Samuli Lehtonen

Leon Perrie

André L De Gasper

Regina Hirai

Jefferson Prado

Alexandre Salino

Bruno Senterre

Lara Shepherd

Michael Sundue

Ackowledgements -Remerciements

Ce travail de trois ans n'aurait pas été possible sans la contribution précieuse de nombreuses personnes, sur plusieurs plans qu'ils soient professionnels ou personnels.

Je remercie premièrement mes encadrants et mon directeur de thèse, Germinal, Myriam et Marc-André, pour m'avoir donné cette opportunité unique qu'est le doctorat au Muséum. J'aurai vécu une expérience de trois ans avec vous, non sans difficultés, mais qui aura été professionnellement très enrichissante. Je mentionnerai tout particulièrement Germinal, que je remercie pour avoir partagé avec moi son expérience du terrain à Madagascar.

To the jury members, thank you very much to have accepted my invitation. Especially, I would like to thank the reviewers for their work on my manuscript.

Je remercie également le ministère de l'Enseignement Supérieur et de la Recherche, pour sa dotation ayant financé mes trois années

General introduction

In the middle of 18th century, about 10,000 plant species were known by the scientific community [START_REF] Linnaeus | Species Plantarum[END_REF]. A report from the Kew Royal Botanic Gardens evaluates today to more than 369,000 the number of flowering plants, with around 2,000 plant species described annually [START_REF] Willis | State of the World's Plants 2017[END_REF]. Around half of this diversity is estimated to occur on 2.3% of the terrestrial surface, in 'biodiversity hotpots' [START_REF] Myers | Biodiversity hotspots for conservation priorities[END_REF]. To define an area as a hotspot, 0.5% or 1,500 endemic plants have to be listed in an area under threat that have lost 70% or more of its primary vegetation. Today, 35 biodiversity hotspots are defined [START_REF] Myers | Biodiversity hotspots for conservation priorities[END_REF][START_REF] Mittermeier | Hotspots Revisited: Earth's Biologically Richest and Most Endangered Ecoregions[END_REF][START_REF] Williams | Forests of East Australia: The 35th Biodiversity Hotspot[END_REF] and on the basis of the number of endemic plants, the five most important ones are the Tropical Andes, Sundaland, the Mediterranean Basin, Madagascar and the Indian Ocean Islands, and the Brazil's Atlantic Forest. Why is biodiversity so localized to these precise areas and what are the underlying evolutionary, ecological and biogeographical processes behind?

Out of the 35 biodiversity hotspots [START_REF] Myers | Biodiversity hotspots for conservation priorities[END_REF][START_REF] Mittermeier | Hotspots Revisited: Earth's Biologically Richest and Most Endangered Ecoregions[END_REF][START_REF] Mittermeier | Biodiversity Hotspots In[END_REF][START_REF] Williams | Forests of East Australia: The 35th Biodiversity Hotspot[END_REF], nine are exclusively composed of islands (Caribbean, Wallacea, Philippines, East Melanesian Islands, Japan, Madagascar and the Indian Ocean Islands, New Caledonia, New Zealand and Polynesia-Micronesia). They correspond to a very small area (ca. 10% of all hotspots) but to 21% of the species diversity of all hotspots, highlighting disequilibrium between the surface and the number of species on continents vs. islands.

Islands have played a crucial role in understanding the evolutionary mechanisms in nature, in particular the Moluccas islands in Indonesia and the Galápagos, where Alfred Russel Wallace and Charles Darwin respectively observed an extraordinary biodiversity that influenced their research [START_REF] Darwin | On the origin of species by means of natural selection, or the preservation of favoured races in the struggle for life[END_REF][START_REF] Wallace | The geographic distribution of animals[END_REF]. Islands provide exceptional study models by their isolation and their relative simplicity compared to continents, and permit easier developments of models to be later applied on more complex systems [START_REF] Emerson | Evolution on oceanic islands: Molecular phylogenetic approaches to understanding pattern and process[END_REF][START_REF] Losos | Adaptation and diversification on islands[END_REF][START_REF] Warren | Islands as model systems in ecology and evolution: prospects fifty years after MacArthur-Wilson[END_REF][START_REF] Santos | New directions in island biogeography[END_REF][START_REF] Crawford | Island floras as model systems for studies of plant speciation: Prospects and challenges: Island floras as models of plant speciation[END_REF]. Moreover, islands vary in their geologic origin, topology, size and localization in diverse bioclimatic regions. The existence of numerous islands provides replicates for evolutionary scientists to test hypotheses about how evolutionary, geologically or spatial processes have shaped biodiversity. However, despite 150 years of island biogeography, the island systems remain a source of many questions about the evolutionary processes: in the study of global diversity patterns, the 'study of relative roles of spatial, historical and ecological processes in driving taxonomic, phylogenetic and functional diversity patterns of island systems' was notably among the first priority issues of the scientific community in island biogeography [START_REF] Patiño | A roadmap for island biology: 50 fundamental questions after 50 years of The Theory of Island Biogeography[END_REF].

MADAGASCAR

1.1. CHARACTERISTICS Madagascar and the Western Indian Ocean islands are located South East of the African coast (Figure 1). It includes Madagascar, the fourth biggest island in the world with ca. 590,000 km² (equal to Spain and Portugal together), the Mascarenes (Réunion, Maurice, Rodrigues; 4,575 km²), the Comoros archipelago (1,862 km²), the Seychelles archipelago (454 km²) and the Scattered Islands (48 km²).

Thereafter, Madagascar and the Indian Ocean islands will be named 'Western Indian Ocean' (WIO) and 'MCS islands' will refer to the Mascarenes, Comoros and Seychelles archipelagos.

Madagascar nests an extraordinary biodiversity that remains poorly known and estimation of species diversity is regularly revised [START_REF] Goodman | The Natural History of Madagascar[END_REF], 2005;[START_REF] Callmander | The endemic and non-endemic vascular flora of Madagascar updated[END_REF]. The endemism is also remarkable, 86% of 5,800 macroinvertebrate species are endemic, but also 84% of 879 vertebrate species and several taxa are endemic (e.g. Malagasy non-flying mammals, Plecoptera, Megaloptera, Ephemera, terrestrial Gastropoda and scorpions, [START_REF] Goodman | Updated estimates of biotic diversity and endemism for Madagascar[END_REF]. About vascular plants, more than 10,000 species of angiosperms are referenced in the Catalogue of the Vascular Plants of Madagascar, of which 84% are endemic, as well as four families and 310 of the 1,730 genera [START_REF] Callmander | The endemic and non-endemic vascular flora of Madagascar updated[END_REF][START_REF] Buerki | Spatio-temporal history of the endemic genera of Madagascar[END_REF].

The ecosystem diversity is also high. Madagascar is remarkable by its humidity gradient increasing from West to East, driven by two main factors: the humid winds coming from the Indian Ocean, and a mountain barrier running along almost all the eastern coast, holding these winds and leading to rainfalls (Figure 2A-B). Tropical rainforests are found all along the eastern coast in the humid and subhumid zones. The high central plateau of Madagascar is characterized by a subhumid climate and a dry climate is found along the Western coast. The South, where is found a subarid climate, is less influenced by this gradient (Figure 2B).

The species and ecologic diversity encountered in Madagascar could be explained by the past geographic, geologic and climatic history of Madagascar [START_REF] Yoder | Has Vicariance or Dispersal Has Vicariance Been the Predominant Force in Biogeographic Madagascar? Only Time Will Tell[END_REF][START_REF] Agnarsson | The generation of a biodiversity hotspot: biogeography and phylogeography of the western Indian Ocean islands[END_REF]. The island was formerly part of Gondwana, a supercontinent of the Southern Hemisphere from the Paleozoic to Mesozoic [START_REF] Mcloughlin | The breakup history of Gondwana and its impact on pre-Cenozoic floristic provincialism[END_REF][START_REF] Seton | Global continental and ocean basin reconstructions since 200 Ma[END_REF]. The Gondwana break-up started in the beginning of Jurassic with the separation of Antarctica, Africa-South America and Madagascar-India (165-162 Ma, Figure 3). Africa and South America separated from each other during Lower Cretaceous. Madagascar was geologically isolated after its separation with India at the end of Cretaceous . At this time, Madagascar was most likely covered by an arid forest, similar to the forest found today in the South [START_REF] Buerki | Spatio-temporal history of the endemic genera of Madagascar[END_REF]. From the Paleocene, the Madagascar northward migration allowed the island to leave this arid climatic zone, now restricted to the extreme South of the island [START_REF] Wells | Geology and Soils[END_REF]. Moreover, the humid winds from the Indian Ocean, formerly stopped by India, could have started to increase the humidity from 60-35 Ma, leading to the gradient of humidity still observed today [START_REF] Wells | Geology and Soils[END_REF]. Beside these tectonic events, volcanic activities and other geologic events have also shaped the Malagasy landscape, notably the northern Montagne d'Ambre or the Western karstic Tsingy of Bemahara that offer plenty of original habitats. [START_REF] Cornet | Essai de cartographie bioclimatique à Madagascar[END_REF], map modified from www.mobot.org/mobot/research/madagascar/gazetteer/. C. Phytogeographic domains from [START_REF] White | The vegetation of Africa[END_REF]. Pie charts represent in dark green the percent of the total diversity of pteridophytes found in the different domains, from Rakotondrainibe (2003a).

BIOGEOGRAPHY OF MALAGASY SPECIES

A complex biogeographical history

The modern assemblage of Malagasy species is most likely the result of a complex biogeographical history, involving many biogeographical processes like Gondwanan vicariance, dispersal from various source pools, anagenesis, cladogenesis and extinction [START_REF] Yoder | Has Vicariance or Dispersal Has Vicariance Been the Predominant Force in Biogeographic Madagascar? Only Time Will Tell[END_REF][START_REF] Agnarsson | The generation of a biodiversity hotspot: biogeography and phylogeography of the western Indian Ocean islands[END_REF]. However, compared to oceanic islands like Hawaii or the Galapagos, the biogeography of species of continental islands like Madagascar and the relative importance of these processes remain poorly studied.

When Madagascar became isolated at the end of Cretaceous, it favored an independent evolution of its biome and vicariance due to the break-up of Gondwana. Vicariance can occur when a population is divided (in two or more) subsequently to the formation of a barrier like a mountain or a continental break-up. If the organisms fail to maintain sufficient gene flow, isolation will result in independent evolution on each side of the barrier and so to vicariant speciation. This isolation is a main factor in the biogeographical history of Malagasy species, giving the original biodiversity we know today and represented by some iconic endemic groups like the lemurs, or by the absence of others like the salamanders [START_REF] Yoder | Has Vicariance or Dispersal Has Vicariance Been the Predominant Force in Biogeographic Madagascar? Only Time Will Tell[END_REF]. Vertebrate fossils shared between Madagascar, India and South America however suggest that a terrestrial connection remained between these lands after the Gondwanan break-up until 80 Ma, via the Gunnerus and Kerguelen Plateau and Antarctica [START_REF] Yoder | Has Vicariance or Dispersal Has Vicariance Been the Predominant Force in Biogeographic Madagascar? Only Time Will Tell[END_REF], but some authors have doubts about this connection [START_REF] Ali | Late Cretaceous bioconnections between Indo-Madagascar and Antarctica: refutation of the Gunnerus Ridge causeway hypothesis[END_REF].

Reviews on the biogeographical history of Malagasy biotas based on molecular studies reach a common conclusion: Cenozoic dispersal events have mostly shaped the modern assemblage of Malagasy taxa [START_REF] Marticorena | Reconciling the origins of Africa, India and Madagascar with vertebrate dispersal scenarios[END_REF][START_REF] Yoder | Has Vicariance or Dispersal Has Vicariance Been the Predominant Force in Biogeographic Madagascar? Only Time Will Tell[END_REF][START_REF] Agnarsson | The generation of a biodiversity hotspot: biogeography and phylogeography of the western Indian Ocean islands[END_REF][START_REF] Samonds | Spatial and temporal arrival patterns of Madagascar's vertebrate fauna explained by distance, ocean currents, and ancestor type[END_REF][START_REF] Buerki | Spatio-temporal history of the endemic genera of Madagascar[END_REF]. Based on phylogenies and the distribution of Malagasy sister taxa, reviews on the flora and the fauna showed diverse biogeographical affinities but especially that the nearest continent, Africa, would be the main source pool for Madagascar [START_REF] Yoder | Has Vicariance or Dispersal Has Vicariance Been the Predominant Force in Biogeographic Madagascar? Only Time Will Tell[END_REF][START_REF] Agnarsson | The generation of a biodiversity hotspot: biogeography and phylogeography of the western Indian Ocean islands[END_REF]. This observation is concordant with the Theory of Island Biogeography for which the main species source pool for an island would be the nearest continent [START_REF] Macarthur | The theory of island biogeography[END_REF]. Among the angiosperms, on the basis of floristic affinities, this tendency was well retrieved with 81% of the Malagasy non-endemic species also found in Africa and 39% shared only with Africa [START_REF] Callmander | The endemic and non-endemic vascular flora of Madagascar updated[END_REF]. A study on the Malagasy endemic genera of angiosperms also retrieved a main African biogeographical affinity [START_REF] Buerki | Spatio-temporal history of the endemic genera of Madagascar[END_REF]. However, Africa is not the only species source pool for Madagascar. In one of the reviews that showed a major African influence [START_REF] Yoder | Has Vicariance or Dispersal Has Vicariance Been the Predominant Force in Biogeographic Madagascar? Only Time Will Tell[END_REF], 31% of all the biogeographical affinities were found with Asia (once all the Asian subdivisions are gathered), against 38% for Africa (flora plus fauna). The Asian biogeographical affinities became even more important than the African ones when only the vertebrates were studied (32% for Asia, 29% for Africa). Biogeographical affinities between Asia and Madagascar could be explained by vicariance, winds across Indian Ocean (monsoons, South Indian Ocean gyre), stepping-stone dispersal events by the Seychelles since its separation from Madagascar 65 Ma [START_REF] Mcloughlin | The breakup history of Gondwana and its impact on pre-Cenozoic floristic provincialism[END_REF], by the drifting Indian landmass and by a chain of stepping-stone islands that formed between India and Madagascar during the last 34 Ma [START_REF] Warren | Why does the biota of the Madagascar region have such a strong Asiatic flavour?[END_REF]and references therein).

The third main area of origin by dispersal found in the literature is South America. For the angiosperm endemic genera, it was found in fourth position with 7.7% of biogeographical affinity, behind Africa (22.4%), Southeast Asia (9.1%) but before India (6.2%) or Australasia (5.6%, [START_REF] Buerki | Spatio-temporal history of the endemic genera of Madagascar[END_REF]. Neotropics are however largely behind if all the Asian affinities are combined (22.8%, India-Asia-Southeast Asia-Australasia, against 7.7%). Biogeographical affinities with the Neotropics were also retrieved by [START_REF] Yoder | Has Vicariance or Dispersal Has Vicariance Been the Predominant Force in Biogeographic Madagascar? Only Time Will Tell[END_REF] for plants and animals, but with higher biogeographical affinities for plants.

Diversification: generation of a regional source pool

Biologists have also examined Madagascar as a model system to study diversification [START_REF] Yoder | Has Vicariance or Dispersal Has Vicariance Been the Predominant Force in Biogeographic Madagascar? Only Time Will Tell[END_REF][START_REF] Vences | Madagascar as a model region of species diversification[END_REF][START_REF] Schneider | Rapid Radiations and Neoendemism in the Madagascan Biodiversity Hotspot[END_REF][START_REF] Agnarsson | The generation of a biodiversity hotspot: biogeography and phylogeography of the western Indian Ocean islands[END_REF]. The geographical isolation, the habitat heterogeneity and the climatic fluctuations could be main drivers that explain diversification in Madagascar [START_REF] Vences | Madagascar as a model region of species diversification[END_REF][START_REF] Schneider | Rapid Radiations and Neoendemism in the Madagascan Biodiversity Hotspot[END_REF]. Diversification is also correlated to habitats, high elevation range and habitat heterogeneity being drivers of species richness and in situ diversification (e.g. [START_REF] Hortal | Island Species Richness Increases with Habitat Diversity[END_REF][START_REF] Stein | Environmental heterogeneity as a universal driver of species richness across taxa, biomes and spatial scales[END_REF].

It was widely assumed that islands are sinks for biodiversity, and that island lineages never colonize a continental area [START_REF] Heaney | Is a new paradigm emerging for oceanic island biogeography?[END_REF]. However, Madagascar has played a role of source pool, firstly for the other islands in the WIO but also for Africa. Strong biogeographical affinities with the Mascarenes, Seychelles and Comoros archipelagos were shown based on the study of sister taxa [START_REF] Yoder | Has Vicariance or Dispersal Has Vicariance Been the Predominant Force in Biogeographic Madagascar? Only Time Will Tell[END_REF][START_REF] Buerki | Spatio-temporal history of the endemic genera of Madagascar[END_REF] and biogeographical analyses have also provided a growing body of evidences based on estimation of the ancestral areas (e.g. [START_REF] Krüger | Molecular phylogeny of the tribe Danaideae (Rubiaceae: Rubioideae): Another example of out-of-Madagascar dispersal[END_REF][START_REF] Strijk | In and out of Madagascar: Dispersal to peripheral islands, insular speciation and diversification of Indian Ocean daisy trees (Psiadia, Asteraceae)[END_REF][START_REF] Bukontaite | In or Out-of-Madagascar? Colonization Patterns for Large-Bodied Diving Beetles (Coleoptera: Dytiscidae)[END_REF][START_REF] Bacon | Biogeography of the Malagasy Celastraceae: Multiple independent origins followed by widespread dispersal of genera from Madagascar[END_REF][START_REF] Kainulainen | Island hopping, long-distance dispersal and species radiation in the Western Indian Ocean: historical biogeography of the Coffeeae alliance (Rubiaceae)[END_REF]. Moreover, dispersal hypotheses out of WIO were also documented to Asia in animals like beetles [START_REF] Bukontaite | In or Out-of-Madagascar? Colonization Patterns for Large-Bodied Diving Beetles (Coleoptera: Dytiscidae)[END_REF] and in angiosperms [START_REF] Bacon | Biogeography of the Malagasy Celastraceae: Multiple independent origins followed by widespread dispersal of genera from Madagascar[END_REF].

In the Yoder & Nowak's analysis of the Malagasy sister taxa (2006), only one taxon of nonseed plants was included (Plagiochila, a Marchantiophyta genus), highlighting the obvious lack of data for spore-bearing plants. Malagasy ferns have been poorly studied compared to angiosperms and were not mentioned in reviews [START_REF] Yoder | Has Vicariance or Dispersal Has Vicariance Been the Predominant Force in Biogeographic Madagascar? Only Time Will Tell[END_REF][START_REF] Agnarsson | The generation of a biodiversity hotspot: biogeography and phylogeography of the western Indian Ocean islands[END_REF]. Until 2014, tree ferns Cyatheaceae were the only ferns on which a biogeographical analysis focused on Madagascar was done, showing a biogeographical history dominated by multiple African colonizations followed by radiation (Janssen et al., 2008). However, there is a growing body of phylogenetic evidences showing other biogeographical patterns for Malagasy ferns, maybe driven by a higher connectivity among the southern continents, especially between Madagascar and the Neotropics [START_REF] Rouhan | Molecular phylogeny of the fern genus Elaphoglossum (Elaphoglossaceae) based on chloroplast non-coding DNA sequences: Contributions of species from the Indian Ocean area[END_REF](Rouhan et al., , 2007a)).

INTRODUCTION TO FERNS

SYSTEMATICS

Polypodiopsida, or 'ferns', form a monophyletic group in the tracheophytes (vascular plants) and they are often called in the literature together with lycophytes under the names 'seed-free vascular plants', 'pteridophytes' or 'ferns and ferns allies', but these terms refer to non-monophyletic taxa as they name the tracheophytes without the seedplants (Figure 4). Ferns would represent 90% of extant pteridophyte species diversity.

Since 2016, the pteridologists community has reached a consensus on the classification of ferns, led by the 'Pteridophyte Phylogeny Group' [START_REF] Ppgi | A community-derived classification for extant lycophytes and ferns[END_REF]. This consensus will be followed in the present thesis and the term 'fern' and 'Polypodiopsida' will be considered as equal and will designate a tracheophyte clade including the Equisetidae (horsetails), Ophioglossidae (whisk ferns, moonworts, adder's-tongue ferns), Marattidae, and Polypodiidae (leptosporangiates). Polypodiidae includes the most part of the diversity like the royal ferns, the filmy ferns (Figure 5D), the aquatic ferns (Figure 5G), the tree ferns (Figure 5J) or the polypody. Around 12,000 pteridophyte species are estimated, and classified into 337 genera and 51 families [START_REF] Ppgi | A community-derived classification for extant lycophytes and ferns[END_REF]. It is comparatively small face to the flowering plants diversity of 369,000 species and some authors explain it by: i) high rates of gene flow, thanks to the wind-mediated spores that prevents speciation; ii) plasticity (whereas angiosperms easily form ecotypes); and iii) lack of sexual selection that would be a key driver of radiation in angiosperms [START_REF] Givnish | Ecology of plant speciation[END_REF][START_REF] Patiño | The anagenetic world of spore-producing land plants[END_REF]Ranker & Sundue, 2015).

LIFE CYCLE AND DISPERSAL

Ferns are spore-bearing plants with a life cycle alternating between a haploid and a diploid generation. The gametophyte produces the gametes (sperm and egg cell) and represents the haploid generation. It is unisexual or bisexual. A humid environment is necessary for fecundation, the sperm being dependent on water to swim from antheridia to encounter the egg cell in the archegonia. The diploid embryo will form a sporophyte, the spore-bearer and dominant generation (in most cases), morphologically characterized by a frond (lamina plus petiole) and a rhizome (Figure 6). This life cycle (Figure 6) is one of the possible sexual mating systems in homosporous ferns. Crossing between gametes from two different gametophytes was also documented, like apomixis (alternation of generations without fertilization) and apogamy (sporophytes from somatic cells) from gametophytes or sporophyte buds [START_REF] Sheffield | Alternation of generations[END_REF][START_REF] Sessa | On the widespread capacity for, and functional significance of, extreme inbreeding in ferns[END_REF].

Figure 6. Life cycle of ferns showing gametophyte selfing, a sexual mating system where a single spore germinates into a bisexual gametophyte that produces both eggs and sperm, partially redrawn from [START_REF] Sessa | On the widespread capacity for, and functional significance of, extreme inbreeding in ferns[END_REF].

Spores are also involved in the dispersal of ferns. The first step of a dispersal event is spore shooting by the sporangium, a structure consisting of a capsule measuring about 0.25 mm in diameter, and in which the spores grow [START_REF] Moran | Spore Shooting. A Natural History of Ferns[END_REF]. The process is fast and impressive, and can be summarized as a catapult: 1) the physical and chemical properties of water allow bending the sporangium cell wall, slowly opening it and exposing the spores (Figure 7a-c); 2) when the bending reaches a critical point, all the accumulated pressure is suddenly released (8d), shooting the spores out of the sporangium, and the sporangium retrieves its initial position (8e). Some authors reported presence of spores on animals [START_REF] Lewis | First evidence of bryophyte diaspores in the plumage of transequatorial migrant birds[END_REF], but their small size (15-150 µm) allow them to be transported by wind [START_REF] Tryon | The biogeography of species, with special reference to ferns[END_REF]. Atmospheric samplings at high altitudes, notably jet streams, have revealed the presence of fern spores resisting low temperatures and UV radiations [START_REF] Moran | Diversity, biogeography, and floristics[END_REF]and references therein). The importance of wind for spore-bearing plants have notably been showed in the Southern Hemisphere [START_REF] Munoz | Wind as a Long-Distance Dispersal Vehicle in the Southern Hemisphere[END_REF], in particular for ferns [START_REF] Parris | Circum-Antarctic continental distribution patterns in pteridophyte species[END_REF]Sundue, Rouhan, & Moran, 2010b) to explain wide distributions of species or higher taxa. In fact, the great dispersal ability of ferns has even made some authors to consider that the dispersal ability as a variable or as a limiting factor can be eliminated in the study of fern biogeography [START_REF] Tryon | Endemic areas and geographic speciation in tropical American ferns[END_REF].

These high dispersal abilities are retrieved in the biogeography of ferns that on average represent 3.6% of the flora on continents but 15.3% on islands [START_REF] Kreft | Contrasting environmental and regional effects on global pteridophyte and seed plant diversity[END_REF] and they are overrepresented on remote islands by representing 16-60% of the flora [START_REF] Moran | Diversity, biogeography, and floristics[END_REF]. A lower endemism compared to angiosperms was also noticed, with for example 89% of endemic angiosperms in Hawaii, against 76% for ferns [START_REF] Ranker | Microevolutionary patterns and processes of the native Hawaiian colonizing fern Odontosoria Chinensis (Lindsaeaceae)[END_REF][START_REF] Ranker | What do we know about Hawaiian ferns and lycophytes?[END_REF]. In the literature, these observations are explained by the high vagility of spores [START_REF] Smith | Comparison of Fern and Flowering Plant Distributions with Some Evolutionary Interpretations for Ferns[END_REF][START_REF] Moran | Diversity, biogeography, and floristics[END_REF].

If spores provide dispersal abilities to ferns, some gametophytic morphologies or habitats could provide supplementary advantages. For example, a disharmony was observed in island flora in favor of epiphytic species with gametophytic gemmae (tissue fragments that could develop into a new gametophyte), which would increase success of colonization [START_REF] Dassler | Significance of gametophyte form in long-distance colonization by tropical, epiphytic ferns[END_REF]. Even continental islands like Madagascar displays the same disharmony compared to Africa [START_REF] Dassler | Significance of gametophyte form in long-distance colonization by tropical, epiphytic ferns[END_REF].

Even if the important role of dispersal in fern biogeography is undeniable, there is still a debate to understand the relative importance of intrinsic and extrinsic factors, dispersal and vicariance, in shaping the ranges of ferns [START_REF] Wolf | Geographic distributions of homosporous ferns: Does dispersal obscure evidence of vicariance?[END_REF][START_REF] Haufler | Genetics, phylogenetics, and biogeography: Considering how shifting paradigms and continents influence fern diversity[END_REF].

WORLDWIDE DISTRIBUTION OF FERN SPECIES

Fern species can be terrestrial (e.g. Figure 5J), aquatic (Figure 5G), epilithic (Figure 5K) or epiphytic (e.g. Figure 5A) and are found on every continent except Antarctica. The species diversity follows a strong latitudinal and altitudinal gradient: highest species richness is retrieved between the tropics and in mountains, and the Neotropics and Southeast Asia nest the highest species diversity, with respectively ca. 3,500 and 4,500 fern and lycophyte species (Figure 8).

ORIGIN AND PERIODS OF SPECIES DIVERSIFICATION

Leptosporangiate ferns would have originated during the Carboniferous [START_REF] Galtier | Diversification of early ferns[END_REF] and would have undergone successive radiations: an initial radiation in the Carboniferous (giving rise to several, now extinct families), a second in the late Paleozoic and early Mesozoic (first diverging families of living leptosporangiate ferns like Hymenophyllaceae, Cyatheaceae or Salviniaceae), and a third one in the Cretaceous giving rise to most families represented in the Paleogene [START_REF] Rothwell | Phylogeny and evolution of ferns: a paleontological perspective[END_REF][START_REF] Schuettpelz | Evidence for a Cenozoic radiation of ferns in an angiosperm-dominated canopy[END_REF]. The last radiation, occurring during the Cenozoic, coincide with the proliferation of angiosperm forests that would have offered new habitats, both on forest undergrounds and in forest canopies as epiphytes. However, no evidence of differential rates of diversification among terrestrial and epiphytes was found [START_REF] Schuettpelz | Evidence for a Cenozoic radiation of ferns in an angiosperm-dominated canopy[END_REF][START_REF] Testo | A 4000-species dataset provides new insight into the evolution of ferns[END_REF].

In contrast to the common idea that ferns are 'old plants', being wrongly called 'livingfossils' by the general public, the modern fern species arose quite recently during the Cenozoic compared to their deep phylogenetic roots in the Carboniferous. This relative youth has obvious consequences on our understanding of their biogeographical history.

FERNS OF MADAGASCAR

SYSTEMATICS AND ECOLOGY

The study of the Malagasy fern diversity started from the end of the 19 th century, notably thanks to Baker and Bonaparte (e.g. Baker, 1887;1915-25), on the basis of collection from famous explorers and naturalists (e.g. Commerson, Boivin, Humblot, Hildbebrandt, Perrier de la Bâthie, Decary or Humbert). Major works were provided by [START_REF] Christensen | Pteridophyta of Madagascar[END_REF] who listed and described more than 500 Malagasy fern species, and twenty-years after by Tardieu-Blot who published the Flore de Madagascar et des Comores (1951-71) under the direction of Humbert, in the Muséum national d'Histoire naturelle (MNHN). Today, the research on the Malagasy fern flora is still mainly led by researchers at the MNHN, especially by Rakotondrainibe and Rouhan who also have been contributing to enrich the fern herbarium collection from Madagascar over the past 30 years. In 2003, 586 species and varieties of pteridophytes representing 106 genera were estimated (Rakotondrainibe, 2003a), but a new estimation would be closer to 700 species (Rakotondrainibe, pers. com.).

The Malagasy ferns are terrestrial, epilithous, epiphyte or aquatic, and a species is most often characterized by only one of these habitats (Rakotondrainibe, 2003b). One genus, Lygodium, is lianescent (Figure 8F). Studies on ecological gradients in four Malagasy forests showed a climatic influence, especially a moisture effect on ferns: the percent of epiphytes decreased with the water deficit and increased with the elevation. Furthermore, 43.3% and 85.0% of the total diversity is found respectively in the Eastern and Central domains of Madagascar (Figure 2C; Rakotondrainibe, 2003b). A high number of species in the Central domain are endemic to this part of the island (37.4%), probably because of the important altitudinal zonation and the moisture. The dry to subarid Western and Southern domains are comparatively poor (with respectively 15.4% and 4.6% of the total diversity represented).

Based on Rakotondrainibe's checklist (2003a), 45.2% of the Malagasy pteridophytes are endemic (against 84.0% for angiosperms ;[START_REF] Callmander | The endemic and non-endemic vascular flora of Madagascar updated[END_REF]. Moreover, no higher taxon is endemic to Madagascar (genus or family). The most diversified genera are Asplenium (65 species; 35.4% of endemic species and varieties), Cyathea (43 spp.; 90.7% of endemism, it is the highest endemism level observed for Malagasy ferns at a generic level) and Elaphoglossum (34 spp.; 58.8% of endemism).

The Catalogue of the Plants of Madagascar (www.tropicos.org/Project/Madagascar; accessed 26 th June, 2017) counts today 721 accepted pteridophytes species and varieties, classified in 120 genera. Therefore, the database includes 135 more pteridophytes species and varieties, and 30 additional genera compared to the Rakotondrainibe's checklist. Forty genera (ca. 33%) are represented in Madagascar by one non-endemic species and five by one endemic species. The increasing number of species is a sign of recent improvements in the knowledge of Malagasy diversity (e.g. Rouhan, Rakotondrainibe, & Moran, 2007b;Janssen & Rakotondrainibe, 2008;Rakotondrainibe, 2010a), but these numbers should be treated carefully as a lot of information remains to be checked in the database. The increasing use of molecular markers has notably permitted the circumscription of species or higher taxa hardly distinguishable on the basis of their morphology, notably in ferns (e.g. [START_REF] Ranker | Phylogeny and evolution of grammitid ferns (Grammitidaceae): a case of rampant morphological homoplasy[END_REF][START_REF] Rothfels | Toward a monophyletic Notholaena (Pteridaceae): Resolving patterns of evolutionary convergence in xericadapted ferns[END_REF]. However, the systematics of Malagasy ferns was poorly studied with the aid of molecular data [START_REF] Rouhan | Molecular phylogeny of the fern genus Elaphoglossum (Elaphoglossaceae) based on chloroplast non-coding DNA sequences: Contributions of species from the Indian Ocean area[END_REF](Rouhan et al., , 2007a[START_REF] Rouhan | Not so neotropical after all: the Grammitid fern genus Leucotrichum (Polypodiaceae) is also paleotropical, as revealed by a new species from Madagascar[END_REF].

BIOGEOGRAPHICAL HISTORY OF THE MALAGASY FERNS: CLUES FROM DIFFERENT DATA

Several sources of information can be used to understand the biogeography of the Malagasy ferns: fossils, floristic affinities, phylogenies, dating analyses and ancestral area estimates.

A poorly known fossil record

Paleobotanical data on Malagasy ferns are scarce and restricted to Appert's studies about the Jurassic and Cretaceous [START_REF] Appert | Die Pteridophyten aus dem Oberen Jura des Manamana[END_REF][START_REF] Appert | Die fossile Makroflora der Unterkreide (Hauterivian) von Manja in Südwest-Madagasckar. Farne und Schachtelhalme (Filicatae und Equisetatae)[END_REF]. A temperate fern flora was present in Late Jurassic in the Manamana region (South-West), with Schizeaceae, Gleicheniaceae, Matoniaceae and Dipteridaceae [START_REF] Appert | Die Pteridophyten aus dem Oberen Jura des Manamana[END_REF]. A study of macrofosssils from the Early Cretaceous (133-129 Ma) was conducted in the Manja region (South-West; [START_REF] Appert | Die fossile Makroflora der Unterkreide (Hauterivian) von Manja in Südwest-Madagasckar. Farne und Schachtelhalme (Filicatae und Equisetatae)[END_REF]. It revealed a flora dominated by Bennettitales (cycadeoid fossil plants) but ferns were also found, representing several families: Marattiaceae, Osmundaceae, Matoniaceae, Dipteridaceae, Gleicheniaceae, Hymenophyllaceae, Dicksoniaceae and Polypodiaceae s.l. This assemblage suggests a warm, probably tropical and seasonally humid climate, probably moderated by the proximity of the sea. Wild fires are also suggested, due to the presence of charred plant debris.

Therefore, the biogeographical history of the Malagasy ferns cannot be understood on the basis of the fossil record only. The Appert's contributions however highlighted a bioclimatic turnover, from temperate fern species in the Late Jurassic to species of warm and humid climate.

Floristic affinities

On the basis of the Catalogue of the Plants of Madagascar (www.tropicos.org/Project/ Madagascar; accessed 26 th June, 2017), 18% of the Malagasy pteridophytes were shared with the whole Western Paleotropics (WIO plus Africa), 11% with other WIO islands, 12% with Africa and at least 14% were shared with other tropical regions (Figure 9A). Therefore, at least 41% of the non-endemic Malagasy species show affinities with another Western Paleotropical region. Floristic affinities with distant areas were also highlighted in previous floristic surveys with the Neotropics [START_REF] Moran | Phytogeographic relationships between neotropical and African-Madagascan pteridophytes[END_REF] or tropical Asia [START_REF] Kramer | The Lindsaeoid ferns of the Old World: IX Africa and Its Islands[END_REF].

In lycophytes (Figure 9B), very close results were found with 55% of endemism, 15% of the Malagasy lycophytes being distributed in Madagascar and Africa, 10% in the WIO, 10% being pantropical, 8% being distributed in all the Western Paleotropics and 2% being shared with the Neotropics. These results suggest that ferns and lycophytes may have similarities in their historical biogeography, leading to similar floristic affinities. This could result from shared intrinsic factors (dispersal by spores, ecological preferences). By contrast, angiosperms showed a higher level of endemism (84%; Figure 9C), highlighting the dissimilarities between seed and spore-bearing plants. At a regional scale, the Malagasy ferns endemic to the WIO were mostly shared with the Mascarenes (43% of the non-endemic Malagasy species shared only with the Mascarenes), then with the Comoros-Mascarenes (20%), and with the Comoros (16%, Figure 9D). Malagasy angiosperms however showed the highest floristic affinity with the Comoros (50%), then the Mascarenes (31%), and relatively few species are distributed in Madagascar and two other WIO archipelagos, suggesting less exchange between the WIO islands compared to ferns (Figure 9E). The higher affinities found with the Comoros rather than with the Mascarenes in angiosperms may be correlated to ecological factors, like lower elevation range in the Comoros (ferns being especially diversified in the mountainous rainforests of Madagascar, Figure 2).

Molecular phylogenies, dating and ancestral area estimates

In historical biogeography, methods rely on the idea that the past biogeographical distribution can be inferred from the current distribution of species and their phylogenetic relationships [START_REF] Ronquist | Phylogenetic Methods in Biogeography[END_REF]. Additionally, time-calibrated molecular phylogenies combined to biogeographical analyses allow inferences of the biogeographical history of taxa: the areas of origin and the underlying processes like vicariance, dispersal, diversification, and the timing of these processes. [START_REF] Rouhan | Molecular phylogeny of the fern genus Elaphoglossum (Elaphoglossaceae) based on chloroplast non-coding DNA sequences: Contributions of species from the Indian Ocean area[END_REF] were the first to make inferences about the areas of origin of Malagasy ferns on the basis of phylogenetic relationships estimated from molecular data (Table 1). Their work on Elaphoglossum suggested that at least 13 long-distance dispersal events (LDD) occurred between the Neotropics and the Western Paleotropics, notably Madagascar. Such Neotropical connections were notably confirmed in Lomariopsis (Rouhan et al., 2007a). The first biogeographical analysis including estimates of ancestral areas focused on Malagasy ferns was conducted on Cyatheaceae. It brought evidences for three independent dispersal events from African ancestors during the Miocene, all followed by radiation in Madagascar (Janssen et al., 2008;[START_REF] Korall | Global biogeography of scaly tree ferns (Cyatheaceae): Evidence for Gondwanan vicariance and limited transoceanic dispersal[END_REF].

Since then, numerous phylogenies were published but often relied on a poor sampling of the worldwide and/or Malagasy species diversity, making sometimes hazy to infer the areas of origin. Moreover, the sampling of widely distributed species often blurred the inferences that could be more easily retrieved on the basis of the sampling of Malagasy endemics. In Table 1, the studies including Malagasy endemics were recorded, as well as the most likely ancestral range of the Malagasy lineage (estimated by analyses or inferred by hand).

Neotropical origins hypothesized by [START_REF] Rouhan | Molecular phylogeny of the fern genus Elaphoglossum (Elaphoglossaceae) based on chloroplast non-coding DNA sequences: Contributions of species from the Indian Ocean area[END_REF]Rouhan et al. ( , 2007a) ) were observed at least in grammitid ferns (Sundue et al., 2014). If this study relied on a poor sampling of the Malagasy species diversity, it however highlighted that multiple trans-Atlantic dispersal events occurred from the last 15 Ma from the Neotropics to the Western Paleotropics. About Africa, tree ferns would not be the only ferns to have colonized Madagascar from this continent, as other dispersal events from African ancestors were inferred in Parapolystichum and Dryopteris over the last 25 Ma [START_REF] Labiak | Phylogeny and historical biogeography of the lastreopsid ferns (Dryopteridaceae)[END_REF][START_REF] Sessa | Into Africa: Molecular phylogenetics and historical biogeography of sub-Saharan African woodferns (Dryopteris)[END_REF]. Biogeographical affinities were also found with the Eastern Paleotropics (Asia, Southeast Asia to Australasia and the Pacific) in Lindsaeaceae and Hymenophyllaceae, but only [START_REF] Chao | Molecular phylogeny and biogeography of the fern genus Pteris (Pteridaceae)[END_REF] clearly inferred Asian dispersal events by ancestral areas estimates over the last 10 Ma.

In Hymenophyllaceae, the old divergence of the family (ca. 280 Ma, [START_REF] Schuettpelz | Evidence for a Cenozoic radiation of ferns in an angiosperm-dominated canopy[END_REF] can also allow vicariance hypotheses subsequently to tectonic events, as the separation of Madagascar from India dated to ca. 90 Ma (McLoughlin, 2001). Therefore, dating analyses remain to be done to known if the age of the Malagasy lineages coincide with this event. Most of the families distributed in Madagascar have appeared after the isolation of Madagascar [START_REF] Schuettpelz | Evidence for a Cenozoic radiation of ferns in an angiosperm-dominated canopy[END_REF], so the biogeographical origins of Malagasy ferns would be mainly explained by dispersal events. The ages of dispersal recorded in Table 1 notably show that all the events that have been inferred so far would postdate the end of Paleogene (< 25 Ma). Dating analyses are for now too scarce to know if this tendency can be generalised, but these results highlighted that factors could have been limiting in the colonization of Madagascar by vascular spore bearing plants. Finally, in situ diversifications were observed in at least 10 genera, suggesting that the process would be a driver of Malagasy species diversity. Some biogeographical origins remained unknown as they cannot be directly inferred from the phylogeny and the distribution, due to the diversity of the distribution of Malagasy sister lineages (e.g. Platycerium), lack of resolution (e.g. Bolbitis) or widely distributed Malagasy species (e.g. Dryopteris, Table 1). Also, ancestral areas estimates could not lead to clear results (e.g. Pteris, Table 1

AIMS AND GLOBAL APPROACH

The aim of this thesis was to understand how the Malagasy fern flora has originated, by unraveling its biogeographical history. Especially, some questions were at the heart of this thesis.

 What are the biogeographical origin(s) of Malagasy ferns and their relative importance? Most of the Malagasy lineages would have arrived from dispersal, due to the young age of divergence of the modern ferns. Therefore, what are the areas of origin of these dispersal events and their relative importance? As previously highlighted, the Theory of Island Biogeography predicts that the nearest continent would be the main source pool of species for an island. However, studies proved that further sources like the Neotropics and tropical Asia could be sources as well. These observations firstly highlighted that Madagascar could be highly connected with distant areas in the Southern Hemisphere and secondly called into question the importance of the nearest continent Africa in the biogeographical history of the Malagasy ferns.

 How old are the Malagasy ferns?

After its isolation from the Gondwana, many fern lineages would have colonized and diversified on the island, but the rate of colonization could have stayed steady over time or could have varied. Do the first fern colonizations coincide with events like the establishment of the Malagasy rainforests, the onset of wind currents between some source regions and Madagascar or events in the other tropical regions of the world?

MATERIAL

Five groups were analyzed: the grammitid ferns (Polypodiaceae), Rumohra Raddi (Dryopteridaceae), Blechnoideae (Blechnaceae), Lindsaea Dryand. (Lindsaeaceae) and the lycophyte genus Phlegmariurus Holub. (Lycopodiaceae) (Table 2). These taxa were chosen on several criteria:

-their species diversity in Madagascar and especially the relative number of endemic species compared to the whole Malagasy diversity -as non-endemics could add uncertainties in the inferencse of the biogeographical history; -the availability of a worldwide phylogenetic study including a representative sampling of the global distribution and species diversity; -the existence of a recent taxonomic treatment; -the availability in the Paris herbarium of silica-dried samples for most Malagasy taxa, allowing DNA extraction (although a field trip was performed, in 2015, to complete this sampling as much as possible).

In total, these five groups include 84 of the ca. 600 Malagasy species and 50 endemics (Table 2). Biogeographical analyses have to rely on a clear taxonomy, that's why taxa were chosen if a recent taxonomic treatment was available. In this dissertation, the evolutionary concept species was adopted [START_REF] Simpson | The species concept[END_REF][START_REF] Wiley | The Evolutionary Species Concept Reconsidered[END_REF][START_REF] Mayden | A hierarchy of species concepts: the denouement in the saga of the species problem[END_REF], implying that a species is a group of populations that share a common ancestor and maintains its identity from other such groups, whether or not the morphology has changed during the process. The taxonomic treatments available relied on morphological traits alone, yet morphology can be misleading and molecular data revealed systematic issues, especially in taxa known for their homoplasic features like in grammitid ferns [START_REF] Ranker | Phylogeny and evolution of grammitid ferns (Grammitidaceae): a case of rampant morphological homoplasy[END_REF]. A first step of the work was to test the monophyly of species, to ensure that they formed evolutionary distinct entities from other such groups in the biogeographical analyses.

METHODS

For each group, the following approaches were adopted:

A first step was to sample the Malagasy species and to obtain the plastid DNA sequences of the markers used in the worldwide phylogeny of reference. When it was possible, duplicates per species were sampled to test the monophyly of species. The final datasets were composed of two parts: sequences from the worldwide phylogeny of reference and newly acquired sequences, from Madagascar, but also from other WIO islands and Africa, to complete as much as possible the worldwide framework.

Secondly, the species phylogenetic relationships were inferred on the basis of two statistical methods: Maximum Likelihood (ML) and Bayesian Inference (BI). The obtained phylogenies relied on the broadest taxonomic sampling available.

Thirdly, a dating analysis was conducted on a reduced sampling, by keeping one sample per species or one sample per lineage in case of non-monophyletic species (assuming that a polyphyletic species could represent distinct evolutionary lineages not defined by morphological approaches). Divergence time estimates were calculated using a Bayesian approach implemented in BEAST.

Finally, the ancestral ranges were estimated using statistical biogeographical models, depending on the taxonomic group (see the following Chapters).

ORGANIZATION OF THE DISSERTATION

The first chapters of the present thesis aimed to document the biogeographical history of the grammitid ferns, Rumohra, Blechnoideae, Lindsaea (together with Odontosoria) and Phlegmariurus. They are followed by an overview of the biogeographical history of the Malagasy ferns (Chapter VI).

Chapter I -Grammitid ferns These ferns are renowned for their homoplasic morphological features, highlighted by molecular phylogenetic analyses (e.g. [START_REF] Ranker | Phylogeny and evolution of grammitid ferns (Grammitidaceae): a case of rampant morphological homoplasy[END_REF]. However, the taxonomy of Malagasy species was poorly studied on the basis of molecular data and their sampling could reveal systematic issues.

Moreover, floristic and biogeographical affinities between the Neotropics and Madagascar were observed [START_REF] Moran | Phytogeographic relationships between neotropical and African-Madagascan pteridophytes[END_REF]Sundue et al., 2014), but remained to be confirmed. Chapter II -Rumohra Rumohra was a good candidate to study the biogeographical connections between continents of the Southern Hemisphere. Two centres of diversity are observed in the genus, in the Neotropics and in Madagascar, which nest three endemic species each. In contrast, the widespread Rumohra adiantiformis is retrieved in the Neotropics, Western Paleotropics, Australasia and temperate circumaustral regions.

The manuscript has been accepted in the Botanical Journal of the Linnean Society:

Chapter III -Blechnoideae

Blechnoideae is another taxon showing a most diverse southern distribution and provided a good replicate to understand the biogeographical history of a taxon distributed in Madagascar and in other regions of the Southern Hemisphere.

The group was subject to recent taxonomic re-delimitations in agreement with a molecular phylogeny (de Gasper et al., 2016a,b), by the re-assignation of Blechnum s.l. species in several genera, including the Malagasy species (although poorly sampled in the phylogeny). The monophyly of these new genera was here tested.

Chapter IV -Lindsaea and Odontosoria

Whereas connections between the Neotropics and Madagascar were highlighted, few evidences of Asian dispersal were provided by biogeographical analyses. The Malagasy species of Lindsaea and Odontosoria were good candidates, as close biogeographical affinities with Asia were evidenced by phylogenetic analyses [START_REF] Lehtonen | Phylogenetics and classification of the pantropical fern family Lindsaeaceae[END_REF]. However, the phylogenetic position of the newly sampled L. marojejyensis sp. nov. was unknown, and no dating analyses focused on Lindsaea and Odontosoria were done.

Chapter V -Phlegmariurus

This chapter was focused on Phlegmariurus, a genus of lycophytes widely distributed in the Southern Hemisphere. It provided a replicate in an independent lineage of vascular spore-bearing plants. Malagasy angiosperms showed important differences, in their biogeography (main African origin and high level of endemism) compared to preliminary results on ferns. These differences were notably explained by ferns vagility, related to spores, but could other vascular spore-bearing plants have experienced similar biogeographical histories as ferns?

In addition, some Malagasy Phlegmariurus species show strong morphological convergences with Neotropical and Asian lineages, but also singular morphological traits.

The study of the biogeography was completed by a discussion on the systematics of these intriguing species.

This chapter will be submitted to Molecular Phylogenetics and Evolution.

Bauret L, Field AR, Gaudeul M, Selosse MA, Rouhan G. First insights on the biogeographical history of Phlegmariurus (Lycopodiaceae), with a focus on Madagascar. In prep.

Chapter VI -Overview

This chapter included an overview of the biogeographical history of the Malagasy ferns, based on the results presented in the previous chapters and the literature. It aimed to present a first insight on the biogeographical history of the Malagasy ferns. What are the biogeographical origins? How old are the Malagasy ferns? A biogeographical scenario was also proposed, which has to be confirmed by more data on Malagasy ferns,

ABSTRACT

Based on a worldwide phylogenetic framework filling the taxonomic gap of Madagascar and surrounding islands of the Western Indian Ocean (WIO), we revisited the systematics of grammitid fern species (Polypodiaceae). We also investigated the biogeographic origin of the extant diversity in Madagascar and estimated the relative influence of vicariance, long-distance dispersals (LDD) and in situ diversification.

Phylogenetic inferences were based on five plastid DNA regions (atpB, rbcL, rps4-trnS, trnG-trnR, trnL-trnF) and the most comprehensive taxonomic sampling ever assembled (224 species belonging to 31 out of 33 recognized grammitids genera). 31 species from Madagascar were included representing 87% of the described diversity and 77% of the endemics. Our results confirmed a Paleotropical clade nested within an amphi-Atlantic grade. In addition, we identified three new major clades involving species currently belonging to Grammitis s.l., Ctenopterella and Enterosora. We resolved for the first time Grammitis s.s. as monophyletic, and Ctenopterella (newly tested here) and Enterosora as polyphyletic. The Neotropical genus Moranopteris was shown to also occur in Madagascar through a newly discovered species. Most importantly, we suggest a >30% inflation of the species number in the WIO due to the hidden diversity in >10 cryptic lineages, best explained by high morphological homoplasy.

Molecular dating and ancestral areas reconstruction allowed identifying the Neotropics as the predominant source of LDD to the African-WIO region, with at least 12 colonization events within the last 20 Ma. Repeated eastward migrations maybe explained by transoceanic westerly winds transporting the dust-like spores. Tropical Asia s.l. would also have played a (minor) role through one dispersal event to Madagascar at the end of the Oligocene. Last, within the complex Malagasy region made of a mosaic of continental and oceanic islands located close to the African continent, we showed that contrary to theoretical expectations and empirical evidence in angiosperms, Africa does not act as a dispersal source and Madagascar seems to have a more important influence on the regional dynamics: we observed both in situ species diversification and dispersal out of Madagascar. This influence also extends beyond the region, since one dispersal event probably originated from Madagascar and reached the Subantarctic island of Amsterdam.

KEYWORDS

Biogeography, Ferns, Long-distance dispersal, Madagascar, Phylogeny, Western Indian Ocean

INTRODUCTION

Madagascar is a continental island of the Western Indian Ocean (WIO) known to host an extraordinary biodiversity, with about 12,000 vascular plant species [START_REF] Callmander | The endemic and non-endemic vascular flora of Madagascar updated[END_REF], and listed as one of the world's hotspots of biodiversity [START_REF] Myers | Biodiversity hotspots for conservation priorities[END_REF]. Eighty-three percent of vascular plants, 52% of birds and 86% of invertebrates are endemics, and this proportion reaches 100% for terrestrial Gastropoda and non-volant Mammalia [START_REF] Goodman | Updated estimates of biotic diversity and endemism for Madagascar[END_REF]. However, this biological diversity is still underdocumented and the evolutionary processes explaining its emergence are poorly known, since only a few phylogenetic studies are available. In particular, assessing the relative contributions of vicariance due to plate tectonics, trans-oceanic long-distance dispersal (LDD) and in situ species diversification remains a central question.

Investigating the origin and evolutionary history of Malagasy lineages is challenging because Madagascar is not strongly isolated from the East African coast, and is also surrounded by several archipelagos. Thus, Madagascar must be studied in the broader context of the WIO, involving a complex geologic history of continental and volcanic islands [START_REF] Agnarsson | The generation of a biodiversity hotspot: biogeography and phylogeography of the western Indian Ocean islands[END_REF]. Most importantly, Madagascar was once part of the supercontinent Gondwana that began to breakup 155-118 Ma, with the separation of the America/Africa block from the Madagascar/India/Australia/ Antarctica block. America and Africa split shortly after (110 Ma). Later on (118-84 Ma), India/Seychelles broke away from Madagascar before colliding with Asia 50 Ma, followed by the separation of the Seychelles Plateau (100-95 Ma; [START_REF] Seward | An insight into the breakup of Gondwana: Identifying events through low-temperature thermochronology from the basement rocks of Madagascar[END_REF]. In addition, the WIO is characterized by two volcanic archipelagos, the Comoros and Mascarenes, which respectively emerged within the last ca. 15 Ma [START_REF] Emerick | Age progressive volcanism in the Comores Archipelago, western Indian Ocean and implications for Somali plate tectonics[END_REF][START_REF] Nougier | The Comores archipelago in the western Indian Ocean: volcanology, geochronology and geodynamic setting[END_REF]) and 8 Ma [START_REF] Mcdougall | Isotopic Dating and Geomagnetic Polarity Studies on Volcanic Rocks from Mauritius, Indian Ocean[END_REF]. Whereas some studies underlined the impact of continental drift on the distribution of species occurring in Madagascar, others have more recently emphasized a greater role of LDD during the Cenozoic period [START_REF] Yoder | Has Vicariance or Dispersal Has Vicariance Been the Predominant Force in Biogeographic Madagascar? Only Time Will Tell[END_REF][START_REF] Renner | Biogeography of the Monimiaceae (Laurales): A role for East Gondwana and long-distance dispersal, but not West Gondwana[END_REF][START_REF] Warren | Why does the biota of the Madagascar region have such a strong Asiatic flavour?[END_REF][START_REF] Agnarsson | The generation of a biodiversity hotspot: biogeography and phylogeography of the western Indian Ocean islands[END_REF][START_REF] Buerki | Spatio-temporal history of the endemic genera of Madagascar[END_REF][START_REF] Bacon | Biogeography of the Malagasy Celastraceae: Multiple independent origins followed by widespread dispersal of genera from Madagascar[END_REF]. At least, the role of dispersal is undisputable in the origin of lineages on the recent volcanic islands surrounding Madagascar.

In this context, ferns are a very interesting biological model to study the biogeographic origin of the Malagasy and WIO diversity. As many as 600 fern species are listed in Madagascar, among which ca. 45% are endemic (Rakotondrainibe, 2003a;[START_REF] Goodman | Updated estimates of biotic diversity and endemism for Madagascar[END_REF][START_REF] Roux | Synopsis of the Lycopodiophyta and Pteridophyta of Africa, Madagascar and neighbouring islands[END_REF]. This proportion is high, although not as high as for flowering plants and some other groups cited above, probably because ferns dust-like spores have stronger dispersal abilities that facilitate species arrival and ultimately slow down the speciation process [START_REF] Smith | Comparison of Fern and Flowering Plant Distributions with Some Evolutionary Interpretations for Ferns[END_REF]. Spore dispersal is assumed to occur mostly through air currents, although dispersal mediated by bats [START_REF] Sugita | Possible spore dispersal of a birdnest fern Asplenium setoi by Bonin flying foxes Pteropus pselaphon[END_REF] or birds [START_REF] Lewis | First evidence of bryophyte diaspores in the plumage of transequatorial migrant birds[END_REF] has been documented. This high capacity of spore movement, combined to the relatively recent origin of extant fern lineages (especially in the species-rich Polypodiales) since the Cretaceous (<150 Ma; [START_REF] Schuettpelz | Evidence for a Cenozoic radiation of ferns in an angiosperm-dominated canopy[END_REF][START_REF] Rothfels | The evolutionary history of ferns inferred from 25 low-copy nuclear genes[END_REF], suggests a major influence of LDD compared to Gondwanan vicariance in the origin of the African-WIO groups. In particular, connections between the Neotropics and Madagascar were previously highlighted based either on floristic affinities [START_REF] Moran | Phytogeographic relationships between neotropical and African-Madagascan pteridophytes[END_REF] or on molecular phylogenetic analyses. Among the latter studies, LDD between the two areas were hypothesized for numerous Elaphoglossum lineages [START_REF] Rouhan | Molecular phylogeny of the fern genus Elaphoglossum (Elaphoglossaceae) based on chloroplast non-coding DNA sequences: Contributions of species from the Indian Ocean area[END_REF][START_REF] Vasco | Circumscription and phylogeny of the Elaphoglossum ciliatum group (E. sect. Lepidoglossa, Dryopteridaceae) based on cpDNA sequences[END_REF], and in the genera Lomariopsis (Rouhan et al., 2007a), Stenogrammitis (as Lellingeria in [START_REF] Labiak | Molecular phylogeny, character evolution, and biogeography of the grammitid fern genus Lellingeria (Polypodiaceae)[END_REF], Leucotrichum [START_REF] Rouhan | Not so neotropical after all: the Grammitid fern genus Leucotrichum (Polypodiaceae) is also paleotropical, as revealed by a new species from Madagascar[END_REF] and other Polypodiaceae [START_REF] Janssen | Origin and diversification of African ferns with special emphasis on Polypodiaceae[END_REF].

Transatlantic LDD was also inferred based on dated phylogenies in Alsophila (Janssen et al., 2008) and Parapolystichum [START_REF] Labiak | Phylogeny and historical biogeography of the lastreopsid ferns (Dryopteridaceae)[END_REF]. Claims for Asiatic origins have also been documented, highlighting dispersal routes from Asia e.g. in the genera Pteris [START_REF] Chao | Molecular phylogeny and biogeography of the fern genus Pteris (Pteridaceae)[END_REF], Nephrolepis (Hennequin et al., 2010b), and Deparia [START_REF] Kuo | Historical biogeography of the fern genus Deparia (Athyriaceae) and its relation with polyploidy[END_REF]. At a more restricted scale, data on ferns are almost completely lacking within the African-WIO region, although a few insights from Platycerium [START_REF] Kreier | Phylogeny and biogeography of the staghorn fern genus Platycerium (Polypodiaceae, Polypodiidae)[END_REF] and Alsophila (Janssen et al., 2008) might support continental Africa as a source of dispersal to Madagascar. This trend, implying migration across the Mozambique Channel, is strongly supported in other plant groups [START_REF] Agnarsson | The generation of a biodiversity hotspot: biogeography and phylogeography of the western Indian Ocean islands[END_REF].

Our study focused on grammitid ferns that had long been considered as a family, 'Grammitidaceae', until they were shown to form a clade nested within the larger Polypodiaceae family using molecular data [START_REF] Schneider | Unraveling the phylogeny of polygrammoid ferns (Polypodiaceae and Grammitidaceae): Exploring aspects of the diversification of epiphytic plants[END_REF][START_REF] Ranker | Phylogeny and evolution of grammitid ferns (Grammitidaceae): a case of rampant morphological homoplasy[END_REF]Sundue et al., 2014). Comprising around 1500 species, Polypodiaceae is the second largest family of ferns. The estimated 900 species of grammitid ferns [START_REF] Perrie | Chloroplast DNA sequences indicate the grammitid ferns (Polypodiaceae) in New Zealand belong to a single clade, Notogrammitis gen. nov[END_REF] belong to 33 genera, many of which were described in the last decade based on molecular phylogenetic studies that revealed extensive polyphyly as a recurrent issue resulting from morphological homoplasy [START_REF] Ranker | Phylogeny and evolution of grammitid ferns (Grammitidaceae): a case of rampant morphological homoplasy[END_REF]Sundue, Islam, & Ranker, 2010a). Grammitid ferns are mostly found as epiphytes in tropical montane forests, and distributed in two main phytogeographic zones [START_REF] Parris | The distribution of Grammitidaceae (Filicales) inside and outside Malesia[END_REF]: (i) around 400 species in the Neotropics, tropical Africa, and the WIO (including Madagascar, Mascarenes, Comoros and Seychelles); and (ii) around 500 species in tropical Asia s.l., including Malesia and the Pacific Ocean islands. The Neotropics and the WIO were grouped in the same phytogeographic zone because they share several taxa: the genera Alansmia, Ceradenia, Cochlidium, Enterosora, Grammitis, Leucotrichum, Melpomene, Stenogrammitis, and Zygophlebia, and even some species (Alansmia elastica, Cochlidium serrulatum and Melpomene flabelliformis). In contrast, only a few taxa are known to be shared by the two phytogeographic zones: (i) Ctenopterella is mainly distributed in Malesia and the South-Pacific Ocean islands, but also in the WIO although its monophyly has never been tested;

(ii) Stenogrammitis is mainly Neotropical but also distributed in Africa, the WIO, Hawaii and the South-Pacific Ocean islands; (iii) Notogrammitis has a circumaustral distribution, from Australia and New Zealand to South Africa and South America.

A recent phylogenetic and biogeographic study showed that grammitids evolved from a Neotropical ancestor between the end of the Eocene and beginning of the Paleocene (45-37 Ma; Sundue et al., 2014). In agreement with the distribution patterns and delimitation of the two phytogeographic zones, the inferred phylogeny exhibited a clear geographic pattern: a single clade from tropical Asia s.l. (comprising Australia and Melanesia) was nested in a Neotropical grade, which also included the WIO species. This result was explained by one LDD from the Neotropics to tropical Asia s.l. at the end of the Paleocene, and repeated LDD from the Neotropics to the WIO since molecular dating suggested relatively recent diversification and allowed excluding vicariance hypotheses linked to Gondwana breakup. However, the sampling of Sundue et al. (2014) included only eight species occurring in the WIO, so that many questions remain about the systematics and biogeography of grammitid species in this area.

For the WIO and Africa, Roux (2009) listed 51 species of grammitid ferns belonging to nine genera, and in particular 31 species in Madagascar including 13 endemics (Table 1; Figure 1). However, taking into account several taxa awaiting description based on morphological evidence, the actual diversity could reach >40 species in Madagascar alone.

In addition, generic delimitations have to be revised for some genera already identified as non-monophyletic at the worldwide scale (especially Grammitis and Zygophlebia), and may also have to be for some others (in particular Ctenopterella, which is shared between Tropical Asia s.l. and the WIO; Table 1). Based on an extended sampling and using phylogenetic inference, molecular dating and ancestral area estimation, we aim at improving the systematics of the Malagasy and other WIO grammitids, better understanding their biogeographic history, and shedding light on the evolutionary mechanisms that led to their emergence. More specifically, our goals are: (i) to further test the monophyly of grammitid genera, particularly those diversified in the WIO, namely Grammitis, Zygophlebia and for the first time Ctenopterella; (ii) more broadly, to improve the systematics of grammitid ferns by delimiting species as monophyletic groups; (iii) to test the global biogeographic scenario proposed by Sundue et al. (2014); (iv) to infer the biogeographic origin of the Malagasy and other WIO species (i.e., did they emerge after dispersal events from the Neotropics only, as suggested by Sundue et al. (2014)? How many such events explain the extant diversity in the area?);

Genus

(iv) to assess to what extent dispersal occurred and the predominant migration routes at the regional scale, in the WIO; and v) to check whether diversification occurred within the WIO.

MATERIALS AND METHODS

TAXONOMIC SAMPLING

The sampling was composed of two parts: the first one, based on the worldwide grammitid phylogeny of

DNA SEQUENCING

Total genomic DNA was extracted using the Qiagen DNeasy Plant Mini Kit (Valencia, California, USA) either from silica-dried leaves whenever available, or from herbarium specimens. The manufacturer's protocol was followed but slightly modified for herbarium samples, adding 30 mL proteinase K (20 mg/mL) and 30 mL beta-mercaptoethanol for the initial lysis step, which was carried out at 42°C during 24 h on a tipping plate.

The polymerase chain reaction (PCR) was used to amplify five plastid DNA regions: the two coding genes atpB and rbcL, and the three non-coding intergenic spacers: rps4-trnS, trnG-trnR and trnL-trnF. PCR were carried out in a 25 µL volume containing 1x PCR buffer, 2.5mM MgCl2, 250 µM of each dNTP, 1M betaine, 0.4 µM of each primer, 0.75 U Taq polymerase (Taq CORE kit; MP Biomedicals, Illkirch, France), and 0.75 µL of template DNA. Primer sequences and thermal cycling conditions are reported in Table 2. The resulting PCR products were checked on a 1% agarose gel and sequenced in both directions at the Centre National de Séquençage (Evry, France), using the amplification primers and additional, internal primers for atpB, rbcL and trnG-trnR (Table 2). Forward and reverse DNA strands were assembled in Sequencher 4.9 (GeneCodes Corporation, Ann Arbor, Michigan, USA). The newly obtained consensus sequences were submitted to GenBank (accession numbers listed in Appendix 1.1).

PHYLOGENETIC ANALYSES

The sequences were aligned with the MAFFT plugin [START_REF] Katoh | Parallelization of the MAFFT multiple sequence alignment program[END_REF] in Jalview 2.8.2 [START_REF] Waterhouse | Jalview Version 2 -a multiple sequence alignment editor and analysis workbench[END_REF] using the default parameters. The alignments were then checked and revised manually when necessary. For each DNA region, the most suitable model of nucleotide substitution was determined with MrModelTest 2.3 [START_REF] Nylander | MrModeltest ver. 2.3. Program distributed by the author[END_REF], following the Akaike Information Criterion. A data matrix was then built by concatenation of all five regions using Sequence Matrix 1.7.8 [START_REF] Vaidya | SequenceMatrix: concatenation software for the fast assembly of multi-gene datasets with character set and codon information[END_REF], each DNA region constituting a distinct partition in the final dataset.

Phylogenetic trees were inferred based on two probabilistic methods: Maximum Likelihood (ML) and Bayesian Inference (BI), as respectively implemented in RAxML-HPC2 8.2.6 [START_REF] Stamatakis | RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies[END_REF] and MrBayes 3.2.3 [START_REF] Ronquist | MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space[END_REF]. Gaps were treated as missing data and analyses were performed on the CIPRES science gateway [START_REF] Miller | Creating the CIPRES Science Gateway for inference of large phylogenetic trees[END_REF]. Parameters for the RAxML analysis were determined on the CIPRES interface. We used the GTRGAMMA+I model of nucleotide substitution for each partition, performed 1000 rapid bootstrap (BS) replicates and searched for the bestscoring ML tree. In MrBayes, we conducted two independent but parallel analyses with four chains each (one cold and three incrementally heated at a temperature of 0.1). The BI analyses were run for 15 million generations each, sampled every 1500 generations, and performed with the GTR+I+C model of nucleotide substitution for each partition and parameters unlinked. Tracer 1.6.0 [START_REF] Rambaut | Tracer 1.6[END_REF] was used to check that effective sample sizes were higher than recommended (>200) and that the two runs had converged to the stationary distribution. The 25% initial trees were discarded as burn-in, the post-burn-in trees (15,000 total trees) were pooled and a 50% majority-rule consensus was computed with average branch lengths and posterior probability (PP) estimates for all nodes. This tree and the best ML tree were visualised with FigTree 1.4.2 [START_REF] Rambaut | FigTree 1.4.2 software[END_REF].

DIVERGENCE TIME ESTIMATION

Divergence time estimation was performed on the CIPRES science gateway using BEAST 1.8.0 [START_REF] Drummond | Bayesian Phylogenetics with BEAUti and the BEAST 1.7[END_REF]. Our biogeographic analyses were performed at the species level and focused on Madagascar. Therefore, given that the BEAST outputs were used as inputs for the estimation of ancestral areas, we reduced our ingroup sampling to 149 samples representing 139 species for the dating analysis. For genera that included Malagasy species, we kept one sample per species that was retrieved as monophyletic and as many samples as retrieved lineages when species were poly-or paraphyletic. For genera without any Malagasy species, we retained at least two samples of two distinct species including the type species of the genus whenever available, and the species that was recovered as the most early-diverging lineage (in order not to underestimate the diversification date of the genus). For genera with no resolution on the crown node, we kept all the sampled species branched on the polytomous node.

Partitions and models of nucleotide substitution were the same as for the BI. An uncorrelated lognormal relaxed clock was used, with a Yule tree prior [START_REF] Gernhard | The conditioned reconstructed process[END_REF] and a random starting tree. Based on a large-scale, fossil-based study on leptosporangiate ferns [START_REF] Schuettpelz | Evidence for a Cenozoic radiation of ferns in an angiosperm-dominated canopy[END_REF], we used four secondary calibration points corresponding to four well-supported clades within the Polypodiaceae (nodes 367, 368, 378, 382 in Schuettpelz & Pryer, 2009; figured as black squares on Figure 4) that were also used by Sundue et al. (2014) Suchard, 2008). Two analyses of 20 million generations each were performed with tree and parameters sampling every 2000 generations. Tracer 1.6.0 was used to define burnin length and the first 1000 trees (10%) were discarded for each run. We used LogCombiner v1.8.0 to combine results from the two runs and TreeAnnotator v1.8.0 [START_REF] Drummond | Bayesian Phylogenetics with BEAUti and the BEAST 1.7[END_REF] to compute the maximum clade credibility tree. FigTree 1.4.2 [START_REF] Rambaut | FigTree 1.4.2 software[END_REF] was used to visualize the maximum clade credibility tree and the associated chronogram.

ANCESTRAL AREAS ESTIMATION

We used both the statistical Dispersal-Vicariance Analysis S-DIVA [START_REF] Yu | S-DIVA (Statistical Dispersal-Vicariance Analysis): A tool for inferring biogeographic histories[END_REF] and the Bayes-Lagrange S-DEC [START_REF] Beaulieu | A Southern Hemisphere origin for campanulid angiosperms, with traces of the break-up of Gondwana[END_REF]) models implemented in the RASP software [START_REF] Yu | RASP (Reconstruct Ancestral State in Phylogenies): A tool for historical biogeography[END_REF] to estimate ancestral ranges at all nodes. Nine biogeographic regions were defined (see Figure 2 et al. (2014), and on herbarium specimens (mostly from the Paris Herbarium) and personal observations for all other samples. The taxonomic identification of all herbarium specimens was checked. We considered polyphyletic species as distinct lineages and coded as many distinct distributions as retrieved lineages. The maximal number of ancestral areas was set to two and, owing to the high wind-dispersal ability of fern spores over long distances, we considered that dispersal probability was not correlated to geographic distance. The frequencies of an ancestral range at a node were averaged over 100 random, post burn-in trees taken from the BEAST output. The condensed tree was the maximum clade credibility tree estimated in BEAST.

RESULTS

PHYLOGENETIC ANALYSES

Our combined DNA sequence matrix of the five plastid regions was composed of 401 specimens and 5593 base pairs. Table 3 reports the percentage of samples successfully sequenced and other statistics, for each DNA region and the combined alignment. The phylogenetic hypotheses produced by the ML analysis and BI resulted in very similar topologies, with a few minor, not statistically supported differences. Consequently, only the BI topology is summarized in Figure 2 (see Appendix 1.2 for the full tree with all terminals).

Both the ML analysis and BI supported grammitid ferns as a strongly-supported clade (BS = 100; PP = 1; Figure 2). The resulting phylogeny was almost fully resolved at the species level. Most nodes were strongly supported, especially those supporting genera (BS = 95 and/or PP = 0.95; Figure 2), although more moderate sup-port values were retrieved for the backbone nodes and some nodes within clade-1 (Figure 2). The inferred topology almost fully agreed with the most recent phylogenetic study on the group (Sundue et al., 2014), with two notable exceptions: we recovered Grammitis s.s. as monophyletic (BS = 100; PP = 1), and three new clades were supported (highlighted as grey-filled triangles, Figure 2) involving species currently classified in Grammitis, Ctenopterella and Enterosora (as detailed later). (atpB, rbcL, trnG-trnR, trnL-trnF and rps4-trnS), and figured as a summary phylogeny (infrageneric branches are shown in Appendix 1.2). Generic lineages are represented by triangles (whose heights are proportional to the numbers of samples included), with names of genera preceded by colored squares figuring their geographic distribution (see map) and followed by (number of species analyzed / number of samples included). Non-monophyletic genera are indicated in bold and their names are followed by symbols to show the distinct lineages of a given genus. The three grey-filled triangles are the three newly evidenced clades, and circled numbers (1 to 3) correspond to clades detailed in Figure 3. Unless mentioned next to the nodes, support values were BS≥95 and PP≥0.95.

The phylogeny was geographically structured, with a Paleotropical clade (BS = 78; PP = 0.86) nested within a large grade (Figure 2). The Paleotropical clade included 15 genera mostly distributed in tropical Asia s.l. and the Pacific Ocean islands. Notably, the Paleotropical clade also comprised eight species from the WIO and Africa, belonging to Ctenopterella and Grammitis and all together forming clade-3 (BS = 100; PP = 1; Figure 2). This clade is a newly recovered one for grammitids. The relationships between clade-3, Chrysogrammitis, and the rest of the Paleotropical clade were not resolved.

The rest of the tree consisted of a large grade, hereafter called amphi-Atlantic grade. It included 17 genera showing either an exclusively Neotropical distribution for six genera, or a distribution on both sides of the Atlantic Ocean (including Africa and the WIO) for 10 genera (with the exceptions of Stenogrammitis and Grammitis s.s., which include a few additional species from the Pacific Ocean islands, tropical Asia s.l. or the circumaustral region; and Adenophorus restricted to Hawaii; Figure 2).

Out of the 31 genera that we sampled, monophyly could not be assessed for Acrosorus and Lomaphlebia (represented by only one species each). Twenty-two genera were recovered as monophyletic, including Moranopteris that was exclusively described from the Neotropics to date and that was also represented in this study by an undescribed, endemic species to Madagascar (Moranopteris sp. 1). By contrast, seven genera were not recovered as monophyletic: Ceradenia, Ctenopterella, Enterosora, Grammitis, Oreogrammitis, Radiogrammitis and Zygophlebia (indicated in bold, Figure 2). In particular, Grammitis, Ctenopterella and Enterosora were retrieved as highly polyphyletic: Grammitis was retrieved in the clade-1 of the amphi-Atlantic grade (as Grammitis s.s.), but also as four distinct lineages within the Paleotropical clade (two lineages in clade-3, one clade sistergroup to Notogrammitis, and G. stenophylla as sister lineage to the Acrosorus-Ctenopterella denticulata clade; Figures 2 and3). Ctenopterella species formed three distinct lineages within the Paleotropical clade: C. denticulata was included in the clade Acrosorus-Grammitis stenophylla clade, C. lasiostipes and two other undescribed species were sistergroup to Grammitis-Notogrammitis, and two species were included in clade-3; Figures 2 and3). Enterosora was retrieved as four lineages belonging to the amphi-Atlantic grade: two species were sister-group to Adenophorus in clade-1 and, in clade-2, two distinct lineages were nested within Zygophlebia (counting four and one species, respectively) and one species within Ceradenia (Figure 3).

Our molecular sampling included multiple individuals per species, especially for those from the WIO, and also allowed the identification of several cases of polyphyly at the species level. Twenty-eight species were thus recovered as non-monophyletic (Appendix 1.2). They belonged to 15 genera and included 12 species from the WIO and Africa (Table 4). These 12 non-monophyletic species were mostly found in Grammitis, with four nonmonophyletic species in Grammitis s.s. (highlighted in distinct colors; Figure 3, clade-1; Table 4) and six non-monophyletic species which could be classified in one to several new genera in order to accommodate their placement in clade-3 (Figure 3; Table 4). 4A). The Paleotropical clade was dated to 24.9 Ma for the stem age (95% HPD: 19.6-28.1; Figure 4B).

DNA region

Divergence dates (stem ages) of generic lineages ranged between 13.1 Ma (divergence between Acrosorus and Ctenopterella denticulata; 95% HPD: 9.0-18.1; Figure 4B) and 32.1 Ma (divergence between Terpsichore and its sister-clade; 95% HPD: 26.5-38.7; Figure 4A), while their diversification (crown) ages ranged between 2.0 and 14.6 Ma for Xiphopterella and Ascogrammitis respectively (Figure 4B). In fact, diversification could also have occurred earlier: several new genera will have to be newly described based on this study (see Table 3 and Discussion) and as a result, the potential genus corresponding to clade-V would have started to diversify 21.1 Ma.

Ancestral areas estimation

S-DIVA and S-DEC analyses produced very similar results. When they differed, S-DEC inferred slightly broader ancestral areas (i.e., including an additional region, but with a low probability), but the areas inferred by S-DIVA were also always the most probable ones inferred by S-DEC (results not shown). The only notable difference was an ancestral area covering both Madagascar and the Neotropics for the crown node of Stenogrammitis and its next outer node by S-DEC, vs. Madagascar only by S-DIVA (Figure 4B).

Grammitid ferns originated and diversified in the Neotropics (Figure 4A) and a Neotropical origin was also inferred for all the generic lineages of the amphi-Atlantic grade, with two exceptions: the ancestral area of Adenophorus was inferred in the Neotropics and the Pacific Ocean islands, while Stenogrammitis would have originated in the Neotropics and Madagascar. 3). For some species, several issues emerged and were distinguished by i/ and ii/, while the distinct lineages of non-monophyletic species were distinguished by a/ and b/.

The Paleotropical clade originated in tropical Asia s.l. and the Neotropics (Figure 4B). Within this clade, all genera have an exclusively tropical Asian origin, except Notogrammitis (for which the circumaustral area was also inferred) and clade-V if considered as a new genus (for which Madagascar was also inferred).

Focus on Madagascar, surrounding islands and Africa

The lineages occurring in this region were dispersed throughout the phylogeny. They originated by 13 LDD events dated from the end of the Oligocene or more recently (indicated by black arrows on branches; Figure 4): 12 from the Neotropics and one from tropical Asia s.l., leading to clade-V. However, this latter event was not statistically supported since the node grouping the African-WIO clade-V with the rest of the Paleotropical clade (excluding the Asian genus Chrysogrammitis) had PP = 0.45. Five LDD were inferred to Madagascar (black arrows for LDD-3, LDD-5, LDD-10, LDD-12 and LDD-13; Figure 4). These events resulted in three species endemic to Madagascar: Grammitis ebenina-Rouhan1180 (LDD-3), Leucotrichum madagascariense (LDD-5) and Moranopteris sp. 1 (LDD-12). The two other dispersal events to Madagascar were at the origin of the genus Stenogrammitis (LDD-10) and of clade-V (LDD-13 from Asia). One LDD only reached Africa (LDD-8). Seven other LDD gave rise to lineages distributed in several areas, with no possibility to infer whether one or several dispersal events occurred, and which area(s) was(were) colonized at first (LDD-1, 2, 4, 6, 7, 9 and 11). Only one transatlantic LDD from Madagascar back to the Neotropics was suggested, within the genus Stenogrammitis.

At a regional scale, several dispersal events were also inferred in all directions between Madagascar, Africa and the neighbouring islands, but most of them originated from Madagascar to give rise to Grammitis melanoloma endemic to Réunion, and for others to expand their original ranges (Grammitis cryptophlebia, Zygophlebia devoluta-Rouhan1379, Zygophlebia torulosa, Enterosora barbatula-Rouhan1186, Stenogrammitis oosora, Grammitis synsora, Grammitis pygmaea, Ctenopterella zenkeri and Ctenopterella parvula). In two cases, dispersal originated in other WIO islands: Ceradenia sechellarum dispersed to Africa, and Ceradenia comorensis to Madagascar. Last, only one dispersal was inferred from Africa towards Madagascar and the other WIO islands, which gave rise to clade-III (Zygophlebia-Enterosora; Figure 4).

The analysis suggested that out of the 13 LDD that gave rise to lineages of the WIO and Africa, five were followed by species diversifications in the region (clades I to V, Figure 4).

DISCUSSION

Our phylogenetic analyses included 25% of all grammitid species and especially filled major gaps in the Malagasy and other WIO taxa (e.g. 87% of the described Malagasy diversity and 77% of the known endemics are now included vs. 22% and 0%, respectively in Sundue et al., 2014). This allowed improving our understanding of both the worldwide systematics and the biogeographic history of the group, as hereafter discussed.

SYSTEMATIC IMPLICATIONS

Our results generally supported those previously obtained with a more limited sampling (Sundue et al., 2014): grammitid ferns formed a strongly supported clade, and the same global topology was recovered although support values of deeper nodes were more moderate. In addition, 22 genera were confirmed as monophyletic and four as polyphyletic (Grammitis, Oreogrammitis, Radiogrammitis and Zygophlebia; the assessment was not possible for Lomaphlebia and Acrosorus, represented by only one species each, and for Luisma and Archigrammitis still to be sampled; Figure 2).

Besides these, our results revealed six new major findings: (i) Grammitis s.s. was resolved as monophyletic; (ii) all other species of Grammitis s.l. were retrieved across four lineages, reinforcing the polyphyly of this genus; (iii) for the first time, Ctenopterella (newly tested here) and Enterosora were recovered as polyphyletic; (iv) three new major clades were supported (grey-filled triangles 1, 2, and 3, in Figure 2), involving species currently classified in Grammitis s.l., Ctenopterella and Enterosora; (v) three new species, suspected based on morphological evidence, were confirmed as distinct molecular lineages and will be described elsewhere (Moranopteris sp. 1 as endemic to Madagascar, whereas the genus was known only from the Neotropics to date; Stenogrammitis sp. 1 as endemic to Amsterdam Island, which is the new southernmost occurrence for the genus; and Zygophlebia sp. 1 as endemic to the Comoros); and (vi) a high level of cryptic species was suggested. Some of these findings being related to each other, they are hereafter discussed by genus or new major clade.

Grammitis s.s. is monophyletic

Grammitis s.s. was newly resolved as monophyletic and sister-clade to Cochlidium (Figure 2), whereas it was previously interpreted as paraphyletic with respect to Cochlidium (Sundue et al., 2014). Our result is in agreement with morphological observations, which suggested that all the ca. 20 species showing distinct, blackish sclerotic lamina margins (e.g. G. copelandii; Figure 1E) were close relatives (Parris, 2007). All such species are indeed placed within Grammitis s.s. in our molecular phylogeny, and we also anticipate that the type species of the genus (G. marginella, not included here) belongs to this group. However, G. cryptophlebia and G. coriaceifolia ined. are also both nested within Grammitis s.s. based on molecular data, although their laminae do not exhibit blackish margins (Figure 3, clade-1). It suggests that this character was lost at least once during the evolution of the clade. Consequently, the blackish sclerotic margin adds to the long list of homoplastic morphological characters in the evolution of grammitids [START_REF] Ranker | Phylogeny and evolution of grammitid ferns (Grammitidaceae): a case of rampant morphological homoplasy[END_REF], which resulted in the recent description of many genera.

Grammitis s.l. and Ctenopterella are highly polyphyletic, and lead to the identification of two new major clades

Apart from the Grammitis s.s. clade, other Grammitis species were retrieved in four lineages (Figure 2) that are consequently in need of new generic concepts. These phylogenetic placements were described previously for G. stenophylla (sister lineage to Acrosorus and Ctenopterella denticulata), and for the three-species clade sister to Notogrammitis [START_REF] Perrie | Chloroplast DNA sequences indicate the grammitid ferns (Polypodiaceae) in New Zealand belong to a single clade, Notogrammitis gen. nov[END_REF]Sundue et al., 2014). In addition, we identified two new lineages nested within clade-3 (Figure 2). The latter clade-3 is new for the grammitid phylogeny. Exclusively composed of African and WIO species, it was unexpected due to its singular placement within the large Paleotropical clade otherwise only composed of Asian and Oceanian taxa, and due to its grouping of six species of Grammitis with two species of Ctenopterella (Figures 2 and3). Laminar dissection was commonly used to distinguish Grammitis (simple, undivided laminae; Figure 1E) from Ctenopterella (pinnatisect laminae; Figure 1C) but the grouping of species from the two genera, in clade-3, supports leaf dissection as homoplastic as evidenced within other grammitid genera like Ceradenia [START_REF] Ranker | Phylogeny and evolution of grammitid ferns (Grammitidaceae): a case of rampant morphological homoplasy[END_REF]. This explains why the modern generic classification of grammitids is rather based on characters of the rhizomes, rhizome scales and frond hairs [START_REF] Parris | New genera of Malesian Grammitidacae (Monilophyta). Blumea -Biodiversity[END_REF][START_REF] Sundue | A morphological cladistic analysis of Terpsichore (Polypodiaceae)[END_REF]Sundue et al., 2010a). However, many of these morphological characters are variable among the species clustered in clade-3 (e.g. rhizome symmetry is either dorsiventral or radial, rhizomes scales are concolorous or bicolor, and clathrate or not). Clade-3 could nevertheless be supported by the presence of hydathodes, hypothesizing one reversion in the anhydathodous G. obtusa (Figure 3). This clade could be treated as one or several new genera distinct from Grammitis, which should ultimately be restricted to Grammitis s.s. Another possibility would be to accommodate the six species of Grammitis of clade-3 in an expanded concept of Ctenopterella. However, the placement of Ctenopterella in the whole tree is uncertain because the type species of the genus (C. blechnoides) has never been sampled and moreover, we recovered the three other sampled species of Ctenopterella as another distinct, new clade of the grammitid phylogeny (Figure 2).

Of this new Ctenopterella lineage, retrieved as sister to the clade formed by Notogrammitis and three species of Grammitis (Figure 2), two species are endemic to New Caledonia (C. lasiostipes and Ctenopterella sp. 1) and the third, Ctenopterella sp. 2, occurs in eastern Papua New Guinea, Solomon Islands and Vanuatu (Parris unpubl.; Appendix 1.2). We speculate that most, if not all other species from Oceania and South-eastern Asia (including the type species C. blechnoides) could belong here, i.e., 16 out of the ca. 21 species in the genus [START_REF] Parris | New genera of Malesian Grammitidacae (Monilophyta). Blumea -Biodiversity[END_REF][START_REF] Parris | Ctenopterella gabonensis, a new species of grammitid fern (Polypodiaceae) from Gabon, Africa[END_REF]. In contrast, the four Ctenopterella species from Africa and the WIO [START_REF] Parris | Ctenopterella gabonensis, a new species of grammitid fern (Polypodiaceae) from Gabon, Africa[END_REF] likely all cluster in clade-3 (as observed for the two species included here, C. zenkeri and C. parvula).

Enterosora is highly polyphyletic, notably revealing a new major grammitid clade

Enterosora was here recovered as polyphyletic for the first time (Figure 2). Although the genus was previously hypothesized as paraphyletic with respect to Zygophlebia (Sundue et al., 2010a), it was recently supported as monophyletic (Sundue et al., 2014). Our extended sampling included nine out of ca. 17 Zygophlebia species plus seven out of 11 Enterosora species, and led to two findings.

First, the close relationship between these two genera was confirmed, two lineages of Enterosora being nested within Zygophlebia (Figure 3, clade-2). The lack of morphological apomorphy supporting Enterosora [START_REF] Ranker | Phylogeny and evolution of grammitid ferns (Grammitidaceae): a case of rampant morphological homoplasy[END_REF][START_REF] Sundue | A morphological cladistic analysis of Terpsichore (Polypodiaceae)[END_REF] argues for including the five concerned species (E. enterosoides, E. trifurcata, E. trichosora, E. percrassa and E. barbatula) into Zygophlebia (the additional segregate lineage of E. barbatula from Réunion Island, retrieved within Ceradenia, is discussed in the next section, 4.1.4).

Second, the two species E. parietina and E. sprucei formed a new clade, placed as sistergroup to Adenophorus (Figures 2 and3, clade-1). This grouping is meaningful since E. parietina and E. sprucei are morphologically most closely related to each other within the genus. It is also in agreement with [START_REF] Bishop | Revision of the Fern Genus Enterosora (Grammitidaceae) in the New World[END_REF], who underlined that the affinity of E. sprucei (as E. gilpinae) and E. parietina to other species of Enterosora was not obvious, especially considering unique characters like medial soral placement and the number of annulus cells in the sporangia. All these characters should help to define a new genus accommodating this new clade. The type species of the genus, E. campbellii, has not been sampled yet, however we expect it to reside within clade-2 based on its assemblage of morphological characters. Within the new clade, E. parietina and E. sprucei were not monophyletic with respect to each other, in agreement with [START_REF] Bishop | Revision of the Fern Genus Enterosora (Grammitidaceae) in the New World[END_REF] who regarded them as conspecific in the Neotropics (as E. parietina). In fact, our results even support recognition of only one species on both sides of the Atlantic Ocean, as suggested by Parris [START_REF] Parris | New Species and New Combinations in African Grammitidaceae (Filicales)[END_REF][START_REF] Parris | Grammitidaceae[END_REF] and contrary to [START_REF] Bishop | Revision of the Fern Genus Enterosora (Grammitidaceae) in the New World[END_REF] who distinguished E. parietina in the Neotropics from E. gilpinae in Africa and Madagascar.

High level of cryptic species as revealed by a dense sampling on Madagascar

Our sampling, especially focused on Madagascar and other WIO islands and Africa, included at least two individuals from each of 30 species from this geographical region. This allowed assessment of monophyly at the species level. Based on our molecular data, a total of 12 species were revealed as non-monophyletic, although we could not identify morphological characters to differentiate the distinct lineages recovered for each nominal species (Table 4, Appendix 1.2). Therefore, nine of these species are best interpreted as cryptic species [START_REF] Bickford | Cryptic species as a window on diversity and conservation[END_REF]. The three remaining ones (Stenogrammitis oosora, Stenogrammitis sp. 1, and Enterosora sprucei) deserve further investigation since they could actually turn out to represent a single species each (see Table 4). In three cases of polyphyly (Grammitis ebenina (Figure 3, clade-1), Grammitis kyimbilensis (Figure 3, clade-1) and Enterosora barbatula (Figure 3, clade-2), the segregate lineages occurred in disjunct geographic areas. This provides an additional line of evidence to describe new species (respectively, two new species for Madagascar and one for Madagascar/Africa) that would accommodate the segregate, allopatric species with monophyly (Table 4). By contrast, for the six other cryptic species, only an in-depth study of integrative taxonomy combining molecular data, morphology, anatomy, cytometry and cytology might help to identify discriminating characters. Given that most grammitid ferns are epiphytes, a possibility of differential host-plant specificity should also be explored.

We do not know the evolutionary processes underlying cryptic speciation, but the apparent morphological similarity must be either a plesiomorphy due to shared ancestry (morphological stasis), or a homoplastic result of parallel or convergent evolution. Morphological stasis is rather expected to result from non-ecological vicariant speciation, e.g. when the topography is complex and populations are isolated [START_REF] Britton | Topography as a driver of cryptic speciation in the high-elevation cape sedge Tetraria triangularis (Boeck.) C. B. Clarke (Cyperaceae: Schoeneae)[END_REF]. In contrast, parallel or convergent evolution usually suggests the influence of selection, e.g. to adapt to extreme environmental conditions [START_REF] Bickford | Cryptic species as a window on diversity and conservation[END_REF] such as high elevations for many grammitid ferns [START_REF] Parris | New genera of Malesian Grammitidacae (Monilophyta). Blumea -Biodiversity[END_REF][START_REF] Sylvester | The world's highest vascular epiphytes found in the Peruvian Andes[END_REF]. We tend to favour the latter mechanism given the high dispersal capacities of ferns and the well-known homoplastic nature of several morphological traits in this group [START_REF] Ranker | Phylogeny and evolution of grammitid ferns (Grammitidaceae): a case of rampant morphological homoplasy[END_REF]. Hybridization might also be at the origin of some cryptic species [START_REF] Mallet | Hybrid speciation[END_REF] and is thought to be especially frequent in ferns compared to angiosperms [START_REF] Barrington | Hybridization, Reticulation, and Species Concepts in the Ferns[END_REF][START_REF] Haufler | Species and speciation[END_REF]. Hybrids are often postulated based on morphological intermediary between the two putative parents, but they sometimes retain the overall morphology of only one parent. In such a case, the comparison of plastid-and nuclear-based phylogenetic analyses may eventually provide evidence of such reticulate evolution, and explain the incongruence between morphological and molecular plastid data.

Our results showed that the identification of morphologically cryptic lineages increased the number of sampled species from 36 to >50 in the African-WIO region (some cryptic species have to be confirmed, and their exact number cannot be firmly established). Whatever the evolutionary origins of the cryptic species, failure to distinguish them greatly underestimates species richness [START_REF] Gill | Cryptic species diversity reveals biogeographic support for the 'mountain passes are higher in the tropics' hypothesis[END_REF], and consequently the impact of habitat destruction that is already a very serious threat in the Malagasy region [START_REF] Harper | Fifty years of deforestation and forest fragmentation in Madagascar[END_REF]. The inclusion of several samples per a priori delimited species is therefore crucial in a conservation perspective, to uncover the possible hidden but threatened Malagasy diversity.

Finally, taking into account all our phylogenetic findings, we suggest that the African-WIO region harbours >68 grammitid species (>50 analyzed here, plus 18 non-sampled species) instead of the 51 previously listed [START_REF] Roux | Synopsis of the Lycopodiophyta and Pteridophyta of Africa, Madagascar and neighbouring islands[END_REF]; that is, we document a >30% increase in the species richness of the region. Although some taxa are still missing and the extinction of some lineages may bias the inferences as in all biogeographic studies, our extended sampling provides valuable insights into the biogeographic events and evolutionary processes underlying the emergence of the species in the region.

BIOGEOGRAPHIC HISTORY OF GRAMMITID FERNS, AND ORIGINS OF THE AFRICAN-WIO SPECIES

At the worldwide scale: A Neotropical origin, followed by numerous LDD events

At the global scale, as in Sundue et al. (2014), our results supported the Neotropical origin of grammitids and the divergence and start of diversification of the group were dated to the Eocene and early Oligocene (39 and 34 Ma, respectively). This relatively recent timing confirms that dispersal, rather than vicariance linked to continental fragmentation, explains species distribution pat-terns. The high dispersal ability of dust-like spores has been previously invoked to explain LDD in fern lineages of diverse ages and in different areas (Hennequin et al., 2010b;[START_REF] Labiak | Molecular phylogeny, character evolution, and biogeography of the grammitid fern genus Lellingeria (Polypodiaceae)[END_REF][START_REF] Labiak | Phylogeny and historical biogeography of the lastreopsid ferns (Dryopteridaceae)[END_REF][START_REF] Lu | Phylogenetic relationships of Chinese Adiantum based on five plastid markers[END_REF][START_REF] Chao | Molecular phylogeny and biogeography of the fern genus Pteris (Pteridaceae)[END_REF][START_REF] Chen | A phylogeny and biogeographic analysis for the Cape-Pondweed family Aponogetonaceae (Alismatales)[END_REF][START_REF] Wei | Eurasian origin, boreotropical migration and transoceanic dispersal in the pantropical fern genus Diplazium (Athyriaceae)[END_REF][START_REF] Péchon | A well-sampled phylogenetic analysis of the polystichoid ferns (Dryopteridaceae) suggests a complex biogeographical history involving both boreotropical migrations and recent transoceanic dispersals[END_REF]. In addition, epiphytism with occurrence of long-lived and slow growing gametophytes, as observed in grammitids [START_REF] Stokey | The gametophyte of the Grammitidaceae[END_REF][START_REF] Parris | Grammitidaceae[END_REF], may allow to delay sexual reproduction until a second gametophyte germinates nearby and confer an additional advantage for successful colonization [START_REF] Dassler | Significance of gametophyte form in long-distance colonization by tropical, epiphytic ferns[END_REF][START_REF] Moran | Phytogeographic relationships between neotropical and African-Madagascan pteridophytes[END_REF][START_REF] Sessa | On the widespread capacity for, and functional significance of, extreme inbreeding in ferns[END_REF].

Origin of the African-WIO grammitids: A clearly predominant role of the

Neotropics, with one possible migration from tropical Asia s.l Based on the phylogenetic pattern composed of 'a monophyletic tropical Asian clade nested within a primarily Neotropical and African grade', Sundue et al. (2014) inferred the expansion and diversification of grammitids throughout the tropics. From the Neotropics, they inferred at least six dispersal events to Madagascar, two to the Hawaiian Islands in the Pacific, and only one to tropical Asia s.l. where the group underwent a striking species diversification (referred to as the Paleotropical clade, emerging in the late Oligocene 25 Ma). From tropical Asia s.l., they showed that the group further dispersed towards the Hawaiian Islands on the one hand, and to the circumaustral region on the other hand.

In contrast to those previous findings, we recovered the existence of an African-WIO clade nested within the Paleotropical clade, and composed of species sampled for the first time (clade V, Figure 4). This suggests the occurrence of a newly inferred dispersal from Tropical Asia s.l. to the African-WIO region (see map, Figure 4), which would be the oldest LDD event to this region observed in grammitids, at the end of the Oligocene. However, this inference remains to be confirmed since the branching pattern of the African-WIO clade with the rest of the Paleotropical clade was not well-supported statistically. Therefore, we cannot fully exclude that dispersal actually occurred from the Neotropics to Africa-WIO, and either later on from Africa-WIO to Tropical Asia s.l., or independently from the Neotropics to Tropical Asia s.l.

In spite of this new finding, our study strengthened the scenario of Sundue et al. (2014) of repeated dispersals from the Neotropics to the African-WIO region (Figure 4): while they inferred at least six such events, our data showed that at least 12 (occurring within the last 20 Ma and including species of 10 distinct genera) must actually be hypothesized to explain the current species richness of the region. This was in line with the observed distribution patterns: indeed, no genus is shared between the African-WIO region and Tropical Asia s.l. (only Ctenopterella and Grammitis were thought to be shared but turned out to be polyphyletic, with distinct lineages in both regions), whereas 11 genera are shared between the African-WIO region and the Neotropics. We do not exclude that the generic affinities between the Neotropics and the African-WIO region could be even greater since two genera were discovered recently in Madagascar, namely Leucotrichum [START_REF] Rouhan | Not so neotropical after all: the Grammitid fern genus Leucotrichum (Polypodiaceae) is also paleotropical, as revealed by a new species from Madagascar[END_REF] and Moranopteris (this study), which were previously considered endemic to the Neotropics. At the species level, even four species (A. elastica, C. serrulatum, E. sprucei and M. flabelliformis) are shared: this co-occurrence in the Neotropics and WIO may be explained by recent dispersal events (<4 Ma; and, therefore, insufficient time for geographically disjunct populations to diverge genetically) or by repeated dispersals, causing recurrent gene flow and preventing genetic differentiation.

Another eastward transatlantic migration of grammitid ferns is exemplified by the sister relationships between the Neotropical G. paramicola and G. ebenina, which is endemic to the mid-South Atlantic Ocean island of St. Helena, although this island is geographically closer to Africa (Figure 4). A similar closer evolutionary relationship between species from St. Helena and the Neotropics has been reported in the genus Elaphoglossum [START_REF] Vasco | Circumscription and phylogeny of the Elaphoglossum ciliatum group (E. sect. Lepidoglossa, Dryopteridaceae) based on cpDNA sequences[END_REF].

In contrast to these 12 eastward dispersal events, only one back-dispersal from the African-WIO region to the Neotropics was inferred, in Stenogrammitis (clade-IV; Figure 4). An additional such westward back-dispersal may have occurred in the Zygophlebia-Enterosora clade, where the African Zygophlebia cf. devoluta was retrieved as basal to a dichotomy of a Neotropical and an African-WIO clades: this pattern suggested either two independent dispersal events from the Neotropics to Africa-WIO, or one migration followed by a back-dispersal. In any case, transatlantic migrations appear highly skewed in their directions, with a predominant eastward direction.

The much higher affinity and closer phylogenetic relationships of grammitid ferns of the WIO with those of the Neotropics, compared to those of Tropical Asia s.l., may be due neither to ecological specificities -in all regions, most species occur in mountain forests -nor to lower dispersal abilities of taxa occurring in Tropical Asia s.l. -most of which have large distribution areas. Therefore, we rather hypothesize a higher potential for dispersal from the Neotropics than from Tropical Asia s.l. due to environmental factors, even if the Neotropics do not seem to be a major area in the biogeographic history of other Malagasy vascular plants: in their broad-scale survey, [START_REF] Buerki | Spatio-temporal history of the endemic genera of Madagascar[END_REF] identified only two undisputable cases of American ancestry for Malagasy angiosperms (in Haematodendron, Myristicaceae; and Tsoala, Solanaceae). More recently, [START_REF] Smedmark | Inferring geographic range evolution of a pantropical tribe in the coffee family (Lasiantheae, Rubiaceae) in the face of topological uncertainty[END_REF] and [START_REF] Janssens | Dispersing towards Madagascar: Biogeography and evolution of the Madagascan endemics of the Spermacoceae tribe (Rubiaceae)[END_REF] provided two additional examples of such dispersal from the Neotropics to Africa-WIO in Saldinia and Astiella and closely-related genera, respectively (both Rubiaceae). However, this pattern remains scarce in flowering plants. In contrast, it has been inferred in several fern groups (see Introduction). In some of them (e.g. Parapolystichum and Lastreopsis; [START_REF] Labiak | Phylogeny and historical biogeography of the lastreopsid ferns (Dryopteridaceae)[END_REF] connections between the Neotropics and the WIO could be facilitated by overland dispersal events via Antarctica, which were possible until the Late Cretaceous [START_REF] Buerki | Spatio-temporal history of the endemic genera of Madagascar[END_REF][START_REF] Yoder | Has Vicariance or Dispersal Has Vicariance Been the Predominant Force in Biogeographic Madagascar? Only Time Will Tell[END_REF]. However, it cannot be invoked in grammitids, whose stem lineage is younger (here dated to the Eocene at the earliest). Therefore, the most likely hypothesis for the strong link between the Neotropical and the WIO grammitids involves transoceanic LDD. Their highly predominant occurrence in the eastward direction could be due to transport of spores through winds blowing from the west, either surface winds over the Central Atlantic Ocean (10°S-5°N; even if these are subject to significant year-to-year changes), or the jet streams always blowing from the west and that may extend across the entire Atlantic basin [START_REF] Renner | Bayesian analysis of combined chloroplast loci, using multiple calibrations, supports the recent arrival of Melastomataceae in Africa and Madagascar[END_REF]. In fact, prevailing westerly trade winds existing at even higher latitudes (30-60°S latitude) could also have contributed to skewed dispersals [START_REF] Munoz | Wind as a Long-Distance Dispersal Vehicle in the Southern Hemisphere[END_REF], as suggested for many other fern genera with a circumaustral distribution including Madagascar [START_REF] Parris | Circum-Antarctic continental distribution patterns in pteridophyte species[END_REF]Sundue, Rouhan, & Moran, 2010b;[START_REF] Labiak | Phylogeny and historical biogeography of the lastreopsid ferns (Dryopteridaceae)[END_REF]. Such a very southern trajectory is likely to reach Madagascar and the other WIO islands through the counter clockwise gyre over the South Atlantic Ocean, moving over the ocean south of Africa and arriving in Madagascar, as modelled for spores of Ophioglossum reticulatum [START_REF] Torres | Distribution of Ophioglossum reticulatum L. in South America. A case of long-distance jump dispersal?[END_REF].

At the regional African-WIO scale: Madagascar, rather than Africa, acts as a

major source of dispersal Many species co-occur in Africa, Madagascar or the other WIO islands: 20 species are shared by at least two of these areas, out of the 51 species recorded in the overall region [START_REF] Roux | Synopsis of the Lycopodiophyta and Pteridophyta of Africa, Madagascar and neighbouring islands[END_REF]. In agreement with these shared distribution patterns, species that are endemic to one territory were most often retrieved as sister-species to others distributed in nearby areas, showing a high level of dispersal at this regional scale.

Strikingly, we inferred only one possible dispersal event from Africa towards Madagascar and the other WIO islands, which gave rise to clade-III (Figure 4). In all other cases, the origin of dispersal within the region appeared to be either Madagascar or the other WIO islands. Therefore, Africa does not seem to be a source region for grammitid species in the WIO, contrary to what could be expected based on the Theory of Island Biogeography [START_REF] Macarthur | The theory of island biogeography[END_REF] and empirical evidence for most of the angiosperms studied [START_REF] Yoder | Has Vicariance or Dispersal Has Vicariance Been the Predominant Force in Biogeographic Madagascar? Only Time Will Tell[END_REF][START_REF] Buerki | Spatio-temporal history of the endemic genera of Madagascar[END_REF][START_REF] Janssens | Dispersing towards Madagascar: Biogeography and evolution of the Madagascan endemics of the Spermacoceae tribe (Rubiaceae)[END_REF][START_REF] Bacon | Biogeography of the Malagasy Celastraceae: Multiple independent origins followed by widespread dispersal of genera from Madagascar[END_REF]. Actually, there is a growing body of evidence against the paradigm postulating that continents and islands respectively act as sources and sinks of species diversity [START_REF] Heaney | Is a new paradigm emerging for oceanic island biogeography?[END_REF], and an increasing awareness of the importance of islands as cradles of diversity themselves: it has been documented for the WIO islands [START_REF] Agnarsson | The generation of a biodiversity hotspot: biogeography and phylogeography of the western Indian Ocean islands[END_REF][START_REF] Krüger | Molecular phylogeny of the tribe Danaideae (Rubiaceae: Rubioideae): Another example of out-of-Madagascar dispersal[END_REF] and for the Macaronesian islands [START_REF] Patiño | Approximate Bayesian Computation Reveals the Crucial Role of Oceanic Islands for the Assembly of Continental Biodiversity[END_REF]. Although the observed patterns may be overestimated due to missing African species in our study (we included 14 out of 26 African species), grammitid ferns corroborate the latter scenario, and provide another example contradicting the traditional view. This was also suggested by the higher species diversity described from Madagascar compared to continental Africa, which harbour ca. 31 and 26 species, respectively, although Africa is 50 times larger in area. Such a lower taxonomic diversity in Africa compared to Madagascar was also observed in many other fern genera [START_REF] Kornas | The Significance of Historical Factors and Ecological Preference in the Distribution of African Pteridophytes[END_REF][START_REF] Roux | Synopsis of the Lycopodiophyta and Pteridophyta of Africa, Madagascar and neighbouring islands[END_REF]. It may be due either to the extinction of lineages after much more severe droughts there than in Madagascar during the Late Miocene and Pleistocene [START_REF] Morley | Origin and evolution of tropical rain forests[END_REF][START_REF] Aldasoro | Diversity and distribution of ferns in sub-Saharan Africa, Madagascar and some islands of the South Atlantic[END_REF], which led to a decline of African rainforests [START_REF] Kornas | The Significance of Historical Factors and Ecological Preference in the Distribution of African Pteridophytes[END_REF][START_REF] Morley | Origin and evolution of tropical rain forests[END_REF][START_REF] Linder | The evolution of African plant diversity[END_REF], or to the lack of extensive mountain ranges [START_REF] Moran | The importance of mountains to Pteridophytes, with emphasis on Neotropical montane forests[END_REF], or most probably to several intricate, both historical and more recent causes [START_REF] Couvreur | Odd man out: why are there fewer plant species in African rain forests?[END_REF].

From Madagascar and/or the neighbouring islands, dispersal also occurred over larger geographic distances, as evidenced by the colonization of the Subantarctic island of Amsterdam by the genus Stenogrammitis: the phylogeny showed that the Neotropical S. jamesonioides was sister-species to a clade formed by two species, one from Madagascar and Réunion, and the other from Amsterdam. The most likely biogeographic scenario involves a dispersal event from the Neotropics to Madagascar and/or Réunion, later followed by dispersal to Amsterdam (Figure 4). Whereas Sundue et al. (2014) suggested that circumaustral taxa only originated in Tropical Asia, our results therefore suggest that the WIO area also played a role in the range expansion of grammitids to this temperate area.

THE OCCURRENCE OF POST-DISPERSAL DIVERSIFICATION

In total, at least 13 LDD events may explain the origin of the >50 species (including cryptic lineages) sampled in Africa, Madagascar, and other WIO islands. In particular, five LDD gave rise to diversifications counting six to 14 species each. Species diversification probably proceeds at a reduced pace in ferns compared to flowering plants, because of their strong dispersal capacities that slow down genetic differentiation [START_REF] Gillespie | Longdistance dispersal: A framework for hypothesis testing[END_REF]. We actually noticed that diversification occurred in the most ancient lineages, suggesting that the time elapsed since the colonization of a given lineage may be involved in its diversification. Species diversification was probably favoured by the environmental diversity within Madagascar: with its very diverse ecological conditions, the island is known to host spectacular species radiations [START_REF] Vences | Madagascar as a model region of species diversification[END_REF][START_REF] Soulebeau | The hypothesis of adaptive radiation in evolutionary biology: hard facts about a hazy concept[END_REF]. At the regional scale, the insular system and resulting relative isolation of populations probably also facilitated species diversification, in spite of dispersal. The evolutionary processes involved in such diversification will be investigated in further studies.

ABSTRACT

Rumohra is a fern genus comprising seven species, three in South America, three in Madagascar and one (R. adiantiformis) which is widely distributed across the Southern Hemisphere. Our goals were to assess species delimitation based on molecular data and to infer the biogeographical history that led to such contrasting distributions among species. We sampled all Rumohra spp., with 46 samples including 28 R. adiantiformis accessions from 14 regions, and sequenced eight plastid DNA regions: atpA,atpB,rbcL, The resulting phylogenetic trees showed R. adiantiformis to be polyphyletic, with at least six lineages found in distinct geographical regions. Given the apparent absence of distinctive morphological characters among lineages, they are best understood as cryptic species. Such genetically distinct but morphologically similar populations may result from a recurrent history of hybridization, morphological convergence or (most probably) morphological stasis. Molecular dating and ancestral area estimations showed that Rumohra diverged from the genus Megalastrum c. 46.4 Mya in the Neotropics, and started to diversify 11.2 Mya. Its biogeographical history was probably shaped by seven long-distance dispersal (LDD) events including three initial events from the Neotropics to southern Africa, the Malagasy region and southern South America. The Australasian lineage resulted from a LDD from southern South America, and the three species endemic to Madagascar diversified in situ.

KEYWORDS

Madagascar, molecular phylogeny, pteridophytes, southern Hemisphere, species concept, systematics, western Indian Ocean

INTRODUCTION

Delimiting species is an essential prerequisite for studies of ecology and evolution and the implementation of appropriate conservation measures. Beyond morphological investigations, molecular markers have greatly improved our ability to circumscribe taxonomic units in recent decades, leading to a so-called integrative taxonomy [START_REF] Rouhan | Plant taxonomy: a historical perspective, current challenges, and perspectives[END_REF]. Molecular markers are especially valuable in groups with few morphological attributes and in groups comprising morphologically similar populations that sometimes occur across large geographical areas. In the latter case, a widely distributed morphologically defined species might consist of a single interconnected gene-pool (e.g. if dispersal is frequent), or may be composed of several evolutionarily independent lineages. Indeed, large geographical distances can lead to reduced gene exchange among populations, resulting in neutral genetic divergence under the action of genetic drift. Nevertheless, such genetic divergence is not necessarily accompanied by morphological changes (morphological stasis). Alternatively, morphological similarity in widely distributed taxa can result from convergence towards traits that confer a selective advantage and that are therefore independently selected in lineages that are not closely related [START_REF] Patterson | Phylogeny, concerted convergence, and phylogenetic niche conservatism in the core Liliales: insights from rbcL and ndhF sequence data[END_REF]. The discovery of cryptic species (distinct species that are, or have been, erroneously classified under one species name because of their similar morphology, but are genetically distinct; [START_REF] Bickford | Cryptic species as a window on diversity and conservation[END_REF] is probably still limited by the low variability of molecular markers, especially in plants, and by the sampling schemes adopted, which often consist of a single or few individual/accession(s) per morphologically recognized species. However, a growing number of studies provide evidence for cryptic species in various plant groups [START_REF] Bickford | Cryptic species as a window on diversity and conservation[END_REF]; see also, e.g. [START_REF] Hedenäs | Cryptic speciation, habitat differentiation, and geography in Hamatocaulis vernicosus (Calliergonaceae, Bryophyta)[END_REF][START_REF] Pillon | Cryptic species, gene recombination and hybridization in the genus Spiraeanthemum (Cunoniaceae) from New Caledonia[END_REF][START_REF] Crowl | Embracing discordance: Phylogenomic analyses provide evidence for allopolyploidy leading to cryptic diversity in a Mediterranean Campanula (Campanulaceae) clade[END_REF][START_REF] Bauret | Madagascar sheds new light on the molecular systematics and biogeography of grammitid ferns: New unexpected lineages and numerous long-distance dispersal events[END_REF]. Genetic data can also provide insight into the evolutionary (phylogenetic) relationships among taxa and their diversification history, providing hypotheses to explain the observed species distributions and morphological disparity or, by contrast, morphological uniformity.

Rumohra Raddi is a small fern genus of seven, mostly tropical species. It contains one species with populations spread across the whole Southern Hemisphere [R. adiantiformis (G.Forst) Ching], whereas the remaining six species are restricted to two centres of endemism (Table 1): South America (three endemics; [START_REF] Sundue | Rumohra glandulosissima (Dryopteridaceae) a new species from the Atlantic Rainforest, and revision of the species occurring in Brazil[END_REF] and Madagascar (three endemics; Rakotondrainibe, 2010b). Species are terrestrial, epilithic or epiphytic, and the genus is morphologically characterized by a combination of several features (Figure 1): creeping rhizomes with a dorsal leaf arrangement; elongate ventral meristele; lanceolate to deltate, two-to three-(to four-) pinnate laminae; decurrent leaf margins forming erect wings along the axes; and peltate indusia. Because the architecture of the lamina is fairly uniform across the genus, species are mostly distinguished based on their rhizome habit, rhizome scales and lamina indument (e.g. sessile and/ or stipitate glands). Rumohra belongs to Dryopteridaceae subfamily Elaphoglossoideae [START_REF] Ppgi | A community-derived classification for extant lycophytes and ferns[END_REF] or Polypodiaceae subfamily Dryopteridoideae [START_REF] Christenhusz | Trends and concepts in fern classification[END_REF]. With the genera Megalastrum Holttum (91 species; Moran, Prado, & Sundue, 2014b,c), Lastreopsis Ching (16 species; Labiak et al., 2015b) and Parapolystichum (Keyserl.) Ching (28 species; Labiak et al., 2015b;[START_REF] Testo | A 4000-species dataset provides new insight into the evolution of ferns[END_REF], Rumohra forms a monophyletic group of 142 species referred to as lastreopsid ferns [START_REF] Labiak | Phylogeny and historical biogeography of the lastreopsid ferns (Dryopteridaceae)[END_REF]. To date, no phylogenetic study has focused on Rumohra. The relationships of two species [R. berteroana (Colla) R.Rodr.R. (endemic to the Juan Fernández Islands, Chile) and R. adiantiformis (circumaustral)] have been analysed. These species were recovered as forming a group that is sister to Megalastrum [START_REF] Labiak | Phylogeny and historical biogeography of the lastreopsid ferns (Dryopteridaceae)[END_REF]. Based on sampling from three localities of R. adiantiformis, [START_REF] Labiak | Phylogeny and historical biogeography of the lastreopsid ferns (Dryopteridaceae)[END_REF] also revealed that this wide-spread species may contain more than one lineage. The systematics of Rumohra may thus require revision, and R. adiantiformis is a candidate with which to investigate the alternative evolutionary causes of morphologically similar and widespread populations: morphological convergence vs. morphological stasis.

Besides its systematics, the distribution of Rumohra raises questions regarding the biogeographical history that has led to such contrasting distributions among species, in terms of spatial extent and geographical location, with three species endemic to South America, three endemic to Madagascar and one widespread, circum-austral species. [START_REF] Labiak | Phylogeny and historical biogeography of the lastreopsid ferns (Dryopteridaceae)[END_REF] highlighted the importance of both vicariance and dispersal in the diversification history of lastreopsids and favoured several long-distance dispersal (LDD) events as the most likely explanation for the expansion and diversification of the Megalastrum-Rumohra clade between the Eocene and Oligocene. This is congruent with the well-known abilities of ferns to disperse easily across long distances owing to their dust-like meiospores [START_REF] Barrington | Ecological and Historical Factors in Fern Biogeography[END_REF][START_REF] Moran | Phytogeographic relationships between neotropical and African-Madagascan pteridophytes[END_REF][START_REF] Wolf | Geographic distributions of homosporous ferns: Does dispersal obscure evidence of vicariance?[END_REF]. Nevertheless, this scenario remained tentative for Rumohra, due to limited sampling.

In this study, we focused on Rumohra and, based on an exhaustive species sampling and extensive within-species sampling for the widely distributed R. adiantiformis, we inferred the molecular phylogeny of the genus in a spatiotemporal framework. Our goals were: (1) to assess the monophyly of the genus and its species; (2) more specifically, to identify whether R. adiantiformis represents a single taxonomic unit or several distinct but morphologically similar evolutionary units (cryptic species); and (3) to infer the biogeographical history of the group.

MATERIAL AND METHODS

TAXONOMIC SAMPLING

Our study relied on an exhaustive sampling of Rumohra species diversity, with 46 specimens representing the seven known species. As R. adiantiformis is widespread throughout the tropics, and is mostly of circum-austral distribution, we sampled this species in 14 representative, disjunct localities to cover its large distribution (Table 1). Twelve species were added as outgroups, including five species of the two most closely related genera to Rumohra, namely Megalastrum and Lastreopsis [START_REF] Labiak | Phylogeny and historical biogeography of the lastreopsid ferns (Dryopteridaceae)[END_REF].

Vouchers details are provided in Supporting Information, Appendix 2.

DNA EXTRACTION, AMPLIFICATION AND SEQUENCING

DNA extraction was performed from silica-dried leaf material or, when such material was not available, from herbarium specimens. We used the Qiagen DNeasy Plant Mini Kit (Valencia, CA, USA), and modified the protocol for herbarium specimens by adding 30 µL proteinase K (20 mg/mL) and 30 µL beta-mercaptoethanol for the initial lysis step, which was carried out at 42 °C for 24 h. Eight plastid DNA regions were amplified by PCR: the genes atpA, atpB and rbcL and the non-coding regions atpB-rbcL, rps4-trnS, trnG-trnR, trnH-psbA and the trnL intron plus the trnL-trnF intergenic spacer (trnL/trnL-trnF). All PCRs were carried out in a 25 μL volume containing 1× PCR buffer, 2.5 mM MgCl2, 250 μM each dNTP, 1 M betaine, 0.4 μM each primer, 0.75 U Taq polymerase (Taq CORE kit; MP Biomedicals, Illkirch, France) and 1 μL non-diluted genomic DNA. Primer sequences and thermal cycling conditions are reported in Table 2. PCR products were checked on a 1% agarose gel and sequenced in both directions by Eurofins (Evry, France) using the amplification primers and additional internal primers for atpA, atpB, rbcL and trnG-trnR (Table 2). DNA strands were edited and assembled in Sequencher 4.9 (Gene Codes Corporation, Ann Arbor, MI, USA) and the 292 newly obtained consensus sequences were submitted to GenBank (Supporting Information, Appendix 2.

PHYLOGENETIC ANALYSES

Consensus sequences were automatically aligned in Muscle 3.8.425 [START_REF] Edgar | MUSCLE: multiple sequence alignment with high accuracy and high throughput[END_REF], and the eight resulting alignments were checked by eye and revised manually. After analysis of each marker independently to check the absence of supported conflicts between the estimated topologies, a data matrix was built by concatenation of all eight DNA regions using Sequence Matrix 1.7.8 [START_REF] Vaidya | SequenceMatrix: concatenation software for the fast assembly of multi-gene datasets with character set and codon information[END_REF]. Each region constituted an independent partition in the final dataset, and gaps were treated as missing data.

Bayesian inference (BI) and maximum likelihood (ML) approaches were used to infer phylogenetic relationships and were conducted on the CIPRES science gateway [START_REF] Miller | Creating the CIPRES Science Gateway for inference of large phylogenetic trees[END_REF]. For the BI, we used a Metropolis-coupled Markov chain Monte Carlo (MCMC) method implemented in MrBayes 3.2.6 [START_REF] Ronquist | MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space[END_REF]. For each region, a reversible jump MCMC (rjMCMC; [START_REF] Huelsenbeck | Bayesian phylogenetic model selection using reversible jump Markov Chain Monte Carlo[END_REF]) was used to find the most appropriate model of nucleotide substitution. We allowed the rjMCMC to move across models with +I+Γ. Two independent, but parallel, analyses of three million generations each were conducted, with four chains (one cold and three incrementally heated at a temperature of 0.1) sampled every 300 generations to obtain 10,000 sampled trees. We used Tracer 1.6.0 [START_REF] Rambaut | FigTree 1.4.2 software[END_REF] to check the output parameter estimates through time, the convergence of the two runs to the same stationary distribution and the burn-in length. We discarded the first 2,500 (25%) trees as burn-in, and pooled the 7,500 remaining trees in a 50% majority-rule consensus with average branch lengths and posterior probability (PP) estimates for all nodes.

The ML analysis was performed using RAxML-HPC2 8.2.6 [START_REF] Stamatakis | RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies[END_REF], using the same eight partitions as in MrBayes and with the GTRGAMMA+I model of nucleotide substitution. We performed 1,000 rapid bootstrap (BS) replicates and searched for the best-scoring ML tree. The BI 50% majority-rule consensus tree and ML best tree were visualized in FigTree 1.4.2 [START_REF] Rambaut | FigTree 1.4.2 software[END_REF].

DIVERGENCE TIME ESTIMATION

We performed the dating analyses on a reduced data-set of 26 samples representing all seven Rumohra spp. and 12 outgroups. We kept one sample per species or per lineage in the case of R. adiantiformis (keeping two samples for the lineage including specimens from South Africa and Amsterdam Island; see Results). Divergence time estimates were calculated using BEAST 2.4.2 [START_REF] Bouckaert | BEAST 2: a software platform for Bayesian evolutionary analysis[END_REF] on the CIPRES science gateway. Partitions were the same as for the BI and ML phylogenetic analyses, and nucleotide substitutions followed a +I+G reversible-jump model as implemented in the RBS 1.3.1 BEAST package.

The uncertainty about the placement of fossils of Dryopteridaceae previously led authors not to rely on these fossils [START_REF] Collinson | Cainozoic ferns and their distribution[END_REF][START_REF] Sessa | Phylogeny, divergence times, and historical biogeography of New World Dryopteris (Dryopteridaceae)[END_REF][START_REF] Labiak | Phylogeny and historical biogeography of the lastreopsid ferns (Dryopteridaceae)[END_REF], but a recently described fossil unambiguously assigned to Elaphoglossum Schott ex J.Sm. was dated to 15-20 Mya (early Miocene) and could provide an external calibration point [START_REF] Lóriga | The first fossil of bolbitidoid ferns belongs to the early divergent lineages of Elaphoglossum (Dryopteridaceae)[END_REF]. This fossil was not assigned to any section of Elaphoglossum, and could even belong to an extinct lineage of the genus. We therefore imposed the age constraint at the node between E. decoratum (Kunze) T.Moore and E. amygdalifolium (Mett. ex Kuhn) Christ, the latter being sister to the rest of the genus [START_REF] Rouhan | Molecular phylogeny of the fern genus Elaphoglossum (Elaphoglossaceae) based on chloroplast non-coding DNA sequences: Contributions of species from the Indian Ocean area[END_REF][START_REF] Lóriga | The first fossil of bolbitidoid ferns belongs to the early divergent lineages of Elaphoglossum (Dryopteridaceae)[END_REF]. The age of this node was modelled by a uniform prior from 15 Mya to infinity.

We also used secondary calibration points from two large-scale studies on the timing of the diversification of leptosporangiate ferns [START_REF] Schuettpelz | Evidence for a Cenozoic radiation of ferns in an angiosperm-dominated canopy[END_REF][START_REF] Testo | A 4000-species dataset provides new insight into the evolution of ferns[END_REF]. [START_REF] Testo | A 4000-species dataset provides new insight into the evolution of ferns[END_REF] reported older ages for numerous nodes and explained the contrast between their estimates and those of [START_REF] Schuettpelz | Evidence for a Cenozoic radiation of ferns in an angiosperm-dominated canopy[END_REF] by differences in the fossil calibrations and statistical methods used, notably the use of penalized likelihood by [START_REF] Schuettpelz | Evidence for a Cenozoic radiation of ferns in an angiosperm-dominated canopy[END_REF] vs. an uncorrelated lognormal relaxed clock in their study. We chose to run two separate analyses to successively adopt two calibration points from these two studies, to consider all the available data to date and to compare their influence on dating estimates in Rumohra: the ages of the lastreopsids and Rumohra An uncorrelated lognormal relaxed clock was used, with a birth-death tree prior and a random starting tree. For each analysis, two independent runs of 100 million generations with random seed values were conducted, sampled every 10,000 generations to obtain 10,000 sampled trees. Using Tracer 1.6.0 [START_REF] Rambaut | FigTree 1.4.2 software[END_REF], we checked the convergence of the two runs and set the burn-in length to 10%. We combined the runs with LogCombiner 2.4.2, computed the maximum clade credibility tree with TreeAnnotator 2.4.2, and visualized the maximum clade credibility tree and the associated chronogram in FigTree 1.4.2 [START_REF] Rambaut | FigTree 1.4.2 software[END_REF].

BIOGEOGRAPHICAL ANALYSES

To explore the biogeographical history of Rumohra, we estimated ancestral range variation along the resulting chronogram, using the R package BioGeoBEARS (Biogeography with Bayesian Evolutionary Analysis in R Scripts; [START_REF] Matzke | BioGeoBEARS: BioGeography with Bayesian (and likelihood) evolutionary analysis in R scripts[END_REF] et al., 2013;referred to as BAYAREALIKE in BioGeoBEARS). We performed three analyses using each of these methods (DEC, DIVALIKE, BAYAREALIKE), plus three implementing the additional free parameter j (DEC+j, DIVALIKE+j, BAYAREALIKE+j) that stands for the additional process of a founder event speciation, when a daughter lineage disperses to a new range outside the range of its ancestor. These '+j' models infer ancestral areas at each node and, for example, the DEC+j model has been shown to perform significantly better than the DEC model for island groups and intercontinental distributions [START_REF] Matzke | Model Selection in Historical Biogeography Reveals that Founder-Event Speciation Is a Crucial Process in Island Clades[END_REF].

We then selected from among the six models the one that was best-suited to model our data based on the Akaike information criterion (AIC). The selected model was used to infer the relative probabilities of ancestral ranges along the phylogeny.

We also performed biogeographical stochastic mapping (BSM) implemented in BioGeoBEARS [START_REF] Matzke | Stochastic mapping under biogeographical models[END_REF]. BSM simulates biogeographical histories (called 'realizations') given the phylogenetic topology (here, the one inferred by BEAST) and the best-suited biogeographical model identified under the AIC. Averaging over many realizations will result in the same ancestral range probabilities as those calculated under the likelihood model. As a BSM realization constitutes one of many possible exact histories, biogeographical events can be objectively hypothesized and counted from it. We performed 100 realizations of BSM to observe the most commonly retrieved biogeographical histories, successively considering the two most likely origins inferred for Rumohra, i.e. a Neotropical origin and an Australasian origin.

Geographical distributions were coded as combinations of eight areas: Neotropics; southern (temperate) South America; southern Africa; Comoros; Madagascar; Mascarenes and Seychelles; southern Indian Ocean islands; and Australia-New Zealand-Papua New Guinea (referred to as Australasia). We coded the distributions of whole species (and not only the localities of the included specimens), except for R. adiantiformis. This species was polyphyletic (see Results) and we therefore coded the locality of each sampled specimen. Geographical distributions were based on herbarium specimens (checked for taxonomic identifications), floras [START_REF] Marticorena | Reconciling the origins of Africa, India and Madagascar with vertebrate dispersal scenarios[END_REF][START_REF] Mccarthy | Ferns, gymnosperms and allied groups[END_REF][START_REF] Labiak | Phylogeny and historical biogeography of the lastreopsid ferns (Dryopteridaceae)[END_REF] and personal observations of the authors. The maximum range size was set to two areas, as it is the maximum number of areas today covered by terminal taxa.

RESULTS

PHYLOGENETIC RELATIONSHIPS

We obtained a combined data matrix of 58 specimens and 6926 characters (Table 3). The topologies inferred by the BI and ML analyses were similar and both strongly supported the monophyly of Rumohra (BS = 100; PP = 1), with Megalastrum as sister genus (BS = 99; PP = 1; Figure 2). Rumohra adiantiformis was grossly polyphyletic, being recovered in eight lineages (Figure 2). However, taking into account the lack of resolution in clade A and weak support of the R. adiantiformis-R. linearisquamata clade (BS < 50; PP = 0.66), the results showed that R. adiantiformis formed at least six geographically structured and supported lineages distributed in the Comoros, WIO excluding the Comoros, Neotropics, South Africa and Amsterdam Island [hypothesizing that subclades (3) and (4) in fact group together], southern South America, and Australasia. The other six species were either monophyletic (R. lokohensis, BS = 66 and PP = 0.76; R. madagascarica, BP = 86 and PP = 1; and R. berteroana, BP = 94 and PP = 1) or unresolved (R. glandulosissima, R. linearisquamata, R. quadrangularis).

Rumohra

DIVERGENCE TIME ESTIMATES

Trees obtained from the two dating analyses, based on calibration points from Testo & Sundue (2016) and [START_REF] Schuettpelz | Evidence for a Cenozoic radiation of ferns in an angiosperm-dominated canopy[END_REF], respectively, were similar for both the topology and the node support values (Figure 3). They showed slightly better resolution in clade A (PP = 0.99) than the BI and ML trees estimated in MrBayes and RAxML: a subclade grouped the South African and Amsterdam Island samples of R. adiantiformis (PP = 0.88), and was sister to the Neotropical subclade (including R. quadrangularis, R. glandulosissima and R. adiantiformis; PP = 1) with PP = 0.71. 4). Diversification of extant Rumohra spp. would have started much more recently, during the Miocene, either 11.2 (95% HPD: 8.3-14.4) or 7.2 Mya (95% HPD: 5.1-9.2). Despite these differences among age estimates based on the two calibration sources, the 95% HPD overlapped for all nodes in Rumohra (Figure 4).

ANCESTRAL AREAS ESTIMATION

We identified DEC+j as the best fitting model under the AIC (LnL = -54.61; AIC = 115.2), followed by the DIVALIKE+j (LnL = -55.81; AIC = 117.6) and BAYAREALIKE+j (LnL = -58; AIC = 122). The DEC+j model estimated the Neotropics as the most probable ancestral area for the lineage leading to extant Rumohra spp. (stem node, P = 0.48; followed by Australasia with P = 0.22; Figure 3). However, Australasia and the Neotropics were inferred with nearly equal probabilities at the Rumohra crown node (P = 0.30 and 0.29, respectively). When performing 100 BSM realizations, we counted 37 realizations with a Neotropical origin for the Rumohra lineage (stem node), which showed an ancestral range at the crown node also in the Neotropics for 16 of them. An Australasian origin for Rumohra (stem node) was inferred for 24 realizations out of 100, all showing an ancestral range at the crown node also in Australasia. Focusing on clade B, the DEC+j analysis inferred an Australasian ancestral area as the most probable (crown node; P = 0.60, Figure 3), whereas a southern South America area was less probable (P = 0.39). However, the BSM realizations with a Neotropical stem for the genus, which were the most abundant (see above), were mostly followed by inferences of the Neotropics at the crown node of Rumohra (16 out of 37 realizations), which in turn showed 11 out of 16 realizations (69%) with a southern South America ancestral area for clade B.

Based on the DEC+j and BSM results that both suggested a Neotropical origin for the stem lineage of the genus, Rumohra would have dispersed three times (

DISCUSSION

Our molecular phylogenetic results supported the evolutionary distinctiveness of three (out of seven) Rumohra spp.: the Malagasy endemics R. lokohensis and R. madagascarica and the Juan Fernández endemic R. berteroana. The monophyly of three other species (the Malagasy R. linearisquamata and the Neotropical R. quadrangularis and R. glandulosissima) remained uncertain because of low resolution. Importantly, we observed that the only widely distributed species, R. adiantiformis, was polyphyletic, with the spatial distribution of its phylogenetic lineages exhibiting a clear geographical structure. This polyphyly was in agreement with, and further strengthened, the pattern detected by [START_REF] Labiak | Phylogeny and historical biogeography of the lastreopsid ferns (Dryopteridaceae)[END_REF], who revealed the paraphyly of R. adiantiformis with respect to R. berteroana based on a restricted sampling (i.e. one R. berteroana and three R. adiantiformis samples from Madagascar, Brazil and Australia).

In addition, our results suggest that although Rumohra originated c. 46.4 Mya, its diversification started only 11.2 Mya and most extant species/line-ages evolved < 5 Mya (based on calibration points from Testo & Sundue, 2016; and assuming that all lineages of the genus are still represented today). We propose a biogeographical scenario to explain the current, mostly circum-austral distribution of the genus, involving several LDD events from a Neotropical ancestral area.

POLYPHYLY OF R. ADIANTIFORMIS: IMPLICATIONS FOR SYSTEMATICS AND CONSERVATION

Based on sampling that includes all known regions where R. adiantiformis occurs, we detected at least six (and up to eight) distinct lineages in this species (the exact number remains uncertain owing to the lack of resolution on deep nodes in the phylogeny). Despite this polyphyletic pattern, no clear morphological or anatomical characters that distinguish among these lineages of R. adiantiformis have been found to date (L. Bauret, pers. obs.). Based on current knowledge, lineages of R. adiantiformis therefore do not fit the early morphological or 'typological' species concept [START_REF] Darwin | On the origin of species by means of natural selection, or the preservation of favoured races in the struggle for life[END_REF]. In addition, we do not know whether R. adiantiformis lineages would maintain their molecular distinctness in sympatry, i.e. whether they are reproductively isolated and fit the concept of 'biological' species sensu [START_REF] Mayr | Systematics and the origin of species from the viewpoint of a zoologist[END_REF]. Nevertheless, it is now commonly accepted that species do not have to be fully isolated reproductively, a phenomenon that sometimes leads to (at least transiently) paraphyletic species [START_REF] Queiroz | Species Concepts and Species Delimitation[END_REF][START_REF] Der | Global Chloroplast Phylogeny and Biogeography of Bracken (Pteridium; Dennstaedtiaceae)[END_REF][START_REF] Vanderpoorten | The application of molecular data to the phylogenetic delimitation of species in bryophytes: a note of caution[END_REF]. Furthermore, the lineages of R. adiantiformis appear to fit the current most commonly used 'evolutionary' species concept, according to which a species consists of a group of populations that share a common ancestor and evolve independently from other such groups [START_REF] Simpson | The species concept[END_REF]; reviewed by [START_REF] Mallet | Hybrid speciation[END_REF][START_REF] Queiroz | Species Concepts and Species Delimitation[END_REF]. Therefore, given the absence of well-established morphological disparity and although this result should be checked with other molecular (in particular, nuclear) markers, R. adiantiformis is best understood as a complex of cryptic species [START_REF] Bickford | Cryptic species as a window on diversity and conservation[END_REF]. Cryptic species are increasingly being discovered with the more widespread use of molecular tools, especially in morphologically simple organisms, such as non-vascular plants, that lack obvious characters (see, e.g. [START_REF] Hedenäs | Cryptic speciation, habitat differentiation, and geography in Hamatocaulis vernicosus (Calliergonaceae, Bryophyta)[END_REF], for a case study in mosses). Cryptic species have also been detected in ferns (e.g. [START_REF] Bauret | Madagascar sheds new light on the molecular systematics and biogeography of grammitid ferns: New unexpected lineages and numerous long-distance dispersal events[END_REF], underlining the importance of analysing numerous samples per morphologically delimited species. In addition to further genetic investigations, it would be useful to determine whether a combination of characters (as opposed to a single one) could distinguish among lineages by adopting a morphometric approach, such as successfully applied on the sedge Tetraria triangularis (Boeckeler) C.B. Clarke [START_REF] Britton | Topography as a driver of cryptic speciation in the high-elevation cape sedge Tetraria triangularis (Boeck.) C. B. Clarke (Cyperaceae: Schoeneae)[END_REF].

In such an evolutionary framework, our result should therefore lead to the recognition of at least five additional species. The type specimen of R. adiantiformis was collected in New Zealand [START_REF] Nicolson | The Forsters and the botany of the second Cook Expedition (1772-1775)[END_REF], and the name would therefore have to be retained for the lineage observed in New Zealand, Papua New Guinea and Australia, which are the only Australasian areas where R. adiantiformis occurs. Other species would have to be recognized to account for plants growing in: (1) the Neotropics (Brazil to West Indies);

(2) southern South America (Argentina to the Falkland Islands); (3) Madagascar, Seychelles, Reunion and Mauritius; (4) the Comoros archipelago; and (5) southern Africa and the southern Indian Ocean islands (Amsterdam and St. Paul). The recognition of such species has an obvious consequence and importance in terms of conservation planning. Indeed, species are the fundamental units for biodiversity assessments and management and there would be an increase from one widely distributed species (the former R. adiantiformis) to six species with necessarily smaller distribution areas (the most extreme case being the species/lineage restricted to the Comoros). The newly recognized species would be more susceptible to habitat destruction and extinction, and would consequently deserve more careful consideration and potential protection. The observed lineages represent distinct evolutionary units and should therefore be conserved as much as possible, as the extinction of one of them would result in the extinction of its unique genetic background and associated adaptive potential [START_REF] Bickford | Cryptic species as a window on diversity and conservation[END_REF].

From a practical point of view, there is currently no clear diagnostic morphological character to distinguish among lineages of R. adiantiformis. It could therefore be advocated that this will cause difficulties for identification in the field and application of conservation measures but, based on our data, the lineages appear geographically disjunct. Before the completion of further in-depth morpho-anatomical studies, species identification could thus rely on geographical provenance by field practitioners. As a consequence, if the current result was also supported by nuclear data, six species should be recognized. This will enable both a more adequate conservation management (since each species will represent an evolutionary independent entity), and further studies on the diversification and evolutionary history of the group.

Rumohra linearisquamata and R. adiantiformis were not separated based on our plastid dataset and additional molecular markers should be considered to assess the existence of two distinct clades. However, although these two species share many morphological characters and occur in sympatry, they are easy to distinguish based on the shape and size of their scales on the rhizomes and costae (Figure 1G, I; Rakotondrainibe, 2010b), and their recognition as two distinct entities therefore appears justified. Similarly, R. quadrangularis and R. glandulosissima [START_REF] Sundue | Rumohra glandulosissima (Dryopteridaceae) a new species from the Atlantic Rainforest, and revision of the species occurring in Brazil[END_REF] were not resolved in the plastid phylogenetic tree, but R. glandulosissima clearly differs morphologically by having densely glandular indumenta on all parts of the leaf, with two kinds of glandular hairs (Figure 1H; [START_REF] Sundue | Rumohra glandulosissima (Dryopteridaceae) a new species from the Atlantic Rainforest, and revision of the species occurring in Brazil[END_REF].

POLYPHYLY OF R. ADIANTIFORMIS: WHAT EVOLUTIONARY SCENARIO(S)?

Cryptic species are often (incorrectly) assumed to be recently diverged, which would explain why they would not have had sufficient time to diverge morphologically [START_REF] Bickford | Cryptic species as a window on diversity and conservation[END_REF]. However, in Rumohra, some morphologically differentiated species have evolved more recently than some lineages of R. adiantiformis and this explanation therefore does not hold. We propose three possible (and mutually non-exclusive) scenarios to explain the polyphyly of R. adiantiformis: (1) a complex history of recurrent hybridization events in the genus; (2) morphological convergence among distinct R. adiantiformis lineages; and (3) morphological stasis, i.e. the sharing of ancestral morphological characters among lineages of R. adiantiformis (symplesiomorphies).

Hybridization hypothesis

Hybridization is now accepted as a major evolutionary mechanism in vascular plants [START_REF] Abbott | Genomics of hybridization and its evolutionary consequences[END_REF], and especially in ferns [START_REF] Barrington | Hybridization, Reticulation, and Species Concepts in the Ferns[END_REF][START_REF] Sigel | Genetic and genomic aspects of hybridization in ferns[END_REF]. The resulting reticulate evolution often leads to the formation of species complexes, within which cryptic species have been repeatedly detected (e.g. [START_REF] Paris | Cryptic Species, Species Delimitation, and Taxonomic Practice in the Homosporous Ferns[END_REF]Adjie et al., 2007, and references therein;[START_REF] Pillon | Cryptic species, gene recombination and hybridization in the genus Spiraeanthemum (Cunoniaceae) from New Caledonia[END_REF][START_REF] Crowl | Embracing discordance: Phylogenomic analyses provide evidence for allopolyploidy leading to cryptic diversity in a Mediterranean Campanula (Campanulaceae) clade[END_REF]. Organelles are maternally inherited in ferns [START_REF] Adjie | Independent origins of tetraploid cryptic species in the fern Ceratopteris thalictroides[END_REF][START_REF] Sigel | Genetic and genomic aspects of hybridization in ferns[END_REF], and references therein), and our phylogenetic tree based on plastid data therefore provides information on the history of the maternal component of the genome in Rumohra. Our resulting topology may suggest that (at most) one lineage of R. adiantiformis represents the 'true' R. adiantiformis stem line, whereas others (or possibly all of them) would have resulted from recurrent hybridization events with distinct species as the maternal parent. Each hybrid lineage would thus display either the plastid haplotype of the (possibly now extinct) maternal ancestor or a haplotype that is more or less closely related to the haplotype of another Rumohra sp., reflecting ancient hybridization events and subsequent genetic differentiation from the maternal parent. In all cases, genetic relatedness between lineages of R. adiantiformis and other Rumohra spp. is correlated with geographical proximity, making the hybridization hypothesis plausible. Such a hypothesis of multiple hybrid origins was suggested for other species, e.g. in Polypodium L. and Pteridium caudatum (L.) Maxon, to explain the placement of some species accessions in two parts of phylogenetic trees based on plastid data [START_REF] Der | Global Chloroplast Phylogeny and Biogeography of Bracken (Pteridium; Dennstaedtiaceae)[END_REF][START_REF] Sigel | Evidence for reciprocal origins in Polypodium hesperium (Polypodiaceae): A fern model system for investigating how multiple origins shape allopolyploid genomes[END_REF]. Nevertheless, two observations make this scenario unlikely. First, although all Rumohra spp. were represented by several samples, no other species displays the signature of hybridization events. Second, putative hybrids would always display the morphology of R. adiantiformis and R. adiantiformis would always have acted as the paternal parent; although highly asymmetric patterns of hybrid formation have been observed, for example in the Asplenium nidus L. complex [START_REF] Yatabe | Patterns of hybrid formation among cryptic species of bird-nest fern, Asplenium nidus complex (Aspleniaceae), in West Malesia[END_REF] and in Dryopteris Adans. [START_REF] Xiang | Population-specific gender-biased hybridization between Dryopteris intermedia and D. carthusiana: Evidence from chloroplast DNA[END_REF][START_REF] Testo | Dynamics of asymmetrical hybridization in North American wood ferns: reconciling patterns of inheritance with gametophyte reproductive biology[END_REF], we consider this unlikely. A nuclear-based phylogenetic analysis would bring crucial information to confirm or reject the possible history of reticulate evolution in Rumohra.

Morphological convergence hypothesis

Another possible explanation for the striking polyphyly of R. adiantiformis is morphological convergence among lineages, i.e. the parallel or convergent evolution of a suite of derived characters. Homoplasy of morphological character evolution has previously been shown in ferns, at a broad scale in eupolypods II [START_REF] Sundue | Stasis and convergence characterize morphological evolution in eupolypod II ferns[END_REF] and in smaller groups such as the grammitids [START_REF] Ranker | Phylogeny and evolution of grammitid ferns (Grammitidaceae): a case of rampant morphological homoplasy[END_REF]Sundue et al., 2010a;[START_REF] Bauret | Madagascar sheds new light on the molecular systematics and biogeography of grammitid ferns: New unexpected lineages and numerous long-distance dispersal events[END_REF], bolbitidoids [START_REF] Moran | Phylogeny and Character Evolution of the Bolbitidoid Ferns (Dryopteridaceae)[END_REF], cheilanthoids [START_REF] Rothfels | Toward a monophyletic Notholaena (Pteridaceae): Resolving patterns of evolutionary convergence in xericadapted ferns[END_REF][START_REF] Grusz | Toward a monophyletic Cheilanthes: The resurrection and recircumscription of Myriopteris (Pteridaceae)[END_REF] and in other spore-bearing vascular plants (Lycopodiaceae, [START_REF] Field | Molecular phylogenetics and the morphology of the Lycopodiaceae subfamily Huperzioideae supports three genera: Huperzia, Phlegmariurus and Phylloglossum[END_REF]Selaginellaceae, Weststrand & Korall, 2016). Such observed homoplasy has led to numerous taxonomic changes since the advent of molecular methods in systematics. It can result from morphological convergence, especially when species that are not closely related occur in similar but extreme environments. A character conferring a selective advantage can indeed evolve repeatedly (see, e.g. [START_REF] Patterson | Phylogeny, concerted convergence, and phylogenetic niche conservatism in the core Liliales: insights from rbcL and ndhF sequence data[END_REF]. However, R. adiantiformis occurs in disparate environments (e.g. in Brazil, from evergreen rainforest to sea-side vegetation where it grows in the full sun among the dunes; [START_REF] Sundue | Rumohra glandulosissima (Dryopteridaceae) a new species from the Atlantic Rainforest, and revision of the species occurring in Brazil[END_REF] and can grow terrestrially, as a climber or an epiphyte. Therefore, morphological convergence towards traits adapted to a particular environment appears unlikely.

Morphological stasis hypothesis

The third scenario that we hypothesize to explain the polyphyly of R. adiantiformis is morphological stasis among lineages, i.e. shared ancestral characters (symplesiomorphies). Rumohra adiantiformis displays broad ecological amplitude and high morphological diversity [START_REF] Sundue | Rumohra glandulosissima (Dryopteridaceae) a new species from the Atlantic Rainforest, and revision of the species occurring in Brazil[END_REF]. As a consequence, our inability to identify diagnostic morphological characters among lineages may be due to their morphological diversity, which does not lead to the emergence of particular morphotype(s) in any geographical region or habitat, rather than to the absence of variation. We suggest that from a common ancestor, which was morphologically close to extant R. adiantiformis and exhibited extensive morphological diversity, the six other species differentiated locally and evolved towards contrasting morphologies, whereas the ancestral morphology was retained in lineages dispersed throughout the tropics. Such a mechanism was suggested by [START_REF] Darwin | On the origin of species by means of natural selection, or the preservation of favoured races in the struggle for life[END_REF], who postulated that wide-spread and highly variable species were most likely to give rise to new species compared to more narrowly distributed, less variable species. It would also be congruent with the fact that R. adiantiformis is present in all regions where other species have evolved, and would correspond to the budding speciation mode proposed by [START_REF] Mayr | Change of genetic environment and evolution[END_REF] and later developed in light of molecular phylogenetics (e.g. [START_REF] Vanderpoorten | The application of molecular data to the phylogenetic delimitation of species in bryophytes: a note of caution[END_REF]. In parallel to this occasional pattern of morphological divergence, lineages of R. adiantiformis most probably differentiated genetically as a result of low gene exchange due to spatial separation and the action of genetic drift. Despite the high dispersal capacities of ferns, we indeed inferred only a single successful colonization to each coded geographical region.

Nonetheless, although we tend to favour this third scenario to explain the polyphyly of R. adiantiformis, morphological convergence and morphological stasis might be involved, depending on the character considered, and the impact of hybridization events also cannot be excluded.

HISTORICAL BIOGEOGRAPHY OF RUMOHRA

A genus of late Palaeogene, Neotropical origin

All age estimates along the chronogram for Rumohra differed based on whether the calibration points were taken from older dates obtained on the large-scale fern phylogenetic analysis of [START_REF] Testo | A 4000-species dataset provides new insight into the evolution of ferns[END_REF], or younger dates obtained by [START_REF] Schuettpelz | Evidence for a Cenozoic radiation of ferns in an angiosperm-dominated canopy[END_REF]. Thus, our results suggested an origin of Rumohra (stem node) between c. 46.4 and 30.7 Mya. The latter age is similar to the age of 28.8 Mya found by [START_REF] Labiak | Phylogeny and historical biogeography of the lastreopsid ferns (Dryopteridaceae)[END_REF] in their broad analysis across the lastreopsid ferns, which was also calibrated based on the analysis of [START_REF] Schuettpelz | Evidence for a Cenozoic radiation of ferns in an angiosperm-dominated canopy[END_REF]. Their slightly lower age estimate could result from their more restricted sampling, which included only two Rumohra spp. compared to our exhaustive sampling of seven species (e.g. [START_REF] Linder | Taxon sampling effects in molecular clock dating: An example from the African Restionaceae[END_REF]. Despite the differences observed depending on the calibration points, all age estimates were consistent with the biogeographical history proposed here and we only report estimates based on [START_REF] Testo | A 4000-species dataset provides new insight into the evolution of ferns[END_REF] in the text below, for the sake of clarity.

Based on our results, the austral genus Rumohra started to diversify during the late Miocene. Among lastreopsid genera, it was thus the last to diversify, in agreement with [START_REF] Labiak | Phylogeny and historical biogeography of the lastreopsid ferns (Dryopteridaceae)[END_REF] even when considering the relatively older age estimates in our study. At that time, the southern continents resulting from the breakup of Gondwana were well separated from each other (New Zealand, Australia, South America and Antarctica became isolated from one another during the late Cretaceous and Tertiary; [START_REF] Sanmartín | Southern hemisphere biogeography inferred by eventbased models: plant versus animal patterns[END_REF]. Therefore, contrary to the early range expansion and subsequent divergence of Lastreopsids, which could have been influenced by an Antarctic land bridge that persisted between Australia and southern South America until c. 40 Mya [START_REF] Labiak | Phylogeny and historical biogeography of the lastreopsid ferns (Dryopteridaceae)[END_REF], the diversification history of Rumohra is too recent, even when taking 95% HPDs into account, to explain its southern circumaustral distribution by geological vicariance events. Thus, the geographical disjunctions in Rumohra must rather be explained by transoceanic LDD events.

The ancestral area for the crown node of Rumohra was uncertain based on DEC+j, given the equal probabilities assigned to the Neotropics and Australasia. However, Rumohra most probably diverged from its sister genus Megalastrum in the Neotropics (based on both DEC+j and stochastic mapping at the stem node of Rumohra) and, considering this Neotropical origin, stochastic mapping also recovered the Neotropics as the centre of origin of the genus (crown node). Therefore, we favour a scenario in which the diversification started in the Neotropics and resulted in the two main clades of the genus.

A late Miocene diversification, mostly shaped by three major LDD events

Clade A diversified in situ, in the Neotropics, giving rise to a clade of three species (R. quadrangularis, R. glandulosissima and R. adiantiformis), but it also dispersed twice independently to southern Africa and the western Indian Ocean (Madagascar or Comoros), respectively. These two LDD events (LDD2 and LDD3; Figure 5), which occurred c. 9.8 and 9.4 Mya, are best interpreted as trans-Atlantic LDD events of spores, since the involved lineages clearly postdate the separation of Africa and Madagascar from all other southern continents (especially Antarctica and South America) c. 165-105 Mya (McLoughlin, 2001). Spores were probably transported eastward via the West Wind Drift, a wind current initiated around Antarctica after the opening of the Drake Passage between South America and Antarctica in the Oligocene [START_REF] Sanmartín | West Wind Drift revisited: testing for directional dispersal in the Southern Hemisphere using event-based tree fitting[END_REF].

From the Neotropical ancestor of the genus, clade B probably evolved by an initial dispersal event to south-ern South America reaching as far as the Falkland Islands (LDD1; Figure 5), as supported by stochastic mapping. Then, there was a disjunction between southern South America (R. adiantiformis and R. berteroana) and Australasia (R. adiantiformis). Similar disjunctions have been observed in many other plant groups and three potential dispersal routes were proposed to explain them: a direct transoceanic dispersal; dispersal through intermediate stepping-stone(s); or an out-of-Antarctica scenario involving an origin in Antarctica followed by a bidirectional dispersal [START_REF] Winkworth | Explaining the disjunct distributions of austral plants: the roles of Antarctic and direct dispersal routes[END_REF]. In Rumohra, the disjunction was established <5.3 Mya, i.e.

after complete Antarctic glaciation (which dates back to 14-4 Mya; [START_REF] Zachos | Trends, rhythms, and aberrations in global climate 65 Ma to present[END_REF][START_REF] Siegert | Recent advances in understanding Antarctic climate evolution[END_REF], forcing the South American ancestor to a direct transoceanic dispersal route to Australasia. If considering the shortest route between South America and Australasia, which is across the Pacific Ocean, this LDD event would have occurred westward in an opposite direction to the West Wind Drift. As analysed by [START_REF] Sanmartín | West Wind Drift revisited: testing for directional dispersal in the Southern Hemisphere using event-based tree fitting[END_REF], such an apparent westward direction has in fact frequently been inferred in various plant groups, but it does not exclude the influence of the West Wind Drift: in particular, spore dispersal patterns are indeed more influenced by wind connectivity than by geographical distance in the circum-austral area (Muñoz et al., 2004). Therefore, spores most probably travelled eastward through the Atlantic and Indian Oceans (LDD4; Figure 5), under the action of the West Wind Drift, instead of the shortest west-ward route across the Pacific Ocean. Alternatively, prevailing trade winds blowing at lower latitudes from the western coast of South America to Australasia [START_REF] Gillespie | Longdistance dispersal: A framework for hypothesis testing[END_REF] or birds through ectozoochory [START_REF] Lewis | First evidence of bryophyte diaspores in the plumage of transequatorial migrant birds[END_REF]) may be involved.

The clade B lineage that remained in southern South America includes R. berteroana, which is endemic to the Juan Fernández archipelago. This species formed recently (c. 590,000 years ago) and probably resulted from anagenetic speciation after short range dispersal of the southern South American lineage of R. adiantiformis. The timing of this speciation event is congruent with the date of emergence of these islands < 5 Mya [START_REF] Stuessy | Botanical and geological significance of potassium-argon dates from the Juan Fernandez Islands[END_REF]. Anagenesis is an important model of speciation on oceanic archipelagos, accounting for 36% of the endemic plant species diversity in the Juan Fernández archipelago [START_REF] Stuessy | Anagenetic evolution in island plants[END_REF], and it has been shown to be even more important in spore-producing plants than in seed plants in several other archipelagos [START_REF] Patiño | The anagenetic world of spore-producing land plants[END_REF].

FOCUS ON THE MALAGASY SPECIES HOTSPOT

The two transatlantic eastward LDD events (LDD2 and LDD3), which occurred c. 10 Mya, resulted in a clade comprising all Malagasy, Comorian and other western Indian Ocean lineages on the one hand, and in a clade consisting of a continental African (and southern Indian Ocean) lineage of R. adiantiformis on the other hand. Therefore, African and western Indian Ocean lineages of Rumohra are not closely related despite their geographical proximity. This is in contrast to the numerous biotic affinities found in other groups of plants and animals [START_REF] Agnarsson | The generation of a biodiversity hotspot: biogeography and phylogeography of the western Indian Ocean islands[END_REF][START_REF] Buerki | Spatio-temporal history of the endemic genera of Madagascar[END_REF] and with the African origin reported for many Malagasy angiosperms (e.g. [START_REF] Bartish | Vicariance or long-distance dispersal: historical biogeography of the pantropical subfamily Chrysophylloideae (Sapotaceae)[END_REF][START_REF] Calvino | The role of the Southern Hemisphere in the evolutionary history of Apiaceae, a mostly north temperate plant family[END_REF][START_REF] Janssens | Dispersing towards Madagascar: Biogeography and evolution of the Madagascan endemics of the Spermacoceae tribe (Rubiaceae)[END_REF][START_REF] Bacon | Biogeography of the Malagasy Celastraceae: Multiple independent origins followed by widespread dispersal of genera from Madagascar[END_REF]. As opposed to the apparent absence of dispersal between continental Africa and the western Indian Ocean area, we inferred at least one LDD event between Madagascar and the Comoros (LDD5; Figure 5; the direction remains unknown because of the uncertain ancestral area estimation), one LDD event from Madagascar to Mascarenes/ Seychelles (LDD7) and one LDD event from continental Africa to the southern Indian Ocean islands (LDD6; both LDD6 and LDD7 events were inferred within lineages of R. adiantiformis).

The LDD event inferred from the Neotropics to the Malagasy region (LDD2) reinforces the importance of the dispersal events between these two regions for the origin of the fern flora of Madagascar, as already shown in other fern groups such as Elaphoglossum (13 events; [START_REF] Rouhan | Molecular phylogeny of the fern genus Elaphoglossum (Elaphoglossaceae) based on chloroplast non-coding DNA sequences: Contributions of species from the Indian Ocean area[END_REF], or the grammitid ferns (five or more events; [START_REF] Bauret | Madagascar sheds new light on the molecular systematics and biogeography of grammitid ferns: New unexpected lineages and numerous long-distance dispersal events[END_REF]. However, in Rumohra, the Malagasy hotspot (comprising three endemic species and at least one R. adiantiformis lineage) resulted from a single successful long-distance colonization with subsequent diversification on the island, as otherwise only found in Lomariopsis Fée (Rouhan et al., 2007a), Ctenitis (C.Chr.) C.ChR. [START_REF] Hennequin | Global phylogeny and biogeography of the fern genus Ctenitis (Dryopteridaceae), with a focus on the Indian Ocean region[END_REF] and some grammitid fern genera (Sundue et al., 2014;[START_REF] Bauret | Madagascar sheds new light on the molecular systematics and biogeography of grammitid ferns: New unexpected lineages and numerous long-distance dispersal events[END_REF]. The mechanisms involved in the diversification of Rumohra in Madagascar are unknown. Nowadays, most extant species do not display any obvious difference in their ecological preferences and all occur in rainforests. Rumohra madagascarica, however, pro-vides a probable case of ecological speciation, since it is only observed as an epiphyte on species of Pandanus Parkinson (G. Rouhan, pers. obs.;Rakotondrainibe, 2010b). Species are commonly found in sympatry, without intermediate morphological forms that would indicate the occurrence of interspecific crosses. Whether speciation took place in sympatry or, more likely, whether sympatric sites result from secondary contact between previously, allopatrically derived species remains to be determined.

Chapter III -Biogeographical history of

Blechnoideae in Madagascar: connection with tropical regions of the Southern Hemisphere and two in situ diversifications highlighted

INTRODUCTION

The subcosmopolitan family Blechnaceae comprises around 270 species and three subfamilies: Blechnoideae, Stenochlaenoideae and Woodwardioideae. Most of the species diversity is found in Blechnoideae, with 18 genera and about 240 species (PPGI, 2016).

The family is recognizable in the field by linear sori that are parallel and adjacent to midveins, introrse indusia, and vascular bundles forming a ring in the petiole cross section. All the species are terrestrial, except the New Caledonian Oceaniopteris francii (Rosenst.) Gasper & Salino that is aquatic. In Madagascar, all the Blechnoideae species have entire to pinnate fronds (Figure 1; except Lomaridium biforme that can be pinnatepinnatifid), and dimorphic fronds with the fertile fronds being more or less reduced to the sori (Figure 1C, D, F, G).

De Gasper et al. (2016b) proposed the most recent classification of Blechnaceae, in which the large genus Blechnum was split into 16 genera, all classified in Blechnoideae together with Sadleria Kaulf. and Brainea J.Sm. This revised classification was based both on morphology and molecular data provided by the most comprehensive phylogeny so far, including a sampling of half of the world's species diversity, mostly from the two diversity centres, the Neotropics and Australasia (de Gasper et al., 2016a). The three subfamilies were retrieved monophyletic, with Blechnoideae sister group to Stenochlaenoideae, and all the 24 genera were also monophyletic as the large non-monophyletic Blechnum s.l. was circumscribed in smaller monophyletic genera. In Madagascar, the most recent taxonomic treatment based on morphology estimated 15 Blechnum s.l. species [START_REF] Rakotondrainibe | Révision synoptique du genre Blechnum L. (Blechnaceae) à Madagascar[END_REF] The origin of Blechnaceae was dated to Late Cretaceous by two large-scale, fossil-based studies on leptosporangiate ferns [START_REF] Schuettpelz | Evidence for a Cenozoic radiation of ferns in an angiosperm-dominated canopy[END_REF][START_REF] Testo | A 4000-species dataset provides new insight into the evolution of ferns[END_REF], but the biogeographical history of the family remains unknown. The pantropical distribution of Blechnoideae raises the question of how such a large distribution could be explained, especially since some genera are restricted to small areas (like the Hawaiian endemic Sadleria) whereas others are widely distributed (like Parablechnum in the tropics). The subfamily is particularly diversified in the Neotropics and Australasia (de Gasper et al., 2016a,b), but it is also distributed in Africa and Western Indian Ocean (WIO), southern South America, Tristan da Cunha and in the French Southern Lands. The overall distribution is therefore almost entirely in southern regions, and suggests important biogeographical connections between the Neotropics and Australasia in the history of Blechnoideae. Floristic affinities were retrieved between these two regions in numerous genera [START_REF] Moreira-Muñoz | The Austral floristic realm revisited[END_REF], and phylogenetic studies have unravelled the history of Neotropical-Australasian connections, attributing some to long-distance dispersal and others to trans-Antarctic routes that persisted until the Eocene [START_REF] Sanmartín | Southern hemisphere biogeography inferred by eventbased models: plant versus animal patterns[END_REF][START_REF] Chacón | From East Gondwana to Central America: historical biogeography of the Alstroemeriaceae[END_REF][START_REF] Winkworth | Explaining the disjunct distributions of austral plants: the roles of Antarctic and direct dispersal routes[END_REF]. Antarctica was indeed ice-free and probably covered by near-tropical forests until Early Eocene [START_REF] Pross | Persistent near-tropical warmth on the Antarctic continent during the early Eocene epoch[END_REF]. The trans-Antarctica connection stopped after the opening of South Tasman Sea and Drake passage about 30-35 Ma, leading to the isolation of Antarctica and its cooling, as well as to the establishment of circumaustral currents [START_REF] Sanmartín | West Wind Drift revisited: testing for directional dispersal in the Southern Hemisphere using event-based tree fitting[END_REF][START_REF] Yang | Coupled climate impacts of the Drake Passage and the Panama Seaway[END_REF].

The classification of Malagasy species in five monophyletic genera implies that the Malagasy diversity have originated from multiple distinct biogeographical events (at least four events, as Blechnum and Austroblechnum were retrieved sister by de Gasper et al., 2016b). The family being dated to Late Cretaceous, hypotheses of vicariance linked to the Gondwanan break-up are unlikely because Madagascar was already isolated at this time [START_REF] Mcloughlin | The breakup history of Gondwana and its impact on pre-Cenozoic floristic provincialism[END_REF]. Therefore, the biogeographical history of Malagasy lineages of Blechnoideae is likely to be dominated by dispersal. The species composition of Malagasy Blechnoideae shows affinities with the nearest continent Africa, with four species distributed in both areas (Table 1). Nevertheless, six Malagasy species belong to two mostly Neotropical genera (Lomariocycas and Blechnum) and floristic affinities were highlighted with Neotropical Lomariocycas and Lomaridium species [START_REF] Moran | Phytogeographic relationships between neotropical and African-Madagascan pteridophytes[END_REF].

This chapter aims to study the systematics and biogeographical history of Malagasy Blechnoideae, and specifically: 1) to test the monophyly of Blechnoideae genera distributed in Madagascar and to confirm the classification of de

MATERIAL AND METHODS

SAMPLING

The sequence matrix from de Gasper et al. (2016a) was combined with my dataset, which was mostly focused on Madagascar and included 49 specimens representing 16 species. Ten species were never sampled so far, among which eight Malagasy taxa (Appendix 3).

The whole dataset included 13 species from Africa and WIO (76% of the diversity for this region, and 87% of the Malagasy diversity) and about 62% of the Blechnoideae diversity was included. Eighteen species from the two other subfamilies and four from closely related families were added as outgroups. The whole dataset included 164 species and 202 specimens (Appendix 3).

DNA EXTRACTION, AMPLIFICATION AND SEQUENCING

The protocols for DNA extraction, amplification and sequencing followed those of Chapter II. Four plastid DNA regions were amplified by PCR and sequenced: the two genes rbcL and rps4, and two non-coding regions rps4-trnS and the trnL intron plus the trnL-trnF intergenic spacer (trnL/trnL-trnF). For rps4 and rps4-trnS that were amplified and sequenced together, I used the primers rps4.5' 5'-ATG TCS CGT TAY CGA GGA CCT-3' [START_REF] Small | Amplification of noncoding chloroplast DNA for phylogenetic studies in lycophytes and monilophytes with a comparative example of relative phylogenetic utility from Ophioglossaceae[END_REF] and trnS-r 5'-TAC CGA GGG TTC GAA TC-3' [START_REF] Smith | Intrafamilial Relationships of the Thelypteroid Ferns (Thelypteridaceae)[END_REF] and the following thermal cycling conditions: 5 min 94°C / 5 × (30 s 94°C / 30 s 65-55°C / 1 min 30 s 72°C) / 35 × (30 s 94°C / 30 s 55°C / 1 min 30 s 72°C) / 10 min 72°C. For the first five cycles, 65-55°C stands for a temperature that was increased by 2.5° at each cycle.

PHYLOGENETIC ANALYSES

The analyses followed the protocol detailed in Chapter II about alignments, matrix concatenation and phylogenetic approaches: Maximum Likelihood (ML) and Bayesian Inference (BI). Four partitions were defined by DNA regions: rbcL, rps4, rps4-trnS and trnL/trnL-trnF. The parameters were set as in Chapter II, except for the MrBayes analysis; the runs comprised five million generations and were sampled every 500 generations to obtain 10,000 sampled trees, with a temperature of chains set to 0.05.

AGE ESTIMATES

A reduced dataset of 170 samples was used to perform the dating analysis, representing all 164 species, outgroups included. One sample per species was kept, except in case of statistically supported paraphyly and polyphyly. I followed the same protocol as in Chapter II, using BEAST 2.4.2 [START_REF] Bouckaert | BEAST 2: a software platform for Bayesian evolutionary analysis[END_REF] on the CIPRES science gateway [START_REF] Miller | Creating the CIPRES Science Gateway for inference of large phylogenetic trees[END_REF] and with the specific calibration points mentioned below.

I used a primary calibration point provided by a fossil assignable to Onoclea sensibilis (Onocleaceae; [START_REF] Rothwell | Onoclea sensibilis in the Paleocene of North America, a dramatic example of structural and ecological stasis[END_REF], previously used for dating analyses by [START_REF] Schuettpelz | Evidence for a Cenozoic radiation of ferns in an angiosperm-dominated canopy[END_REF] and [START_REF] Testo | A 4000-species dataset provides new insight into the evolution of ferns[END_REF] and dated to the Paleocene. Therefore, the stem age of this species was calibrated using a uniform prior with a minimum age of 56 Ma. In addition, three secondary calibration points were modeled by normal prior distributions with means from Testo & Sundue (2016) and standard deviations (S.D.) of 10% of the mean values: tree height (85.9 Ma; S.D. = 8.6), Blechnoideae stem node (59.5 Ma; S.D. = 6.0) and Blechnoideae crown node (55.8 Ma; S.D. = 5.6). The more comprehensive sampling (both in terms of markers and taxonomic diversity) led me to favor their results, as calibration sources, relatively to those of Schuettpeltz & Pryer (2007).

An uncorrelated lognormal relaxed clock was used, with a Birth-Death tree prior and a random starting tree. For each analysis, two independent runs of 100 million generations with random seed values were conducted, sampled every 10,000 generations to obtain 10,000 sampled trees.

BIOGEOGRAPHICAL ANALYSES

The BioGeoBEARS R package was used to estimate the ancestral areas [START_REF] Matzke | BioGeoBEARS: BioGeography with Bayesian (and likelihood) evolutionary analysis in R scripts[END_REF], as in Chapter II. Six biogeographical models were considered: DEC, DIVALIKE, BAYAREALIKE, and the same models implementing the additional parameter j, which stands for the founder event speciation. The Akaike Information Criterion (AIC) was then used to select the best model among the six.

I coded species distributions by combinations of eight areas: (A) Madagascar, (B) Mascarenes-Comoros-Seychelles, (C) Africa, (D) Neotropics, (E) Asia-Southeast Asia, (F) Australasia-Oceania (latter referred as Australasia), (G) North America-Europe, and (H) a circumaustral region including the southern South America, Tristan da Cunha archipelago and French Southern Lands (see map of Figure 3). The entire distribution of species was coded, i.e. not only the sampling localities, based on herbarium collections, floras and the GBIF database when necessary. Two species were however coded differently: for Parablechnum montbrisonis, the coding followed the distribution of its two varieties that were found paraphyletic; and for Lomaridium attenuatum, a clade nesting Mascarenes samples was inferred and coded in the area Mascarenes-Comoros-Seychelles (see Results). The maximum range size was set to five areas, as it is the maximum number of areas coded for a terminal taxon.

RESULTS

PHYLOGENETIC ANALYSES

The final matrix included 202 specimens and 3493 characters (Table 2). The topologies inferred by the MrBayes and raxML analyses showed that Blechnaceae and the three subfamilies were monophyletic (Figure 2A). Similar intergeneric relationships were found between the two analyses, with an exception for Diploblechnum that was retrieved sister group to Parablechnum in raxML results (not shown). The Blechnoideae genera were monophyletic, except: i) Oceaniopteris that was found paraphyletic with respect to Doodia (Figure 2C; but with low support values, BS<50, PP=0.77); ii) Parablechnum, as P. chauliodontum was nested within Lomaridium (Figure 2A); and iii) Austroblechnum retrieved as three non-closely related lineages: nineteen out of the 21 sampled species of Austroblechnum formed a clade (Figure 2B), but A. integrifrons was found in Lomaridium (Figure 2A) and A. bakeri was nested in Cranfillia (Figure 2B).

DNA region

Number 2B). The monophyly of several Malagasy species remained uncertain despite the sampling of multiple individuals, due to a lack of resolution. It was the case i) in Lomaridium (Figure 2A) for L. biforme and L. xiphophyllum; and ii) in Lomariocycas (Figure 2C) for L. madagascariensis. The paraphyly of several species was suggested with medium to high statistical supports: Lomaridium attenuatum, Lomaridium simillimum (Figure 2A), the widespread Blechnum australe (Figure 2B), Lomariocycas longipinna and Parablechnum marginatum (Figure 2C). Lomariocycas tabularis was also retrieved paraphyletic but the position of the specimen 'Hennequin R105' was barely supported (BS=63, PP=0.55; Figure 2C). Two species and a variety were found monophyletic: Austroblechnum bakeri, Blechnum punctulatum (BS=100; PP=1; Figure 2B) and Parablechnum marginatum var. humbertii (BS=100; PP=1; Figure 2C). The monophyly of Parablechnum marginatum var. marginatum was not tested, due to the sampling of one specimen only, which was found sister group to Neotropical Parablechnum species.

BIOGEOGRAPHICAL HISTORY

Based on AIC, the DEC model was inferred as the most appropriate (AIC=561.6, Table 2), but the Likelihood Ratio Test (LRT) showed that the null hypothesis could not be rejected (p-value>0.1; H0: model with and without +j process confer equal likelihoods on the data). I therefore considered the results based on both the DEC and DEC+j models, and observed that the most likely ancestral ranges inferred were the same. Blechnoideae would have diverged from their sister group during Early Paleocene (64.1 Ma; Figure 3A, Table 4), most likely in a wide ancestral range covering the Neotropics and the Eastern Paleotropics (Asia-Southeast Asia and Australasia), and would have started to diversify in the Eastern Paleotropics during the Early Eocene (55.4 Ma).

Biogeographical model

Three range expansions from Australasia to the Neotropics were suggested, in Lomaria, Austroblechnum-Blechnum and Parablechnum-Diploblechnum-Doodia-Oceaniopteris-Neoblechnum-Lomariocycas lineages (Figure 3A). Other range expansions resulted in ancestral wide ranges, and making difficult the inference of a clear biogeographical history.

Nevertheless, at least five range expansions to Madagascar can be hypothesized (Figure 3B, Table 4): i) between 50.9-19.7 Ma [between nodes a and b]; ii) most likely between 34.0-18.8 Ma [c-d]; iii) one between 35.8-25.9 Ma [f-g] or two between 25.9-23.1 [g-h] and 25.9-0.0 Ma [g-Blechnum punctulatum]; iv) between 9.6-3.8 Ma [i-j]; and v) between 29.0-12.1 Ma [k-l]. Another range expansion could be estimated, for Blechnum australe (Prada s.n.), but the lineage was only known from a southern South American specimen. Neither precise ages of divergence nor precise areas of origin could be inferred for these Malagasy lineages, due to the number of areas estimated in the ancestral ranges (Figure 3B, Table 4).

DISCUSSION

SYSTEMATICS ISSUES ABOUT MALAGASY SPECIES

The phylogenetic placement of the Malagasy species supports the classification of de Gasper et al. (2016b), except for Austroblechnum bakeri retrieved nested within Cranfillia and Austroblechnum integrifrons within Lomaridium. Several hypotheses could explain these results: wrong genus assignation and misleading genetic processes like hybridization.

The taxonomic identification of our four samples of Austroblechnum bakeri was checked, based on the morphology-based identification key of de Gasper et al. (2016,a,b). The identification actually led to the genus Cranfillia, into which the samples were phylogenetically retrieved (Figure 2B), rather than to Austroblechnum. A combination of A. bakeri into Cranfillia should therefore be published.

Austroblechnum integrifrons is morphologically well distinct from all other Malagasy

Blechnoideae species by being the only one with entire fertile fronds [START_REF] Rakotondrainibe | Révision synoptique du genre Blechnum L. (Blechnaceae) à Madagascar[END_REF]. The key to Blechnaceae genera (de Gasper et al., 2016b) correctly assigns the species to Austroblechnum, even if the pinnae has to be considered as adnate to reach the assignation. Furthermore, the species does not match the description of Lomaridium, into which it was retrieved in the phylogeny, since this genus is characterized by a long creeping rhizome and the absence of hydathodes, whereas A. integrifrons has a shortcreeping to erect rhizome and distinct hydathodes [START_REF] Rakotondrainibe | Révision synoptique du genre Blechnum L. (Blechnaceae) à Madagascar[END_REF]. Only one sample of Austroblechnum integrifrons was successfully sequenced, and additional specimens will be necessary to confirm the phylogenetic position of this taxon. Sequencing a nuclear marker would also allow testing if the specimen(s) or the specieslike other species retrieved non-monophyletic -has a hybrid origin (see also Chapter II, discussion on the hybridization hypothesis).

Only two Malagasy Blechnoideae species (out of 15) and a variety were retrieved monophyletic. The lack of resolution was important in most clades of Malagasy species (e.g. Lomariocycas, Figure 2C), precluding the test of monophyly for three species, and six other species were retrieved paraphyletic (e.g. Lomariocycas longipinna, Figure 2C). Interestingly, we detected a possible case of cryptic species in Lomaridium since a clade nesting the three Lomaridium attenuatum specimens from Mascarenes (Janssen 2673, Hennequin R67, Hennequin 365; Figure 2A), was sister-group to the remaining samples of the species, collected in Comoros and Africa.

AN UNCERTAIN MALAGASY BIOGEOGRAPHICAL HISTORY

The biogeographical history of the Malagasy Blechnoideae could not be very precisely documented, but our results nevertheless provide some information and suggest numerous biogeographical connections between southern regions.

At least three range-expansions were inferred from Australasia to explain the Neotropical distribution of Lomaria, Austroblechnum-Blechnum and Parablechnum-Diploblechnum-Doodia-Oceaniopteris-Neoblechnum-Lomariocycas lineages (Figure 3A). Australasia and South America were connected via Antarctica until the end of Eocene [START_REF] Mcloughlin | The breakup history of Gondwana and its impact on pre-Cenozoic floristic provincialism[END_REF] and such overland migrations via Antarctica were already hypothesized in both directions for ferns in Lastreopsids [START_REF] Labiak | Phylogeny and historical biogeography of the lastreopsid ferns (Dryopteridaceae)[END_REF], Cyatheaceae [START_REF] Korall | Global biogeography of scaly tree ferns (Cyatheaceae): Evidence for Gondwanan vicariance and limited transoceanic dispersal[END_REF] and for many other plant lineages and animals [START_REF] Sanmartín | Southern hemisphere biogeography inferred by eventbased models: plant versus animal patterns[END_REF][START_REF] Bartish | Vicariance or long-distance dispersal: historical biogeography of the pantropical subfamily Chrysophylloideae (Sapotaceae)[END_REF][START_REF] Winkworth | Explaining the disjunct distributions of austral plants: the roles of Antarctic and direct dispersal routes[END_REF]. Migration via Antarctica however stopped at Eocene-Oligocene boundary, due to Antarctic ice-sheets formation [START_REF] Zachos | Trends, rhythms, and aberrations in global climate 65 Ma to present[END_REF]. Therefore, connections between the Neotropics and Australasia after ca. 35 Ma are most likely explained by long distance dispersal events, following the onset of circumaustral winds [START_REF] Munoz | Wind as a Long-Distance Dispersal Vehicle in the Southern Hemisphere[END_REF]. Hypotheses of trans-Antarctica migrations are compatible with range expansions from Australasia to Neotropics in Austroblechnum-Blechnum, Parablechnum-Lomariocycas clades and in Lomaridium, although a direct dispersal event could also lead to Lomaridium (Figure 3).

Hypotheses of Antarctica routes are not compatible with migration to Madagascar as the island was isolated from Antarctica for at least ca. 80 Ma [START_REF] Yoder | Has Vicariance or Dispersal Has Vicariance Been the Predominant Force in Biogeographic Madagascar? Only Time Will Tell[END_REF]. Therefore, the biogeographical history of Malagasy Blechnoideae would be driven by dispersal events from the Neotropics, Australasia, Africa and other WIO islands. Precise areas of origin cannot be inferred from the present results but hypotheses may be proposed in some cases, especially dealing with the Malagasy lineages. In Lomariocycas, the number of endemic species in clade j highly suggests a diversification in Madagascar only, and so a direct dispersal from the Neotropics to Madagascar between 9.6-3.8 Ma.

IN SITU DIVERSIFICATION

In situ diversifications would explained the Malagasy endemic diversity in Lomariocycas (clade j) and in Lomaridium (L. attenuatum-Rouhan1283-L. simillimum-Rouhan1370 clade), giving rise to four and five species respectively. Lomariocycas and Lomaridium seem to have colonized Madagascar and diversified by retaining their original ecological preferences. Malagasy Lomariocycas species are terrestrial with an erect rhizome (often sub-arborescent, Figure 1G) and occur between 800-1900 meters of altitude and mostly found in ericoid and summit forests [START_REF] Rakotondrainibe | Révision synoptique du genre Blechnum L. (Blechnaceae) à Madagascar[END_REF], as well as the Neotropical species like Lomariocycas yungensis (e.g. >2000 meters in Bolivia, [START_REF] Giacosa | Blechnum yungense (Pteridophyta, Blechnaceae), una Nueva Especie de Argentina y Bolivia[END_REF]. Within Lomaridium, the species display the same ecological preferences, growing as epiphytes or hemi-epiphytes (Figure 1D,E), rarely epilithes, in a wide range of altitudes (often higher than 700 m), in Madagascar [START_REF] Rakotondrainibe | Révision synoptique du genre Blechnum L. (Blechnaceae) à Madagascar[END_REF], the Neotropics [START_REF] Dittrich | The family Blechnaceae (Polypodiopsida) in Brazil: key to the genera and taxonomic treatment of Austroblechnum, Cranfillia, Lomaridium, Neoblechnum and Telmatoblechnum for southern and southeastern Brazil[END_REF] and in Australasia [START_REF] Brownlie | Flore de la Nouvelle-Calédonie et dépendances[END_REF].

Chapter IV -Biogeographical history of Lindsaea

and Odontosoria (Lindsaeaceae) in Madagascar: at least two dispersal events from tropical Asia and one in situ diversification highlighted

INTRODUCTION

Lindsaeaceae include seven genera and around 230 species distributed in the Neotropics and the Paleotropics, Lindsaea being the most diversified genus with 180 estimated species [START_REF] Lehtonen | Phylogenetics and classification of the pantropical fern family Lindsaeaceae[END_REF][START_REF] Ppgi | A community-derived classification for extant lycophytes and ferns[END_REF]. Lindsaeaceae species are either terrestrial or epiphyte, and characterized by marginal or sub-marginal sori that open towards the margin at the extremity of veins. Furthermore, many species have dimidiate pinnae, giving them an Adiantum-like appearance (Figure 1A).

The lack of clear morphological features to segregate the Lindsaeaceae genera has led to several classifications before the current consensus [START_REF] Lehtonen | Phylogenetics and classification of the pantropical fern family Lindsaeaceae[END_REF][START_REF] Ppgi | A community-derived classification for extant lycophytes and ferns[END_REF].

The latest and most comprehensive molecular phylogenetic study on Lindsaeaceae showed that Lindsaea was sister-clade to a clade nesting three genera: Nesolindsaea, Osmolindsaea and Tapeinidium [START_REF] Lehtonen | Phylogenetics and classification of the pantropical fern family Lindsaeaceae[END_REF]. However, another analysis also showed Odontosoria as the sister genus to Lindsaea [START_REF] Lehtonen | Diversification of lindsaeoid ferns and phylogenetic uncertainty of early polypod relationships[END_REF], suggesting that the phylogenetic relationships between all these genera could be sensitive to the dataset and the methods used. [START_REF] Lehtonen | Phylogenetics and classification of the pantropical fern family Lindsaeaceae[END_REF] also showed that Odontosoria was still difficult to define morphologically: the small number of sporangia per sorus was the only supporting character, but not shared by all the species. For Lindsaea, several supporting morphological characters were found to discriminate the genus from others, such as short stipes, abaxially keeled rachis, broad rachis sulcus and a vein order of two.

Lindsaea is the most diversified Lindsaeaceae genus in the Western Paleotropics (Africa-Western Indian Ocean) with 14 species all present in Madagascar, followed by Odontosoria with four species (Table 1). Numerous collections from recent field works in Madagascar provide material for molecular studies to test the taxonomy based on morphology, by adopting the evolutionary species concept applied in the previous chapters [START_REF] Simpson | The species concept[END_REF]. In particular, the molecular phylogenetic results will be discussed in the light of an ongoing taxonomic study based on morphological characters (Rakotondrainibe, pers. com.). The sampling of [START_REF] Lehtonen | Phylogenetics and classification of the pantropical fern family Lindsaeaceae[END_REF] already included two specimens of L. blotiana and L. millefolia but the monophyly of numerous Malagasy species remained untested. The ongoing taxonomic revision by Rakotondrainibe also hypothesized synonymies that could be tested on the basis of molecular data (Table 1).

This work will provide the first biogeographical analysis on Lindsaeaceae, with a focus on the Malagasy species of Lindsaea and Odontosoria. The species diversity in Madagascar would be explained by dispersal rather than Gondwanan origins, as Lindsaea diverged from Odontosoria between ca. 45-70 Ma [START_REF] Lehtonen | Diversification of lindsaeoid ferns and phylogenetic uncertainty of early polypod relationships[END_REF][START_REF] Testo | A 4000-species dataset provides new insight into the evolution of ferns[END_REF], after the isolation of Madagascar ca. 90 Ma [START_REF] Mcloughlin | The breakup history of Gondwana and its impact on pre-Cenozoic floristic provincialism[END_REF]. [START_REF] Christensen | Pteridophyta of Madagascar[END_REF] found that the Eastern Paleotropics (Asia to Australasia and the Pacific) have the strongest phytogeographic affinities with the Malagasy species of Lindsaeaceae. These affinities were retrieved by [START_REF] Lehtonen | Phylogenetics and classification of the pantropical fern family Lindsaeaceae[END_REF]: in their results, the Malagasy species were nested in clades of the Eastern Paleotropics, whereas all the Neotropical species were nested in two other clades with no Paleotropical species, suggesting that dispersal events from Eastern Paleotropics (rather than Neotropics) would explain the presence of Lindsaea species in Madagascar. Such affinities with the Eastern Paleotropics were also retrieved in Odontosoria, as the Malagasy endemic O. melleri was found sister species to Eastern Paleotropical species. Within the Western Paleotropics, relatively few exchanges are expected due to the high proportion of Malagasy endemics in Lindsaea (12 out of the 14 Malagasy species, Table 1).

This chapter aims 1) to test the monophyly of the Malagasy species in the light of a current taxonomic revision (Rakotondrainibe, com. pers.)

Endemic to Madagascar

Table 1. Lindsaea and Odontosoria species occurring in Africa and Western Indian Ocean (WIO), species distribution, and hypothesized synonymies based on an ongoing morphological taxonomic revision (Rakotondrainibe, com. pers.). Species sampled for the molecular study are in bold.

MATERIAL AND METHODS

TAXONOMIC SAMPLING

The sampling was composed of two parts: one from the worldwide phylogenetic study of Lindsaeaceae by [START_REF] Lehtonen | Phylogenetics and classification of the pantropical fern family Lindsaeaceae[END_REF], and one from new specimens recently collected in Madagascar. All four Western Paleotropical species of Odontosoria and 11 out of 14 Afro-Malagasy species of Lindsaea were sampled (Table 1,Appendix 4). For Lindsaea, 27 new specimens were added compared to the previous phylogenetic study [START_REF] Lehtonen | Phylogenetics and classification of the pantropical fern family Lindsaeaceae[END_REF], as well as the new species L. marojejyensis sp. nov. ined. Also, ten species were added as outgroups for calibration needs (see 1.4 Divergence time estimation). The whole dataset included 178 specimens representing 149 species. Voucher details are available in Appendix 4.

DNA EXTRACTION, AMPLIFICATION AND SEQUENCING

The protocols for DNA extraction, amplification and sequencing followed those of Chapters II and III. Five plastid regions were sequenced, the two coding regions rpoC1 and rps4, and the three non-coding regions rps4-trnS, trnH-psbA and the trnL intron plus the trnL-trnF intergenic spacer (trnL/trnL-trnF). For rpoC1, specific primers were used: LP1 5'-TAT GAA ACC AGA ATG GAT GG-3' and LP5 5'-CAA GAA GCA TAT CTT GAS TYG G-3' [START_REF] Chase | A proposal for a standardised protocol to barcode all land plants[END_REF] with the following thermal cycling conditions: 5 min 94°C / 40 × (30 s 94°C / 30 s 48°C / 45 s 72°C) / 10 min 72°C.

PHYLOGENETIC ANALYSES

The phylogenetic analyses followed the protocol detailed in Chapter II about alignments, matrix concatenation and phylogenetic approaches (ML, BI). The five plastid markers were concatenated but formed five independent partitions in the MrBayes and raxML analyses. The parameters were set following the Chapter II, except for the MrBayes analysis; the runs were conducted on five million generations and sampled every 500 generations to obtain 10,000 sampled trees.

DIVERGENCE TIME ESTIMATION

The dating analysis was performed on a reduced dataset including one sample per species, or per lineage when species were retrieved non-monophyletic. I followed the same protocol as developed in Chapter II, using BEAST 2.4.2 [START_REF] Bouckaert | BEAST 2: a software platform for Bayesian evolutionary analysis[END_REF] on the CIPRES science gateway and with the specific calibration points mentioned below.

Two fossils identified as Lindsaeaceae have already been used for calibration in the literature: a root system and a leaf, both from the Upper Cretaceous, but the authors could not assign them to one of the extant genera [START_REF] Schneider | An Early Cretaceous root-climbing epiphyte (Lindsaeaceae) and its significance for calibrating the diversification of polypodiaceous ferns[END_REF][START_REF] Regalado | The first fossil of Lindsaeaceae (Polypodiales) from the Cretaceous amber forest of Myanmar[END_REF]. We combined these fossil calibration points with secondary calibrations from a large-scale dating analysis [START_REF] Testo | A 4000-species dataset provides new insight into the evolution of ferns[END_REF].

The age of the Lindsaeaceae stem node was modeled by a uniform prior from 100.5 Ma to infinity, based on the stratigraphic occurrences of the two fossils in the Upper Cretaceous [START_REF] Schneider | An Early Cretaceous root-climbing epiphyte (Lindsaeaceae) and its significance for calibrating the diversification of polypodiaceous ferns[END_REF][START_REF] Regalado | The first fossil of Lindsaeaceae (Polypodiales) from the Cretaceous amber forest of Myanmar[END_REF]. The age of divergence between Odontosoria and Lindsaea was modeled by a normal prior distribution with a mean of 71.1 Ma, the crown node age of Odontosoria with a mean of 61.2 Ma and the stem node age of the Lindsaea Neotropical clade with a mean of 32.0 Ma based on [START_REF] Testo | A 4000-species dataset provides new insight into the evolution of ferns[END_REF]. Standard deviations were set to 10% of the mean estimates.

An uncorrelated lognormal relaxed clock was used, with a Birth-Death tree prior and a random starting tree. For each analysis, two independent runs of 100 million generations with random seed values were conducted and sampled every 10,000 generations to obtain 10,000 sampled trees.

BIOGEOGRAPHICAL ANALYSES

The ancestral ranges were estimated using the R package BioGeoBEARS [START_REF] Matzke | BioGeoBEARS: BioGeography with Bayesian (and likelihood) evolutionary analysis in R scripts[END_REF] in R studio 1.0.44 (RStudio Team, 2015). I conducted six analyses, successively using the models DEC, DEC+j, DIVALIKE, DIVALIKE+j, BAYAREALIKE, BAYAREALIKE+j (see Material and Methods in Chapter II for details). Among these six models, the most adequate to reconstruct the biogeographical history was selected based on the Akaike Information Criterion (AIC).

Six areas were defined to code the geographic distributions of species: (A) Madagascar, (B) Mascarenes-Comoros-Seychelles, (C) Africa, (D) Neotropics, (E) Asia-Southeast Asia, and (F) Australasia-Oceania (later referred as Australasia). The entire species distribution was coded (not only the voucher localities) based on herbarium collections, floras, personal communications (Rakotondrainibe) and the GBIF database when necessary. The maximum range size was set to five areas, as it is the maximum number of areas covered by an extant taxon.

RESULTS

PHYLOGENETIC RESULTS

The whole matrix included 178 specimens and 3314 characters (Table 2). MrBayes and RaxML topologies both supported the monophyly of Lindsaea (Bootstrap (BS)=100; Posterior Probability (PP)=1) and Odontosoria (BS=87; PP=1), which were retrieved sister groups (BS=85; PP=1; Figure 2A). With the other genera Nesolindsaea, Tapeinidium, Osmolindsaea and Sphenomeris, they formed the well-supported clade Lindsaeaceae (BS=100; PP=1; Figure 2A). The clade annotations of [START_REF] Lehtonen | Phylogenetics and classification of the pantropical fern family Lindsaeaceae[END_REF]

AGE AND BIOGEOGRAPHICAL ORIGIN OF MALAGASY LINEAGES

The DEC model was selected based on the AIC value (Table 3), but the Likelihood Ratio Test (LRT) showed that the null hypothesis cannot be rejected (p-value>0.1; H0: models with and without +J process confer equal likelihoods on the data). So, both DEC and DEC+j results were examined but the same ancestral ranges were inferred as most likely. Based on these inferences, Lindsaea and Odontosoria diverged during the Upper Cretaceous in Australasia (Table 4). Extant species of Lindsaea started to diversify during the Middle Eocene (45.8 Ma; HPD: 37.5-55.4) and the two most likely ancestral ranges of diversification inferred were Australasia-Neotropics (p=0.20) and Australasia (p=0.17; Figure 3). An ancestral range covering both the Neotropics and Australasia was also retrieved as the most likely at nodes g-i between Eocene and early Miocene. Clades VII, VIII, IX and X would have originated in Australasia during the Miocene (Figure 3, nodes km). The Malagasy diversity of Lindsaea would be explained by at least two dispersal events: one between 34.0-45.8 Ma from an unknown area as wide ancestral ranges were retrieved (L1, nodes e-f, Table 4) and one from Australasia between 8.6-9.9 Ma (L2). The latter was followed by an in situ diversification in Madagascar that started 6.9 Ma (node p). Two dispersal events could explain the Malagasy diversity of Odontosoria, one from an unknown area, most likely between 36.5-64.4 Ma (O1, nodes b-c) and one from Australasia between 25.0-64.4 Ma (O2, nodes b-c, Table 4). Clade c was estimated to initially originate from Australasia but no range was clearly estimated at crown node; the two most likely ancestral ranges covered Madagascar and four other areas (C or B, D, E and F, Table 4). Therefore, the dispersal event to Madagascar may have originated from any of these other areas. ). Colored squares at tips represent the current distribution, with the following color code: (A) Madagascar (red), (B) Mascarenes-Comoros-Seychelles (orange), (C) Africa (purple), (D) Neotropics (green), (E) Asia-Southeast Asia (yellow), and (F) Australasia-Oceania (light blue, referred in the text as Australasia). For wide ranges (covering several coded areas), their composition is detailed by colored squares next to the corresponding pie section. For the sake of clarity, only the distribution of the most likely ranges were depicted, but details about nodes probabilities are available in Table 4. Red arrows on branches indicate hypothesized dispersal events to Madagascar. The map represents the areas coded in the biogeographical analysis. The stratigraphy follows the 2017 International Chronostratigraphic Chart, the global temperature and tectonic events were mapped following [START_REF] Zachos | Trends, rhythms, and aberrations in global climate 65 Ma to present[END_REF], with (A) Tasmania-Antarctic passage opens and (B) Drake passage opens.

Biogeographical model

DISCUSSION

SYSTEMATICS

In Lindsaea, the tree topology obtained was globally congruent with the one found by [START_REF] Lehtonen | Phylogenetics and classification of the pantropical fern family Lindsaeaceae[END_REF]: the same phylogenetic relationships were retrieved with good support for clades I to VI, no resolution was found between clades VII, VIII-IX and X and the relationships between clades XI, XII and XIII remained unresolved due to low support in both studies (Figure 2B). Within Odontosoria, I found the same phylogenetic results as [START_REF] Lehtonen | Phylogenetics and classification of the pantropical fern family Lindsaeaceae[END_REF] and the position of O. melleri remain uncertain due to the lack of good supports.

Within Lindsaea, the synonymy of Lindsaea millefolia under L. flabellifolia proposed by Rakotondrainibe (com. pers.) cannot be confirmed by the present results: they were found in the same clade but without resolution, suggesting that the two species are phylogenetically close but not necessarily conspecific. In the same clade, my results did not discriminate Lindsaea flabellifolia from L. blotiana, like [START_REF] Lehtonen | Phylogenetics and classification of the pantropical fern family Lindsaeaceae[END_REF]. Based on their morphology, these species are however well segregated with for example Lindsaea flabellifolia having linear ultimate free divisions with one vein connecting one sorus whereas L. blotiana has branching veins connecting two or more sori per ultima division.

The Lindsaea subtilis sample was retrieved in the L. goudotiana clade, supporting the need to place L. subtilis under synonymy, as it was suggested by morphological observations (Rakotondrainibe, com. pers.). [START_REF] Kramer | The Lindsaeoid ferns of the Old World: IX Africa and Its Islands[END_REF] distinguished these species by the width of the ultimate free division and the shape of the segment. However, ongoing taxonomic works on Lindsaea show that the genus displays a continuum of sizes and shapes of the segments (Rakotondrainibe, com. pers.), making hazy taxonomic distinctions based on these characters.

With the synonymy of Lindsaea subtilis under L. goudotiana, the latter was the only monophyletic species retrieved by my phylogenetic analyses. For some species, there was not enough resolution to assess monophyly, suggesting that the markers could be not enough variable at this taxonomic scale (e.g. L. flabellifolia and L. blotiana). Also, several genetic processes can be misleading in the recognition of species and their relationships [START_REF] Naciri | Species delimitation and relationships: The dance of the seven veils[END_REF], notably hybridization that is a process largely recognized for ferns [START_REF] Barrington | Hybridization, Reticulation, and Species Concepts in the Ferns[END_REF][START_REF] Haufler | Species and speciation[END_REF][START_REF] Sigel | Genetic and genomic aspects of hybridization in ferns[END_REF] and previously suggested in Lindsaea [START_REF] Lehtonen | Phylogenetics and classification of the pantropical fern family Lindsaeaceae[END_REF]. This could notably explain the polyphyly of L. leptophylla and L. heterophylla.

BIOGEOGRAPHICAL HISTORY

Disjunction between the Paleotropics and the Neotropics

Ancestral ranges covering both the Paleotropics and the Neotropics were estimated at deep nodes in Lindsaea and Odontosoria (e.g. nodes g to j, Figure 3), although the lineages diversified in only one of the two regions. Such disjunctions in the Southern Hemisphere are usually explained by Gondwanan vicariance, direct dispersal or Antarctica routes [START_REF] Sanmartín | Southern hemisphere biogeography inferred by eventbased models: plant versus animal patterns[END_REF][START_REF] Winkworth | Explaining the disjunct distributions of austral plants: the roles of Antarctic and direct dispersal routes[END_REF].

As developed in Chapter III for Blechnoideae, the biogeographical history of Lindsaea and Odontosoria could be explained by migration via Antarctica and/or direct dispersal mediated by circumaustral wind currents. Compatible ancestral ranges with an Antarctica distribution were estimated in Lindsaea at nodes e to g, and eventually at nodes h and i when the 95% HPD is taken into account. The independent diversification in the Neotropics and Paleotropics could be therefore explained by an isolation of the two regions after ice-sheets formation at the Eocene/Oligocene boundary (Figure 3). In Odontosoria, the wide ranges estimated at node c included the Neotropics and Eastern Paleotropical regions, but also Western Paleotropical areas, suggesting that an ancestral Antarctica distribution does not completely explain the present results and suggest that other processes like dispersal could be involved. After ca. 35-30 Ma, connections between the Neotropics and the Paleotropics in Lindsaea are more likely explained by dispersal events from Australasia to the Neotropics rather than disjunctions of wide ranges consequently to vicariant events.

Biogeographical history of the Malagasy species

Four dispersal events most likely explain the distribution of Lindsaea and Odontosoria in Madagascar during the Cenozoic (O1, O2, L1, L2; Figure 3), since Madagascar was isolated from other landmasses since the Upper Cretaceous [START_REF] Mcloughlin | The breakup history of Gondwana and its impact on pre-Cenozoic floristic provincialism[END_REF]. At least two direct dispersal events between Australasia and Madagascar were suggested by the results (O2, L2; Figure 3). For ferns, dispersal events between these two regions were previously reported, but only during the Neogene and Quaternary (Hennequin et al., 2010b;[START_REF] Chao | Molecular phylogeny and biogeography of the fern genus Pteris (Pteridaceae)[END_REF][START_REF] Péchon | A well-sampled phylogenetic analysis of the polystichoid ferns (Dryopteridaceae) suggests a complex biogeographical history involving both boreotropical migrations and recent transoceanic dispersals[END_REF][START_REF] Kuo | Historical biogeography of the fern genus Deparia (Athyriaceae) and its relation with polyploidy[END_REF][START_REF] Sessa | Into Africa: Molecular phylogenetics and historical biogeography of sub-Saharan African woodferns (Dryopteris)[END_REF]. They were hypothesized to be linked to the onset of Asian monsoons. The age of initiation of Asian monsoons is subject to controversy but the associated winds would have been established at the latest during late Miocene [START_REF] Passey | Strengthened East Asian summer monsoons during a period of highlatitude warmth? Isotopic evidence from Mio-Pliocene fossil mammals and soil carbonates from northern China[END_REF][START_REF] Jacques | Quantitative reconstruction of the Late Miocene monsoon climates of southwest China: A case study of the Lincang flora from Yunnan Province[END_REF][START_REF] Gupta | Evolution of the South Asian monsoon wind system since the late Middle Miocene[END_REF]. The dispersal event O2 was estimated during Paleogene and would may rather be explained by stepping-stone dispersal via the drifting India [START_REF] Warren | Why does the biota of the Madagascar region have such a strong Asiatic flavour?[END_REF].

For L1, the exact area of origin of the dispersal event remains doubtful, due to wide ranges covering different areas estimated at nodes e and f. Moreover, the position of clade I in the BEAST analysis, as sister group to all other Lindsaea species, was poorly supported (PP=0.63) and this clade was instead found at the crown node of Lindsaea by MrBayes and raxML analyses (Figure 2A). Therefore, the biogeographical origins of clade II and Lindsaea plicata remain uncertain. About O1, a range covering multiple areas was inferred at node c and made it impossible to infer the area of origin of the Malagasy lineage.

With at least ten species that would have originated from in situ diversification, that is, 71% of the Lindsaea species diversity in Madagascar, diversification would be an important process to explain the diversity of the genus in Madagascar. Such diversification in Madagascar was also documented in previous chapters of this thesis, in genera of the grammitid ferns and Blechnoideae, in Rumohra, but also in Phlegmariurus.

All extant Lindsaea species of the Malagasy clade (included in clade IX) occur in tropical rainforests, mostly in the centre of the island [START_REF] Ml | Polypodiacées (sensu lato)[END_REF]. Lindsaea species are usually terrestrial, and epiphytes are only retrieved in clades V, VI, and in the Malagasy clade [START_REF] Lehtonen | Phylogenetics and classification of the pantropical fern family Lindsaeaceae[END_REF]. Therefore, speciation of some Malagasy Lindsaea may have been caused by adaptation to the epiphytic habitat. Lindsaea goudotiana and L. leptophylla are specialized epiphytes with host specificity, respectively on tree ferns and palm stipes, and their distant phylogenetic position suggests that epiphytism is most probably a convergence. Other species are occasionally epiphytes, like L. blotiana, L. flabellifolia or L. madagascariensis, but they are found close to the ground or on fallen branches/trunks, suggesting a slightly modified habitat compared to other fully terrestrial Lindsaea species.

ABSTRACT

We explored the biogeographical history of a group of spore-bearing plants focusing on Phlegmariurus (Lycopodiaceae), a genus of lycophytes comprising ca. 250 species. Given its wide distribution in the Southern Hemisphere, Phlegmariurus provides a good model to address questions about the biogeographical processes underlying southern distributions, notably in Madagascar and surrounding islands of the Western Indian Ocean (WIO). Our aims were i) to discuss the systematics of the Malagasy species in the light of molecular phylogenetic results, ii) to provide the first dating analysis focused on Phlegmariurus and iii) to understand the relative role of vicariance, dispersal and diversification in the origin of the Malagasy Phlegmariurus species.

The phylogenetic relationships were inferred based on three plastid DNA regions (rbcL, trnH-psbA and trnL+trnL-trnF) and on a dataset comprising 93 species that includes 16 Malagasy species (80% of the total Malagasy diversity for the genus). Our results highlighted the need to combine Malagasy Huperzia species in Phlegmariurus, as well as the polyphyly of widely distributed species: Phlegmariurus phlegmaria, P. squarrosus and P. verticillatus. This led us to propose new circumscriptions of Phlegmariurus species, especially in the WIO.

Our dating analysis, relying on fossil calibrations, showed that Phlegmariurus would have originated in the Late Cretaceous and diversified in Early Eocene. The biogeographical analysis highlighted uncertainties concerning the biogeographical origins of Phlegmariurus: the genus would have started to diversify in an ancestral range covering at least the Neotropics and Australasia. Hypotheses on the biogeographical history of Phlegmariurus were discussed, especially the roles of long distance dispersal, migration via Antarctica and the Boreotropics. Six long distance dispersal events over the last 40 Ma would explain the Malagasy species diversity of Phlegmariurus, as well as an important in situ diversification starting in Miocene.

KEYWORDS

Biogeography, molecular phylogeny, lycophytes, fossil, Southern Hemisphere, Western Indian Ocean

INTRODUCTION

Madagascar is a large 590,000 km 2 continental island of the Western Indian Ocean (WIO) renowned for its species richness and high level of endemism. It is considered to be one of earths important biodiversity hotspots [START_REF] Myers | Biodiversity hotspots for conservation priorities[END_REF] with ca. 11,000 species of vascular plants, among which 82% are endemic and 95% are angiosperms [START_REF] Callmander | The endemic and non-endemic vascular flora of Madagascar updated[END_REF]. Approximately 600 species of ferns and lycophytes are estimated to inhabit Madagascar, whereas 800 are estimated in all Africa [START_REF] Moran | Diversity, biogeography, and floristics[END_REF]. The level of endemism is also relatively high and evaluated to 45.2% of endemism (Rakotondrainibe, 2003a), more than the Galapagos (7%) or New Caledonia (38.2%) [START_REF] Moran | Diversity, biogeography, and floristics[END_REF][START_REF] Morat | Le référentiel taxonomique Florical et les caractéristiques de la flore vasculaire indigène de la Nouvelle-Calédonie[END_REF][START_REF] Munzinger | FLORICAL: Checklist of the vascular indigenous flora of New Caledonia[END_REF]. These high species richness and level of endemism raise the question about the origin of the Malagasy lineages and the evolutionary processes leading to such diversity.

Madagascar has a Gondwanan origin, having separated from Africa 165 Ma and from India 95-84 Ma [START_REF] Mcloughlin | The breakup history of Gondwana and its impact on pre-Cenozoic floristic provincialism[END_REF]) so ancient vicariant origins are plausible hypotheses to explain the unique divergent biota of Madagascar [START_REF] Yoder | Has Vicariance or Dispersal Has Vicariance Been the Predominant Force in Biogeographic Madagascar? Only Time Will Tell[END_REF]. However, the rise of molecular dating has highlighted more recent Cenozoic origins for most of the Malagasy lineages, suggesting that dispersal would be the main biogeographical process explaining the presence of modern Malagasy lineages [START_REF] Yoder | Has Vicariance or Dispersal Has Vicariance Been the Predominant Force in Biogeographic Madagascar? Only Time Will Tell[END_REF][START_REF] Agnarsson | The generation of a biodiversity hotspot: biogeography and phylogeography of the western Indian Ocean islands[END_REF]). Madagascar's biogeographical affinities have been found to be higher with the nearest continent Africa for animals and for plants [START_REF] Yoder | Has Vicariance or Dispersal Has Vicariance Been the Predominant Force in Biogeographic Madagascar? Only Time Will Tell[END_REF][START_REF] Buerki | Spatio-temporal history of the endemic genera of Madagascar[END_REF] even though its separation from India is more recent than from Africa. In agreement with the prediction of the Theory of Island Biogeography [START_REF] Macarthur | The theory of island biogeography[END_REF], Africa was found as a source of dispersal for numerous taxa towards Madagascar (e.g. [START_REF] Agnarsson | The generation of a biodiversity hotspot: biogeography and phylogeography of the western Indian Ocean islands[END_REF][START_REF] Zhou | Out-of-Africa' dispersal of tropical floras during the Miocene climatic optimum: Evidence from Uvaria (Annonaceae)[END_REF][START_REF] Blair | Multilocus phylogenetic and geospatial analyses illuminate diversification patterns and the biogeographic history of Malagasy endemic plated lizards (Gerrhosauridae: Zonosaurinae)[END_REF][START_REF] Bacon | Biogeography of the Malagasy Celastraceae: Multiple independent origins followed by widespread dispersal of genera from Madagascar[END_REF][START_REF] Forthman | Phylogenetics and biogeography of the endemic Madagascan millipede assassin bugs (Hemiptera: Reduviidae: Ectrichodiinae)[END_REF]. However, long distance dispersal events (LDD) for plants and animals were hypothesized from tropical Asia [START_REF] Warren | Why does the biota of the Madagascar region have such a strong Asiatic flavour?[END_REF][START_REF] Federman | The biogeographic origin of a radiation of trees in Madagascar: implications for the assembly of a tropical forest biome[END_REF][START_REF] Forthman | Phylogenetics and biogeography of the endemic Madagascan millipede assassin bugs (Hemiptera: Reduviidae: Ectrichodiinae)[END_REF] or from the Neotropics in plants [START_REF] Smedmark | Inferring geographic range evolution of a pantropical tribe in the coffee family (Lasiantheae, Rubiaceae) in the face of topological uncertainty[END_REF][START_REF] Janssens | Dispersing towards Madagascar: Biogeography and evolution of the Madagascan endemics of the Spermacoceae tribe (Rubiaceae)[END_REF]. Studies on ferns have highlighted that the Neotropics are an important source of dispersal for Madagascar in vascular spore-bearing plants (e.g. [START_REF] Rouhan | Molecular phylogeny of the fern genus Elaphoglossum (Elaphoglossaceae) based on chloroplast non-coding DNA sequences: Contributions of species from the Indian Ocean area[END_REF][START_REF] Bauret | Madagascar sheds new light on the molecular systematics and biogeography of grammitid ferns: New unexpected lineages and numerous long-distance dispersal events[END_REF]. Evidence of African dispersal events were also found [START_REF] Korall | Global biogeography of scaly tree ferns (Cyatheaceae): Evidence for Gondwanan vicariance and limited transoceanic dispersal[END_REF][START_REF] Sessa | Into Africa: Molecular phylogenetics and historical biogeography of sub-Saharan African woodferns (Dryopteris)[END_REF], as well as Asian affinities [START_REF] Lehtonen | Phylogenetics and classification of the pantropical fern family Lindsaeaceae[END_REF]. LDD from the Neotropics to Madagascar has also been found in bryophytes [START_REF] Scheben | Multiple transoceanic dispersals and geographical structure in the pantropical leafy liverwort Ceratolejeunea (Lejeuneaceae, Porellales)[END_REF] but no biogeographical analyses focused on Malagasy lycophytes have been done so far.

Madagascar is also well known to be a place of diversification of its fauna and flora, notably thanks to its isolation and its past and current habitat heterogeneity (Janssen et al., 2008;[START_REF] Vences | Madagascar as a model region of species diversification[END_REF][START_REF] Wood | Why is Madagascar special? The extraordinarily slow evolution of pelican spiders (Araneae, Archaeidae)[END_REF]. Phylogenetic studies showed that diversification is a major process in the generation of Malagasy endemic fern flora (Bauret et al., 2017, in Press.;Janssen et al., 2008;[START_REF] Chao | Molecular phylogeny and biogeography of the fern genus Pteris (Pteridaceae)[END_REF][START_REF] Labiak | Phylogeny and historical biogeography of the lastreopsid ferns (Dryopteridaceae)[END_REF][START_REF] Hennequin | Global phylogeny and biogeography of the fern genus Ctenitis (Dryopteridaceae), with a focus on the Indian Ocean region[END_REF]. It could be informative to test the monophyly of Malagasy lycophytes to observe if all the vascular spore-bearing plants have capable of such diversifications in Madagascar.

Phlegmariurus Holub is a pantropical genus of lycophytes including about 250 species (PPGI, 2016), occurring in wet tropical forested and montane habitats of tropical regions.

Two primary growth forms occur, hanging epiphytes in mesic forests and erect terrestrials in high montane non-forested areas, with the terrestrials being considered a derivation from ancestrally epiphytic species (Figure 1; [START_REF] Wikström | Epiphytism and terrestrialization in tropical Huperzia (Lycopodiaceae)[END_REF][START_REF] Field | Molecular phylogenetics and the morphology of the Lycopodiaceae subfamily Huperzioideae supports three genera: Huperzia, Phlegmariurus and Phylloglossum[END_REF]. Phlegmariurus is a monophyletic genus of Lycopodiaceae, forming with Huperzia and Phylloglossum the Huperzioideae subfamily (Figure 2A, [START_REF] Field | Molecular phylogenetics and the morphology of the Lycopodiaceae subfamily Huperzioideae supports three genera: Huperzia, Phlegmariurus and Phylloglossum[END_REF].

The biogeographical history of lycophytes is poorly understood and worldwide biogeographical analyses were done only recently on the cosmopolitan Selaginella [START_REF] Klaus | Historical biogeography of the ancient lycophyte genus Selaginella: early adaptation to xeric habitats on Pangea[END_REF], revealing a Devonian origin in Euramerica and a diversification coinciding with the formation of Pangea. On Isoetes, such analyses were provided by [START_REF] Kim | Biogeography of North Pacific Isoëtes (Isoëtaceae) inferred from nuclear and chloroplast DNA sequence data[END_REF] but on a dataset reduced to North Pacific species, and are lacking on Lycopodiaceae genera, like Phlegmariurus. Huge uncertainties remain about the age of divergence of Phegmariurus, with estimates in a large range of ages from 351 to 167 Ma [START_REF] Wikström | Evolution of Lycopodiaceae (Lycopsida): estimating divergence times from rbcL gene sequences by use of nonparametric rate smoothing[END_REF][START_REF] Larsén | Disentangling the Phylogeny of Isoetes (Isoetales), Using Nuclear and Plastid Data[END_REF]. These studies were however not focused on Phlegmariurus. A large diversification of Phlegmariurus has been recovered for the Neotropics and the Eastern Paleotropics (Asia, South-East Asia, Melanesia, Australasia and Pacific islands) in the most comprehensive phylogenetic study [START_REF] Field | Molecular phylogenetics and the morphology of the Lycopodiaceae subfamily Huperzioideae supports three genera: Huperzia, Phlegmariurus and Phylloglossum[END_REF] but low sampling in the Western Paleotropics (Africa, Madagascar, Mascarenes, Seychelles, Comoros) leaves the overall pattern of diversification in the Paleotropics poorly understood. Indeed, only four Western Paleotropical species have previously been sampled out of the 27 estimated in this region (Table 1, Field et al., in prep).

The Western Paleotropical region is outstanding in harboring one of the world's highest proportions of endemic Phlegmariurus with 90 % of endemic species (Table 1, Field et al., in prep.). Madagascar harbors 20 out of the 27 species estimated in the Western Paleotropical species and 14 of these are endemic to Madagascar (Table 1, Field et al. in prep). The Malagasy species of Phlegmariurus exhibit a spectrum of morphological diversity capturing most of the forms found in epiphytic Phlegmariurus globally (Figure 1). Therefore, based on morphological evidence only, it is difficult to interpret if the Malagasy Phlegmariurus result from multiple dispersal events to Madagascar that have converged geographically or if these species have stemmed from an endemic diversification, adaptively exploring congruent habitats to those found elsewhere and thereby repeating the spectrum of adaptive morphologies.

The Western Paleotropical region is also unique for the genus Phlegmariurus as several species exhibit unusual apomorphies, in particular triangular shoots (Figure 1,E,G) and fimbriate leaf margins (Figure 1,I). Since the latter character is only found in two endemic species to Madagascar (P. pecten and P. gagnepainianus), those species were kept separate by [START_REF] Herter | Beiträge zur kenntniis der kattung Lycopodium. Studien über dieuntergattung Urostachys[END_REF] and [START_REF] Nessel | Die Bärlappgewächse (Lycopodiaceae)[END_REF] in Urostachys (Pritz.) Herter subgenus Eurostachys Herter section Selaginurus Herter, suggesting an affinity with species now placed in the genus Huperzia s.s. rather than the genus Phlegmariurus. They were later placed in Huperzia subgenus Tardieaublottia by [START_REF] Holub | Some taxonomic changes within Lycopodiales[END_REF] suggesting they were distantly related to all other species. Most recently they were placed in Phlegmariurus Holub by [START_REF] Field | New and existing combinations in Palaeotropical Phlegmariurus (Lycopodiaceae) and lectotypification of the type species Phlegmariurus phlegmaria (L.)[END_REF], based on their lack of bulbils and relatively unornamented weakly foveolate isotetrahedral spore type. As they have never been placed in a molecular phylogenetic analysis, their evolutionary position remains unclear. Our study aims to improve the systematics of the Malagasy Phlegmariurus and to unravel the biogeographical history of Phlegmariurus, especially regarding Madagascar. The precise goals are (i) to test the monophyly of Malagasy species and to uncover their phylogenetic relationships; (ii) to date Malagasy Phlegmariurus lineage(s) and (iii) to infer the biogeographical history of Malagasy species of the genus. As we investigated the biogeographical history of the Malagasy lineages in a worldwide framework, we also aim to discuss the biogeographical history underlying the pantropical distribution of Phlegmariurus.

MATERIAL AND METHODS

TAXONOMIC SAMPLING

We gathered the largest dataset on Phlegmariurus so far, including 135 specimens representing 93 ingroup species. We included 60 species from the worldwide phylogeny of [START_REF] Field | Molecular phylogenetics and the morphology of the Lycopodiaceae subfamily Huperzioideae supports three genera: Huperzia, Phlegmariurus and Phylloglossum[END_REF] to provide a global framework plus a new dataset mostly focused on Africa and the WIO: 73 new specimens were added, representing 33 species (among which 28 were sequenced for the first time). Compared to the most recent phylogenetic study [START_REF] Field | Molecular phylogenetics and the morphology of the Lycopodiaceae subfamily Huperzioideae supports three genera: Huperzia, Phlegmariurus and Phylloglossum[END_REF], the entire dataset increased the Malagasy diversity from two to 16 species or 80% of the estimated diversity, including 9 out of the 13 Malagasy endemics (Table 1). Two outgroups were used: Huperzia australiana (Herter) Holub and Phylloglossum drummondii Kunze, known to form the sister-group to Phlegmariurus [START_REF] Wikström | Evolution of Lycopodiaceae (Lycopsida): estimating divergence times from rbcL gene sequences by use of nonparametric rate smoothing[END_REF][START_REF] Ji | A molecular phylogenetic study of Huperziaceae based on chloroplast rbcL and psbA-trnH sequences[END_REF][START_REF] Field | Molecular phylogenetics and the morphology of the Lycopodiaceae subfamily Huperzioideae supports three genera: Huperzia, Phlegmariurus and Phylloglossum[END_REF]. This sampling was modified for dating and biogeography (see 1.4). Vouchers details and GenBank accession numbers are reported in Appendix 5.

DNA EXTRACTION, AMPLIFICATION AND SEQUENCING

DNA extraction was performed from silica-dried leaf material or, when such material was not available, from herbarium specimens. The Qiagen DNeasy Plant Mini Kit (Valencia, California, USA) was used and we modified the protocol for herbarium specimens by adding 30 µL proteinase K (20 mg/mL) and 30 µL beta-mercaptoethanol for the initial lysis step, which was carried out at 42 °C during 24 hrs.

We amplified three plastid regions, the gene rbcL, trnL intron plus trnL-trnF spacer (trnL-trnLF) and the intergenic spacer trnH-psbA. All PCRs were carried out in a 25 μL volume containing 1x PCR buffer, 2.5 mM MgCl2, 250 μM of each dNTP, 1M betaine, 0.4 μM of each primer, 0.75 U Taq polymerase (Taq CORE kit; MP Biomedicals, Illkirch, France), and 1 μL of template, non-diluted genomic DNA. Primer sequences and thermal cycling conditions are reported in Table 2. PCR products were checked on a 1% agarose gel and sequenced in both directions by Eurofins (Evry, France) using the amplification primers and additional internal primers for rbcL (Table 2). DNA strands were edited and assembled in Sequencher 4.9 (Gene Codes Corporation) and the resulting consensus sequences were submitted to GenBank (accession numbers in Appendix 5).

DNA region

PHYLOGENETIC ANALYSES

The sequences were aligned with Muscle 3.8.425 [START_REF] Edgar | MUSCLE: multiple sequence alignment with high accuracy and high throughput[END_REF], and the resulting alignments were checked by eye and revised manually. After analysis of each marker independently and control of conflicts between the topologies, the data matrix was built by concatenation of the three alignments with Sequence Matrix 1.7.8 [START_REF] Vaidya | SequenceMatrix: concatenation software for the fast assembly of multi-gene datasets with character set and codon information[END_REF].

Each DNA region constituted an independent partition in the final dataset. Gaps were treated as missing data.

Phylogenetic trees were inferred based on Maximum Likelihood (ML) and Bayesian Inference (BI) approaches, as respectively implemented in RAxML-HPC2 8.2.6 [START_REF] Stamatakis | RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies[END_REF] and MrBayes 3.2.6 [START_REF] Ronquist | MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space[END_REF]. The analyses were conducted on the CIPRES science gateway [START_REF] Miller | Creating the CIPRES Science Gateway for inference of large phylogenetic trees[END_REF].

For the BI, we used a Metropolis-coupled Markov chain Monte Carlo method implemented in MrBayes 3.2.6 [START_REF] Ronquist | MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space[END_REF]. For each region, a reversible jump MCMC (rjMCMC) [START_REF] Huelsenbeck | Bayesian phylogenetic model selection using reversible jump Markov Chain Monte Carlo[END_REF] was used with MrBayes to find the best suited model of nucleotide substitution and we allowed the rjMCMC to move across models with +I+Γ. Two independent but parallel analyses using ten million generations each were conducted, with four chains and a temp set as 0.05 in mcmc command. The trees were sampled every 1,000 generations to obtain 10,000 sampled trees. We used Tracer 1.6.0 [START_REF] Rambaut | Tracer 1.6[END_REF] to check the output parameter estimates through time, and to estimate the point of convergence to the stationary distribution of the two runs: the 25% initial trees were discarded as burn-in. A 50% majority-rule consensus was computed based on the post-burn-in trees with average branch lengths and posterior probability (PP) estimates for all nodes.

The ML analysis was performed with RAxML-HPC2 8.2.6 [START_REF] Stamatakis | RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies[END_REF], using the same three partitions as in MrBayes. Parameters for the RAxML analysis were determined on the CIPRES interface: we used the GTRGAMMA model of nucleotide substitution, performed 1,000 rapid bootstrap (BS) replicates and searched for the best-scoring ML tree.

The BI 50% majority-rule consensus tree and ML best tree were visualized in FigTree 1.4.2 [START_REF] Rambaut | FigTree 1.4.2 software[END_REF].

FOSSIL CALIBRATION AND DIVERGENCE TIME ESTIMATION

The dataset was modified to perform the dating analyses by first reducing the matrix to 96 specimens representing the 91 sampled Phlegmariurus species. We kept one sample per species or one per lineage when the species were retrieved as polyphyletic. We then added 22 outgroup species for dating and biogeographical analyses: Phylloglossum drumondii, 16 Huperzia species, Lycopodiella inundata (L.) J. Holub from the Lycopodielloideae (sensu PPGI, 2016), Diphasium jussiaei (Desv. ex Poir.) Rothm. from the Lycopodioideae (sensu PPGI, 2016), Isoetes flaccida Shuttlew. and two Selaginella species.

Although fossils of vegetative structures have been ascribed to the genus Huperzia s.l.

(meaning Huperzia and Phlegmariurus), they could not be confidently placed within the Huperzioideae and used as reliable calibrations points. Morphological characters of Huperzia s.l. have generally been considered to be plesiomorphic, leading analyses to place fossils of Huperzia s.l. at a basal position within lycophytes [START_REF] Bateman | Do eligulate herbaceous lycopsids occur in Carboniferous strata? Hestia eremosa gen. et sp. nov. from the Mississippian of Oxroad Bay, East Lothian, Scotland[END_REF][START_REF] Xue | Phylogeny of Devonian Lycopsids Inferred from Bayesian Phylogenetic Analyses (Intergovernmental Panel on Climate Change, Ed.)[END_REF]. This basal position is in contradiction with molecular based phylogenies in which Huperzia s.l. is found nested in Lycopodiaceae and exhibit singular vegetative synapomorphies that could preserve in fossils [START_REF] Field | Molecular phylogenetics and the morphology of the Lycopodiaceae subfamily Huperzioideae supports three genera: Huperzia, Phlegmariurus and Phylloglossum[END_REF]. In particular, corticular root emergence is a synapomorphy of Huperzioideae and bulbils in the axils of sporophylls is a synapomorphy of Huperzia [START_REF] Field | Molecular phylogenetics and the morphology of the Lycopodiaceae subfamily Huperzioideae supports three genera: Huperzia, Phlegmariurus and Phylloglossum[END_REF], but these features are presently unknown in the fossil record. Vegetative bulbils are present in the Pragian Hueberia zhichangensis Yang, Li & Edwards [START_REF] Yang | Hueberia zhichangensis gen. et sp. nov, an Early Devonian (Pragian) plant from Yunnan, China[END_REF][START_REF] Xue | New material of Hueberia zhichangensis Yang, Li & Edwards, a basal lycopsid from the Early Devonian of Yunnan, China[END_REF], but this species exhibits anisotomous branching, rounded sporangia and the bulbils that are not associated with sporophylls, contrasting with Huperzia which exhibit isotomous branching, and reniform sporangia and bulbils that are strictly associated with sporophylls.

Huperzioideae are confidently known from spore fossils similar to modern spores of species groups of Phlegmariurus phlegmaria (L.) Holub and Huperzia selago (L.) Bernh., from the fossil record of New Zealand and Australia [START_REF] Cieraad | The New Zealand fossil record of ferns for the past 85 million years[END_REF]. The spore fossil Foveotriletes lacunosus Partridge is a Phlegmariurus phlegmaria type spore that has a relatively continuous record of presence in New Zealand and Australia from the Chatian Oligocene (28.1 Ma) to present day [START_REF] Cieraad | The New Zealand fossil record of ferns for the past 85 million years[END_REF]. However, both Phylloglossum drummondii and all species of Phlegmariurus share the Phlegmariurus phlegmaria spore type, and it is therefore not possible to place Foveotriletes lacunosus in either position as a calibration point. The spore fossil Foveotriletes palaequestrus is a Huperzia selago type spore that is reported to have a relatively continuous record of presence in New Zealand and Australia from the Lutetian Eocene (47.8 Ma), merging with present day Huperzia australiana [START_REF] Cieraad | The New Zealand fossil record of ferns for the past 85 million years[END_REF]. Some doubts exist as to the earliest record of F. lacunosus spores [START_REF] Cieraad | The New Zealand fossil record of ferns for the past 85 million years[END_REF]) and furthermore it is not possible to determine if it be placed with Huperzia australiana or elsewhere within Huperzia as all species share the Huperzia selago spore type.

To fill this gap in useable Huperzioideae fossils, we calibrated our analysis with four confident outgroup fossils, summarized in Table 3. The maximum height of our lycophytes tree was defined on the occurrences of the earliest lycophytes, like Asteroxylon mackiei [START_REF] Kidston | On old red sandstone plants showing structure, from the Rhynie Chert bed, Aberdeenshire. Part III. Asteroxylon mackiei[END_REF], Hueberia zhichangensis Yang, Li & Edwards [START_REF] Bateman | Do eligulate herbaceous lycopsids occur in Carboniferous strata? Hestia eremosa gen. et sp. nov. from the Mississippian of Oxroad Bay, East Lothian, Scotland[END_REF][START_REF] Yang | Hueberia zhichangensis gen. et sp. nov, an Early Devonian (Pragian) plant from Yunnan, China[END_REF][START_REF] Xue | New material of Hueberia zhichangensis Yang, Li & Edwards, a basal lycopsid from the Early Devonian of Yunnan, China[END_REF] and Zhenglia radiata Hao, Wang, Wang & Xue [START_REF] Hao | A New Lycopsid, Zhenglia radiata gen. et sp. nov., from the Lower Devonian Posongchong Formation of Southeastern Yunnan, China, and Its Evolutionary Significance[END_REF]. These fossils were dated in the Pragian Devonian (407.6-410.8 Ma, Lower Devonian) and the lower limit of this stage was used to constrain the maximum age of lycophytes. The lycophyte Baragwanathia longifolia Lang & Cookson has been reported as occurring as early as the Silurian, but doubts remain for some authors on the earliest stratigraphic occurrence [START_REF] Hueber | Thoughts on the Early Lycopsids and Zosterophylls[END_REF], so we kept the more confident Pragian age.

The minimum age of divergence between the Isoetales and the Selaginellales was defined with the occurrence of Yuguangia ordinata, placed by a cladistic analysis in the clade including Isoetes and Selaginella [START_REF] Hao | Yuguangia ordinata gen. et sp. nov., a new lycopsid from the middle Devonian (late Givetian) of Yunnan, China, and its phylogenetic implications[END_REF]. This fossil was found in the Givetian (382.7-387.7 Ma, Middle Devonian) and the upper limit of the stage was used as minimum age and the maximum tree height as the maximum age.

We calibrated the minimum age of the Selaginella crown node with Selaginella resimus, a fossil already used in [START_REF] Klaus | Historical biogeography of the ancient lycophyte genus Selaginella: early adaptation to xeric habitats on Pangea[END_REF] for their Selaginella dating and occurring in the Visean (330.9-346.7 Ma, Carboniferous). We defined the upper limit of Visean as the minimum age. The minimum age of divergence between Lycopodielloideae and Lycopodioideae was defined on the oldest confident occurrence of fossils assigned to this node with Retitriletes spp. (Bomfleur et al., 2014), in the Sinemurian (190.8-199.3 Ma, Lower Jurassic). The upper stratigraphic limit was chosen as the minimum age. Retitriletes is a spore genus of isotetrahedral spores with distinct reticulate ornamentation present on the distal surface that makes it closely comparable with the reticulate distal surface structure in the Lycopodium clavatum spore group that is a synapomorphy of modern Lycopodioideae species (but lost in Pseudolycopodium Holub and Pseudodiphasium Holub) [START_REF] Juhász | Lycopodiaceae spores from Lower Cretaceous deposits of Hungary[END_REF][START_REF] Field | Molecular phylogenetics and the morphology of the Lycopodiaceae subfamily Huperzioideae supports three genera: Huperzia, Phlegmariurus and Phylloglossum[END_REF]. Modern studies comparing Retitriletes and Lycopodioideae spores using scanning and transmission electron microscopies are lacking and it is important to note that several of the species assigned to the genus Retitriletes are dissimilar to modern Lycopodioideae (e.g. [START_REF] Hashemi-Yazdi | A new lycophyte miospore species from the Middle Jurassic of Iran[END_REF] and the genus is likely non-monophyletic.

We performed the dating analyses using BEAST v2.4.2 [START_REF] Drummond | Bayesian Phylogenetics with BEAUti and the BEAST 1.7[END_REF] on the CIPRES science gateway, the same partitions and research of models of nucleotide substitution used for MrBayes and RaxML analyses were defined. The package RBS 1.3.1 was installed in BEAST to implement the rjMCMC research. We used an uncorrelated lognormal relaxed clock with a Birth-Death tree prior and a random starting tree. The fossil calibration points were all set following a uniform prior with values summarized in Table 3. We conducted four runs of 200 million generations with random seed values and sampled every 20,000 generations to obtain 10,000 sampled trees. Tracer 1.6.0 was used to confirm the convergence of the estimated parameters and to define the burn-in at 10%. The post burn-in trees from the four runs were combined using LogCombiner 2.4.2, the maximum clade credibility trees using TreeAnnotator v2.4.2 and visualized with the associated chronogram using FigTree 1.4.2 [START_REF] Rambaut | FigTree 1.4.2 software[END_REF].

ANCESTRAL AREA ESTIMATION

To reconstruct the biogeographical history, we estimated the ancestral ranges using the R package BioGeoBEARS (Biogeography with Bayesian Evolutionary Analysis in R Scripts, [START_REF] Matzke | BioGeoBEARS: BioGeography with Bayesian (and likelihood) evolutionary analysis in R scripts[END_REF] in R studio 1.0.44 (RStudio Team, 2015). It implements in a likelihood framework three commonly used methods: Dispersal-Extinction-Cladogenesis (DEC; [START_REF] Ree | Maximum likelihood inference of geographic range evolution by dispersal, local extinction, and cladogenesis[END_REF], Dispersal-Vicariance Analysis (DIVA; [START_REF] Ronquist | Dispersal-Vicariance Analysis: A New Approach to the Quantification of Historical Biogeography[END_REF]DIVALIKE in BioGeoBEARS) and Bayesian Inference for Discrete Areas (BayArea; [START_REF] Yu | RASP (Reconstruct Ancestral State in Phylogenies): A tool for historical biogeography[END_REF]BAYAREALIKE in BioGeoBEARS). Three analyses using each method (DEC, DIVALIKE, BAYAREALIKE) were performed plus three including the additional parameter j (DEC+J, DIVALIKE+J, BAYAREALIKE+J). The 'j' parameter adds the process of a founder event speciation, when a daughter lineage jumps to a new range outside the range of its ancestor. The Akaike Information Criterion (AIC) was then used to select the best-suited model, then to infer the ancestral ranges along the phylogeny of Phlegmariurus.

Eight areas where defined to code the distribution of the species (see map, Figure 3 . Field). The maximum number of areas coded was set to four as it was the maximum number of area coded for a tip.

RESULTS

PHYLOGENY

Overall topology

The combined dataset was composed of 137 specimens and 2890 characters; summary statistics of the dataset are available in Table 4. BI and ML topologies were similar with a well-supported Phlegmariurus clade (BS=100; PP=1) nesting two clades with less support (Figure 2). Firstly, the Neotropical clade (BS=74; PP=0.89) included mostly Neotropical species and two Paleotropical lineages: 1) one including the African species Phlegmariurus bampsianus and the Western Paleotropic P. ophioglossoides (in N1) and 2) the Western Paleotropical Phlegmariurus verticillatus (in N2). The Macaronesian P. dentatus was also retrieved in the Neotropical clade as well as the wide-ranged P. saururus. Secondly, the Paleotropical clade (BS=73; PP=0.88) nested the remaining two thirds of the sampled diversity with predominantly Paleotropical species and including only one Neotropical species, P. funiformis (Figure 2). Overall the topology inferred was similar to the most recent worldwide phylogenetic study on Phlegmariurus [START_REF] Field | Molecular phylogenetics and the morphology of the Lycopodiaceae subfamily Huperzioideae supports three genera: Huperzia, Phlegmariurus and Phylloglossum[END_REF] but the addition of numerous Western Paleotropical species resulted in a completely new clade (Malagasy clade), included in the Paleotropical clade (Figure 2). The newly sampled Western Paleotropical species were inserted in 8 distinct positions, both in Malagasy clade and across Neotropical and Eastern Paleotropical clades (Figure 2). Within the Paleotropical clade, many of the species were arranged in a polytomy or among one of three Paleotropical clades, the Malagasy, the P1 and the P2 clades.

Number of sequences

Aligned length (in base pairs)

Composition of the two major clades

The Neotropical clade included two subclades, N1 clade (P. attenuatus to P. dichotomus; BS=65; PP=0.76; Figure 2) and N2 (P. ophioglossoides to P. ericifolius; BS=99; PP=1), with both clades including species from Western Paleotropics. All of the six species within N2 clade are hanging epiphytes with markedly heterophyllous biformic shoots with leafy fertile shoots terminated by funiforme-filiforme fertile spikes, whereas the clade N1 includes a spectrum of heterophyllous to homophyllous hanging epiphytes, facultative epiliths and erect terrestrials.

This arrangement is mirrored in the Paleotropical clade which includes two morphologically equivalent subclades both including species from the Western Paleotropics. All of the species within the moderately supported clade P1 (P. tardieuae to P. trifoliatus, BS<50; PP=0.98, Figure 2) are strongly heterophyllous biformic hanging epiphytes with leafy fertile shoots and funiforme to filiform fertile spikes and by comparison the poorly supported clade P2 (P. fordii to P. tetrastichoides, BS<50; PP=0.57, Figure 2) includes a spectrum of heterophyllous to homophyllous hanging epiphytes, facultative epiliths and facultative terrestrials.

Composition of the Malagasy clade

This study was the first to recover a clade comprised entirely of Western Paleotropical species (Malagasy clade, Figure 2) with 11 out of the 20 species estimated in Madagascar (including the enigmatic P. pecten) and out of the 26 estimated in the Western Paleotropics. However, most of the phylogenetic relationships within the Malagasy clade were unresolved. In our phylogeny, P. pecten was inserted among P. gnidioides and P. obtusifolius, confirming it was a Phlegmariurus and not a Huperzia s.s. The most recently described species of Huperzia from Madagascar, H. ambrensis Rakotondr. and H. teretirigida Rakotondr. were inserted in this clade of Phlegmariurus (Figure 2). The Malagasy clade included many morphologically dissimilar Western Indian Ocean endemics such as P. ambrensis comb. ined., P. cavifolius, P. lecomteanus, P. obtusifolius, P. pecten, P. pichianus which repeat the morphological spectrum of Phlegmariurus found elsewhere in the Paleotropics. This clade included both heterophyllous hanging epiphytes, homophyllous epiliths and facultative terrestrials. The morphologically singular species P. gnidioides and P. obtusifolius in particular were each recovered as nonmonophyletic or unresolved. Two large robust nearly homophyllous hanging epiphytes, the tropical east African endemic P. holstii and the Asian-Oceanian P. dalhousieanus were placed as sister to the Malagasy clade, each inserted on a long branch (Figure 2).

Focus on the Western Paleotropical species

The phylogenetic hypotheses inferred were not fully resolved to species level and many closely related species were placed in polytomies, and where structure was recovered, several species were polyphyletic (Figure 2). Phlegmariurus bampsianus was retrieved nested in a clade among P. ophioglossoides collections (= P. rubricus sensu Tardieu-Blot, 1970; and P. rubricus + P. ophioglossoides sensu [START_REF] Field | New and existing combinations in Palaeotropical Phlegmariurus (Lycopodiaceae) and lectotypification of the type species Phlegmariurus phlegmaria (L.)[END_REF]) (clade N2, Figure 2). Phlegmariurus verticillatus s.l. was polyphyletic with specimens sampled from the Mascarenes type population of P. verticillatus inserted in the Neotropical clade with Malagasy and Comoros specimens, whereas specimens sampled from the Asian region were inserted in the Paleotropical clade (Figure 2). Also, P. squarrosus s.l. is polyphyletic, being inserted in three places in the tree recovered, in the Malagasy clade and in two positions in P2 clade. These collections were re-identified in the strict sense as P. lecomteanus from Madagascar (Malagasy clade), P. sp1 'ulcifolius' from Comoros (P1 clade) and P. squarrosus from the Oceanian region (P1 clade). Phlegmariurus lecomteanus is readily distinguished from P. squarrosus by having a red stem wall and non-twisted leaves (Figure 1, H) but is otherwise divergent from the Malagasy species it is related to. Similarly, P. phlegmaria s.l. (e.g. [START_REF] Chinnock | Lycopodiaceae[END_REF][START_REF] Roux | Synopsis of the Lycopodiophyta and Pteridophyta of Africa, Madagascar and neighbouring islands[END_REF] was also recovered as ployphyletic but all collections were inserted in the P1 clade. All P. phlegmaria group species from Western Paleotropics formed an endemic clade that is re-identified in the strict sense as P. tardieuae (Figure 2). Several species were not retrieved in the Malagasy, P1 or P2 subclades of the Paleotropical clade, notably P. cryptomerianus, P. jaegeri, P. parksii a species with P. verticillatus-like morphology and P. perrierianus a species with a P. phlegmaria-like morphology (Figure 2).

Molecularly based clades versus morphologically defined groups

Many of the 21 intuitive morphological species groups proposed by Øllgaard (H2-H22; 1987, 1989) formed molecular clades. The erect Neotropical terrestrial species of the P. reflexus group (H20), the P. saururus group (H21) and the P. brevifolius group (H22) combined formed a well-supported clade (BS=96; PP=1). Within this clade the P. saururus and P. brevifolius groups (H21 & 22) intermingled form a clade (BS=66; PP=1) sister to a clade of the P. reflexus group (H20) including the Macaronesian P. dentatus (BS=57; PP=0.93). The P. phlegmaria group (H12a-k) was polyphyletic with members of its subgroups embedded amongst members of several other groups in both the Palaeotropical and Neotropical clades. Species from the obtusifolius subgroup (H12g) were embedded among species from the P. gnidioides group (H4) and species from the P. carinatus group H3 were embedded in the P. phlegmaria group (H12) and the P. squarrosus group (H13). Members of the P. hippuris group (H8) and squarrosus group (H13) were intermingled. The verticillatus group (H9) was the most markedly polyphyletic with species inserted in five different positions among the species sampled.

Several species included in previous studies were re-identified including H. billardierii from [START_REF] Wikström | Phylogeny of epiphytic Huperzia (Lycopodiaceae): paleotropical and neotropical clades corroborated by rbcL sequences[END_REF] here re-identified as P. varius (R.Br.) A.R.Field & Bostock and a specimen misattributed to P. hamiltonii in [START_REF] Field | Molecular phylogenetics and the morphology of the Lycopodiaceae subfamily Huperzioideae supports three genera: Huperzia, Phlegmariurus and Phylloglossum[END_REF] here tentatively reidentified as P. lenhertii Testo.

BEAST TOPOLOGY AND DIVERGENCE TIME ESTIMATES

Huperzia and Phlegmariurus were found in the same clade (PP=0.87, Figure 3) and strongly supported as monophyletic respectively (PP=1). Phylloglossum drumondii was retrieved sister species to the clade Huperzia-Phlegmariurus (PP=1). Within Phlegmariurus, the topology did not contradict the MrBayes topology and brought more resolution however often weakly supported in several clades, in particular in the Paleotropical clade.

Based on the four calibration points derived from fossils, our analysis estimated that Lycopodiaceae have originated in the Lower Devonian at 404. 3). These two genera would have started their diversification during the Eocene at 47.6 Ma (HPD: 29.1-71.5) for Phlegmariurus and more recently during the Oligocene at 24.5 Ma (HPD: 11.7-42.2) for Huperzia.

ANCESTRAL AREA ESTIMATION

The biogeographical model DEC+J conferred the highest likelihood on the data and the best AIC (LnL= -289.7; AIC= 585.4; followed by DEC model with LnL=-296.3; AIC= 596.6) and the inferred ranges were plotted on the BEAST chronogram (Figure 3).

Uncertainties between estimated ranges were found at Phlegmariurus crown node, as well as the node at divergence between Huperzia and Phlegmariurus. Indeed, numerous ranges were found with small probabilities (p<0.06). Most likely, Huperzia started to diversify in the temperate North Hemisphere (p=0.55) and Phlegmariurus in an uncertain and wide range involving Neotropical and Paleotropical regions: the four most likely inferred ranges were Africa-Neotropics-Australasia (p=0.10), Madagascar-Africa-Neotropics-Australasia (p=0.09), Neotropics-Australasia (p=0.08) and Africa-Neotropics-Asia-Australasia (p=0.07).

Six range expansions by long distance dispersal would explain the species diversity of Phlegmariurus in Madagascar for the last ca. 30 Ma, but with uncertainties as wide ancestral ranges were estimated (except LDD3): from Africa 26.6-19.1 Ma but with Asian-Australasian uncertainties (LDD1), from Africa to WIO 2.0-0.0 Ma (LDD2), from Australasia to Madagascar 1.0 Ma (LDD3), from Australasia 19.8-4.4 Ma but with an Asian uncertainty (LDD4) and from the Neotropics 25.3-5.7 Ma (LDD5) and 38.5-12.3 Ma (LDD6) but with Western Paleotropical uncertainties. A diversification starting exclusively in Madagascar was estimated in the Malagasy clade ca. 10 Ma. It was the only diversification estimated in Madagascar for Phlegmariurus, and so for Huperzioideae. Next to terminals, colored squares depict biogeographical distribution considering eight areas: temperate Northern Hemisphere (grey), circumpolar (dark blue), Neotropics (green), continental and tropical Africa (violet), Madagascar (red), Mascarenes-Comoros-Seychelles islands (orange), tropical Asia (yellow), Australasia-Oceania (light-blue). Colored pies represent the ancestral areas estimated at nodes. When present next to pie charts, colored squares represent the combination of areas covered by a range. These combinations do not necessarily represent the most likely ancestral range estimated at a node. A reduced topology represents the entire BEAST chronogram, simplified in Huperzioideae, with black squares depicting the four fossil calibration points. The stratigraphy follows the 2017 International Chronostratigraphic Chart, the global temperature and the climatic events were mapped following [START_REF] Zachos | Trends, rhythms, and aberrations in global climate 65 Ma to present[END_REF].

DISCUSSION

SYSTEMATICS

The phylogeny presented here provides evidence to address several systematics issues in Phlegmariurus of Madagascar, Africa and the Western Indian Ocean region. Firstly, we establish the placement of P. pecten in the Malagasy clade of Paleotropical Phlegmariurus and we reject the need for its placement in the subgenus Tardieublotia Holub sensu [START_REF] Holub | Some taxonomic changes within Lycopodiales[END_REF] or Huperzia s.s. (sensu [START_REF] Herter | Beiträge zur kenntniis der kattung Lycopodium. Studien über dieuntergattung Urostachys[END_REF][START_REF] Nessel | Die Bärlappgewächse (Lycopodiaceae)[END_REF]. The unusual fringed leaf margins of P. pecten (and its close relative or synonym P. gagnepainianus) (Figure 1, I) appears to be an apomorphy not found elsewhere in the genus Phlegmariurus and is not indicative of a relationship with Huperzia.

Secondly, we show that the recently described species H. ambrensis Rakotondr. and H. teretirigida Rakotondr. are inserted in the Malagasy clade diversification of Phlegmariurus and a new nomenclatural combination is provided for P. ambrensis (Rakotondr. & Jouy) A.R.Field and H. teretirigida is synonymised with the little known species P. humbertii (Nessel) A.R. Field & Bostock (Field et al., in prep.). These species were correctly placed in the gnidioides group by [START_REF] Rakotondrainibe | Nouveautés dans le Genre Huperzia Bernh. (Lycophytes, Lycopodiaceae) à Madagascar[END_REF] and are well supported by morphological similarity as they share slightly enrolled leaf margins with many species in this group.

Thirdly, based on our results we corroborate the findings of [START_REF] Wikström | Epiphytism and terrestrialization in tropical Huperzia (Lycopodiaceae)[END_REF] and [START_REF] Field | Molecular phylogenetics and the morphology of the Lycopodiaceae subfamily Huperzioideae supports three genera: Huperzia, Phlegmariurus and Phylloglossum[END_REF] that P. phlegmaria s.l., P. squarrosus s.l., and P. verticillatus are polyphyletic taxa. We prefer a classification that separates the Eastern Paleotropical P. squarrosus from P. sp1 'ulicifolius' and P. lecomteanus that delimits P. tardieuae as an endemic Malagasy distinct species from the WIO-Asian P. phlegmaria and that separates the Asian-Oceanian P. verticillatus from the Western Paleotropical type population of P. verticillatus s.s. which is nested in the Neotropical clade. Morphological features that distinguish these taxa are presented in Field et al. (in prep).

Future sampling in the Malagasy region should focus on obtaining P. xiphophyllus, which is the only Malagasy member of the Indian-Asian P. hamiltonii group (H2, Øllgaard, 1987) and potentially represents another LDD to Madagascar from the Himalayan region. It should also focus on relocating P. hildebrandtii which is of uncertain affinity possibly related to the P. reflexus group from the Neotropics (Øllgaard, 1989). Future sampling in the African region should focus on biformic species occurring in Africa such as P. afromontanus and P. ellenbeckii. Based on their morphology it is expected these species belong to the Neotropical clade biformic subclade including P. ophioglossoides and their inclusion in future sampling could ascertain whether they represent a single or multiple trans-Atlantic dispersal to Africa. Future sampling across the Atlantic and Indian Oceanic regions should sample the many disparate and disjunct populations of the morphologically heterogeneous P. saururus to ascertain if this species is the result of a single or several long-distance dispersals from the Andean region.

AGE ESTIMATES

Our study provided the first dating analysis focused on Phlegmariurus, showing that despite a Cretaceous divergence, most of the diversity has arisen from diversifications starting during the Eocene. Huperzioideae were already estimated to have diverged 167 Ma and diversified 62 Ma by a study focused on Isoetes [START_REF] Larsén | Disentangling the Phylogeny of Isoetes (Isoetales), Using Nuclear and Plastid Data[END_REF]. These ages are younger than our results (resp. 273.6 Ma and 102.6 Ma) and could be explained by an under-sampling (only two Phlegmariurus species), which has already been correlated with younger age estimates (e.g. [START_REF] Linder | Taxon sampling effects in molecular clock dating: An example from the African Restionaceae[END_REF][START_REF] Testo | A 4000-species dataset provides new insight into the evolution of ferns[END_REF]. Our results are however much younger than ages estimated by [START_REF] Wikström | Evolution of Lycopodiaceae (Lycopsida): estimating divergence times from rbcL gene sequences by use of nonparametric rate smoothing[END_REF], who found respectively 351 Ma and 265 Ma based on a nonparametric rate smoothing analysis and rbcL sequences alone. They also estimated the divergence between the Neotropical and Paleotropical clade at 184 Ma, against 47.6 Ma in our results.

It is however hard to define without additional analyses why they found substantially older ages, with many parameters being different between their analysis and ours, such as the calibrations used, the species and markers sampled and analytical method used.

BIOGEOGRAPHICAL HISTORY OF PHLEGMARIURUS: THREE HYPOTHESES

Phlegmariurus is a genus distributed across the Southern Hemisphere but its species diversity is geographically clustered in three major clades, the Neotropical clade, the Western and the Eastern Paleotropical clades, which would have respectively started to diversify into the Neotropics, Africa, and Australasia during the last 40 Ma. Our biogeographical analysis failed to estimate with confidence the ancestral area of Phlegmariurus, as well as its ancestral area of diversification. Given these uncertainties, three biogeographical processes need to be examined to explain the current, mostly Southern distribution of Phlegmariurus.

The direct dispersal hypothesis

Dispersal is a hypothesis often used to explain the distribution of spore-bearing plants [START_REF] Wolf | Geographic distributions of homosporous ferns: Does dispersal obscure evidence of vicariance?[END_REF][START_REF] Moran | Diversity, biogeography, and floristics[END_REF][START_REF] Norhazrina | Tropical bryophyte floras: a homogeneous assemblage of highly mobile species? Insights from their spatial patterns of beta diversity[END_REF] and biogeographical connections in the Southern Hemisphere have been shown to be correlated with circumaustral wind currents for many taxa of lycophytes, ferns or mosses [START_REF] Parris | Circum-Antarctic continental distribution patterns in pteridophyte species[END_REF][START_REF] Sanmartín | Southern hemisphere biogeography inferred by eventbased models: plant versus animal patterns[END_REF][START_REF] Munoz | Wind as a Long-Distance Dispersal Vehicle in the Southern Hemisphere[END_REF]. If dispersal events cannot be excluded to explain the current distribution of Phlegmariurus across continents, circumaustral wind currents could not have been involved in the biogeographical history of Phlegmariurus before the Oligocene. Indeed, a circumpolar circulation would have established only after the separation of Australia and Antarctica ca. 35 Ma and the Drake passage opening ca. 30 Ma [START_REF] Mcloughlin | The breakup history of Gondwana and its impact on pre-Cenozoic floristic provincialism[END_REF][START_REF] Sanmartín | West Wind Drift revisited: testing for directional dispersal in the Southern Hemisphere using event-based tree fitting[END_REF].

A southern origin hypothesis via Antarctica

Before being the iced continent we know today, Antarctica was covered by subtropical to temperate forests [START_REF] Poole | Valdivian ecosystems in the Late Cretaceous and Early Tertiary of Antarctica: further evidence from myrtaceous and eucryphiaceous fossil wood[END_REF][START_REF] Pross | Persistent near-tropical warmth on the Antarctic continent during the early Eocene epoch[END_REF][START_REF] Cantrill | Paleocene flora from Seymour Island, Antarctica: revision of Dusén's (1908) angiosperm taxa[END_REF] and provided a bridge between South America and Australia, allowing species to be widely distributed across these three landmasses. It was also a bridge for migration or stepping-stone dispersal [START_REF] Winkworth | Explaining the disjunct distributions of austral plants: the roles of Antarctic and direct dispersal routes[END_REF], which has been hypothesized for other vascular spore-bearing plants like ferns [START_REF] Korall | Global biogeography of scaly tree ferns (Cyatheaceae): Evidence for Gondwanan vicariance and limited transoceanic dispersal[END_REF][START_REF] Labiak | Phylogeny and historical biogeography of the lastreopsid ferns (Dryopteridaceae)[END_REF]. Our age estimates are compatible with the hypothesis of an Antarctica connection, with the Phlegmariurus crown node dated to ca. 50 Ma. Antarctica was not an area coded in our biogeographical analysis since no species is currently known from this area, but an equivalent range covering the Neotropics and Eastern Paleotropics was retrieved among the most likely ancestral area at crown node of Phlegmariurus, suggesting an ancestral distribution including Antarctica. The Antarctica connection would have progressively declined by following the global cooling after the Early Eocene climatic optimum and would have been definitively disrupted with the ice-sheet formation ca. 30 Ma (Figure 3). This disruption could have then isolated populations from the Neotropics and the Paleotropics, leading to distinct, geographically structured lineages. However, this hypothesis could not completely explain our results, because Africa were separated from Antarctica between 165-132 Ma and from South America 135-105 Ma [START_REF] Mcloughlin | The breakup history of Gondwana and its impact on pre-Cenozoic floristic provincialism[END_REF].

Fossils proved the presence of vascular spore-bearing plants in Antarctica before icesheets formation [START_REF] Cantrill | Paleocene flora from Seymour Island, Antarctica: revision of Dusén's (1908) angiosperm taxa[END_REF], but no fossils confirm that Phlegmariurus was in Antarctica. Furthermore, Phlegmariurus is the sister lineage to Huperzia, mostly diversified in the Northern Hemisphere, rather suggesting a common history between Southern and Northern lineages.

A northern origin hypothesis via the Boreotropics

A tropical region spanning North America and Eurasia existed during the Cretaceous, at a time when they were geographically closer, facilitating dispersal between the continents that shared numerous taxa within the Boreotropics [START_REF] Wolfe | Some Aspects of Plant Geography of the Northern Hemisphere During the Late Cretaceous and Tertiary[END_REF][START_REF] Morley | Interplate dispersal paths for megathermal angiosperms[END_REF]. The decrease of the global temperature at the Eocene/Oligocene boundary [START_REF] Zachos | Trends, rhythms, and aberrations in global climate 65 Ma to present[END_REF] fragmented the Boreotropical forest belt by forcing the frost-sensitive flora to migrate southward [START_REF] Morley | Interplate dispersal paths for megathermal angiosperms[END_REF]. Several authors explained amphi-Pacific or amphi-Atlantic distributions by the disruptions of the Boreotropics (e.g. [START_REF] Antonelli | Tracing the impact of the Andean uplift on Neotropical plant evolution[END_REF]Hennequin et al., 2010b;[START_REF] Couvreur | Early evolutionary history of the flowering plant family Annonaceae: Steady diversification and boreotropical geodispersal[END_REF][START_REF] Manns | Historical biogeography of the predominantly Neotropical Subfamily Cinchonoideae (Rubiaceae): Into or out of America?[END_REF][START_REF] Liu | Molecular phylogeny of Cissus L. of Vitaceae (the grape family) and evolution of its pantropical intercontinental disjunctions[END_REF][START_REF] Smedmark | Inferring geographic range evolution of a pantropical tribe in the coffee family (Lasiantheae, Rubiaceae) in the face of topological uncertainty[END_REF][START_REF] Wei | Eurasian origin, boreotropical migration and transoceanic dispersal in the pantropical fern genus Diplazium (Athyriaceae)[END_REF], notably explaining disjunction between temperate and tropical regions [START_REF] Weeks | To move or to evolve: contrasting patterns of intercontinental connectivity and climatic niche evolution in "Terebinthaceae" (Anacardiaceae and Burseraceae)[END_REF]. Applied to Phlegmariurus, this hypothesis implies that the ancestor of modern Phlegmariurus was a northern lineage in the Boreotropics. The divergence ca. 50 Ma (HPD: 29.1-71.5) of localized lineages in the Neotropics and the Paleotropics would be explained by southward migrations in less connected continents, facilitating speciation.

Clues about the ancestral ecology of lycophytes could also support the hypothesis of a northern origin of Phlegmariurus. It is likely that lycophytes have a mesic origin as they exhibit physiological features such as passive stomatal control that limit their capacity to ameliorate water loss [START_REF] Brodribb | Passive Origins of Stomatal Control in Vascular Plants[END_REF][START_REF] Mcadam | Fern and Lycophyte Guard Cells Do Not Respond to Endogenous Abscisic Acid[END_REF]. Moreover, an ancestral terrestrial habitat was reconstructed for Lycopodiaceae, with a shift in Phlegmariurus that would have started to diversify as epiphytic [START_REF] Field | Molecular phylogenetics and the morphology of the Lycopodiaceae subfamily Huperzioideae supports three genera: Huperzia, Phlegmariurus and Phylloglossum[END_REF], so Phlegmariurus appears to occupy a relatively xeric biome compared to other living and fossil lycophytes. Diversification linked to epiphytism during Cenozoic was also retrieved in ferns, and is likely correlated with the development of modern tropical forests [START_REF] Schuettpelz | Evidence for a Cenozoic radiation of ferns in an angiosperm-dominated canopy[END_REF] and epiphytism acquisition could be an "enabler" trait mentioned by [START_REF] Donoghue | Biome Shifts and Niche Evolution in Plants[END_REF] to facilitate a biome shift. Phlegmariurus may have originated from northern temperate terrestrial ancestors like its sister group Huperzia, but that the modern species started to diversify as epiphytes in tropical forests.

BIOGEOGRAPHICAL HISTORY OF MALAGASY PHLEGMARIURUS SPECIES

Our sampling greatly improved the number of Malagasy species included in a phylogenetic study on Phlegmariurus, increasing from two [START_REF] Field | Molecular phylogenetics and the morphology of the Lycopodiaceae subfamily Huperzioideae supports three genera: Huperzia, Phlegmariurus and Phylloglossum[END_REF] to 16 species the sampling and so the understanding on the biogeographical history of the group. We estimated at least six LDD from the last 30 Ma to explain the origin of the Malagasy Phlegmariurus, as well as a diversification in Madagascar starting around 10 Ma.

Dispersal in the Southern Hemisphere

Several sources of dispersal to Madagascar were highlighted by our results, all being an area or a combination of areas from the Southern Hemisphere that confirms the biogeographical connections among southern regions (see 3.3.1).

One LDD from Australasia to Madagascar (LDD3) was estimated, and one from Asia and/or Australasia (LDD4), suggesting that spores could have followed westward winds across the Indian Ocean, like those of the Indian monsoon of winter. The initiation of Asian monsoon is subject to controversy but the associated winds would have already been established during the late Miocene [START_REF] Passey | Strengthened East Asian summer monsoons during a period of highlatitude warmth? Isotopic evidence from Mio-Pliocene fossil mammals and soil carbonates from northern China[END_REF][START_REF] Jacques | Quantitative reconstruction of the Late Miocene monsoon climates of southwest China: A case study of the Lincang flora from Yunnan Province[END_REF][START_REF] Gupta | Evolution of the South Asian monsoon wind system since the late Middle Miocene[END_REF], which is compatible with our age estimates.

A precise area of origin for LDD2, 5 and 6 cannot be estimated due to the large distribution of the Malagasy species that make plausible first dispersal events to Africa or other WIO islands before Madagascar. However, LDD5 and LDD6 highlighted connection between Western Paleotropical areas and the Neotropics, retrieved for other vascular sporebearing plants like ferns [START_REF] Rouhan | Molecular phylogeny of the fern genus Elaphoglossum (Elaphoglossaceae) based on chloroplast non-coding DNA sequences: Contributions of species from the Indian Ocean area[END_REF](Rouhan et al., , 2007a;;[START_REF] Janssen | Origin and diversification of African ferns with special emphasis on Polypodiaceae[END_REF][START_REF] Labiak | Phylogeny and historical biogeography of the lastreopsid ferns (Dryopteridaceae)[END_REF][START_REF] Bauret | Madagascar sheds new light on the molecular systematics and biogeography of grammitid ferns: New unexpected lineages and numerous long-distance dispersal events[END_REF] and to a lesser extent for angiosperms (e.g. [START_REF] Buerki | Spatio-temporal history of the endemic genera of Madagascar[END_REF][START_REF] Janssens | Dispersing towards Madagascar: Biogeography and evolution of the Madagascan endemics of the Spermacoceae tribe (Rubiaceae)[END_REF] or bryophytes [START_REF] Scheben | Multiple transoceanic dispersals and geographical structure in the pantropical leafy liverwort Ceratolejeunea (Lejeuneaceae, Porellales)[END_REF]. LDD2 confirms a biogeographical connection between Western Paleotropics and Australasia, previously discussed.

The role of Africa in the biogeographical history of Malagasy Phlegmariurus is ambiguous.

In the Western Paleotropical clade, if the ancestral range estimates showed a diversification starting in Africa, the distribution in the Eastern Paleotropics of the sister lineage to the Malagasy clade adds uncertainties on the area of origin of the Malagasy clade. Africa was however estimated as the second most likely area at the Malagasy stem node, suggesting that Africa could be the area of origin of this Malagasy lineage. Our analysis also relied on a non-exhaustive sampling of the global species diversity. Numerous species from Asia and Australasia remain to be included in a phylogeny and we saw that LDD from these regions to Madagascar area plausible for Phlegmariurus. About LDD2, the distribution of Phlegmariurus tardieuae in all the Western Indian Ocean avoid a clear estimate of the biogeographical origin of the dispersal event to Madagascar, which could be Africa or other WIO islands.

The study of Phlegmariurus brought new evidences about the existence of biogeographical connections between Western Paleotropical regions, in particular Madagascar, and the other continents of the Southern Hemisphere. Phlegmariurus also tends to follow a pattern retrieved in ferns, with an ambiguous role of Africa and other islands of the WIO, but with evidences of trans-oceanic dispersal with other continents. Moreover, studies highlighted the importance of diversification for animals and plants in Madagascar, even for highly dispersive spore-bearing plants like ferns, and the process was also retrieved in lycophytes with Phlegmariurus. Indeed, if multiple LDD could be inferred from our results to explain the Malagasy diversity, diversification is a major process that have generated in a single event at least 11 species out of the 20 estimated in Madagascar (Table 1).

Diversification: a main driver of Malagasy diversity

The diversification of the Malagasy clade is the most localized ever documented for Phlegmariurus and even for Huperzioideae, showing Madagascar as a great catalyst of diversification even for highly dispersive plants. Species in the Malagasy clade showed little molecular divergence in the sequenced markers compared to their broad morphological and ecological heterogeneity (see 2.1.5), which could reflect adaptations to different niches. The Malagasy clade species occupy similar geographic distribution in Madagascar, mostly in the centre region occupied by evergreen forests [START_REF] Ml | Lycopodiacées-Huperziacées[END_REF][START_REF] Rakotondrainibe | Nouveautés dans le Genre Huperzia Bernh. (Lycophytes, Lycopodiaceae) à Madagascar[END_REF], with an exception for P. ambrensis, which is endemic to the Montagne d'Ambre [START_REF] Rakotondrainibe | Nouveautés dans le Genre Huperzia Bernh. (Lycophytes, Lycopodiaceae) à Madagascar[END_REF]. Differences in habitat, growth forms or morphology have been observed after adaptive radiation for angiosperms [START_REF] Givnish | Ecology of plant speciation[END_REF] and for Malagasy animals [START_REF] Wirta | Three parallel radiations of Canthonini dung beetles in Madagascar[END_REF], suggesting that the Malagasy species diversity of Phlegmariurus may have arisen from adaptive radiation. Non-adaptive radiations are rather linked to allopatric speciation and without ecological divergence [START_REF] Rundell | Adaptive radiation, nonadaptive radiation, ecological speciation and nonecological speciation[END_REF].

The diversification in the Malagasy clade also highlighted morphological convergences, with species from similar habitats sharing similar traits, which supports the hypothesis of adaptation in the Malagasy forests. Species with slender filiform-funiform shoots (e.g. P. acerosus, P. verticillatus, P. filiformis, P. pichianus) tend to occur as hanging epiphytes in cloud forest and upper montane rainforest; species with thick bottlebrush shoots comprised of slender spreading leaves like shoots (e.g. P. acutifolius, P. dichotomus, P. lecomteanus, P. squarrosus) tend to occur as mid canopy epiphytes in very wet valley forest; species with broad spreading leaves and markedly biformic shoots (e.g. P. tardieuae, P. phlegmarioides, P. obtusifolius, P. ophioglossoides) are generally canopy epiphytes in midmontane to lowland rainforest, species with thick funiform shoots of adpressed leaves (e.g. P. ambrensis, P. carinatus, P. cavifolius, P. tetrastichus) live in bright light exposed montane habitats and short growing biformic species with lingulate-lanceolate leaves and thick quadrangular or terete fertile species (e.g. P. gnidioides, P. lockyeri, P. megastachyus, P. varius) are commonly facultative epiphytes, epiliths or terrestrials on shallow soils.

Chapter VI -Overview of the biogeographical history of the Malagasy ferns

Madagascar, including nearby islands, is a biodiversity hotspot, comprising 2.3% of all plant species worldwide [START_REF] Myers | Biodiversity hotspots for conservation priorities[END_REF]. It is now widely accepted that Cenozoic dispersal events from Africa have played a great role to explain the presence of living organisms in Madagascar, although dispersal from other further areas and vicariance were also shown [START_REF] Yoder | Has Vicariance or Dispersal Has Vicariance Been the Predominant Force in Biogeographic Madagascar? Only Time Will Tell[END_REF][START_REF] Agnarsson | The generation of a biodiversity hotspot: biogeography and phylogeography of the western Indian Ocean islands[END_REF]. The Malagasy ferns, however, remained poorly studied.

Fern diversity is extremely high in Madagascar with ca. 600 species among which ca. 45% are endemic to the island (Rakotondrainibe, 2003a), and although evolving on a much larger area, the African fern diversity is barely more diversified with ca. 800 species (Introduction-Figure 8). Floristic affinities show that the Malagasy flora is mostly shared with the other islands of the Western Indian Ocean (WIO) and Africa, but also with further regions in the Neotropics and the Eastern Paleotropics (Asia to Australasia and Pacific; see Introduction). The first molecular phylogenetic analyses focused on Madagascar highlighted multiple dispersal from Africa and the Neotropics, as well as important in situ diversifications that could explain the endemism of Malagasy ferns [START_REF] Rouhan | Molecular phylogeny of the fern genus Elaphoglossum (Elaphoglossaceae) based on chloroplast non-coding DNA sequences: Contributions of species from the Indian Ocean area[END_REF](Rouhan et al., , 2007a;;Janssen et al., 2008). Additional molecular phylogenetic studies confirmed a Neotropical and African biogeographical connection with Madagascar but also showed that the Eastern Paleotropics can play a role in the biogeographical history of the Malagasy ferns (e.g. [START_REF] Chao | Molecular phylogeny and biogeography of the fern genus Pteris (Pteridaceae)[END_REF]. The relative importance of these three source pools remain barely known and more data are required to draw a tendency, about the source pools but about the age of colonization as well.

An overview based on the literature and on new data obtained during my thesis will aim at (i) presenting the biogeographical origins of the Malagasy ferns in a spatio-temporal framework, (ii) discussing the factors that could have influenced dispersal, diversification and extinction, and (iii) proposing a summarized scenario of the biogeographical history of the Malagasy ferns.

THREE MAIN SPECIES SOURCE POOLS: AFRICA, THE NEOTROPICS AND THE EASTERN PALEOTROPICS

New analyses more focused on Madagascar, in grammitid ferns, Rumohra, Blechnoideae, Lindsaea, Odontosoria and Phlegmariurus (Figure 1), confirmed that Malagasy lineages of ferns and lycophytes originated from African, Neotropical and Eastern Paleotropical dispersal events. Additionally, another source pool in the Western Indian Ocean was highlighted (grammitid ferns, Figure 1). Information from the studies developed in Chapters I to V and from the literature was summarized in Table 1. Only the studies providing dating and ancestral area estimates were compiled, to compare with relevance the areas of origin and the age of dispersal to Madagascar.

Figure 1. Summary of the results from the Chapters I to V, focused on the dispersal events to Madagascar (arrows) and in situ diversification (+). Each map represents the results of one chapter, with the name of the taxa, followed by numbers: worldwide species diversity/Malagasy species diversity/Malagasy endemic species. The number of dispersal and diversification events inferred are indicated (with the number of species having diversified in Madagascar), together with the detail of the biogeographical sources. On the maps, arrows with dotted lines represent hypothesized (but uncertain) origins and question marks represent unknown areas of origin of Malagasy fern lineages.

NEOTROPICS

The Neotropics were already hypothesized to be an important source of diversity for Madagascar, based on floristic and biogeographical affinities (e.g. [START_REF] Moran | Phytogeographic relationships between neotropical and African-Madagascan pteridophytes[END_REF][START_REF] Rouhan | Molecular phylogeny of the fern genus Elaphoglossum (Elaphoglossaceae) based on chloroplast non-coding DNA sequences: Contributions of species from the Indian Ocean area[END_REF]. Chapter I confirmed the importance of eastward trans-Atlantic dispersal in grammitid ferns, by estimating at least four direct LDD to Madagascar (Figure 1, Table 1). Similar results in two genera belonging to two distinct families, Lomariocycas (Blechnaceae, Chapter III) and Rumohra (Dryopteridaceae, Chapter II, however with uncertainty with Comoros) highlighted that the process was not an exception in the biogeographical history of Malagasy ferns. My results also showed that eastward trans-Atlantic dispersal is a process involved in the biogeographical history of another group of vascular spore-bearing plants, in Phlegmariurus (Lycopodiaceae, Chapter V), but the analysis did not allow to infer whether dispersal occurred directly from the Neotropics to Madagascar, or whether there were intermediate stepping-stones (Malagasy species being widespread in the Western Paleotropics, chapter V). Out of the 40 dispersal events recorded in Table 1 (without uncertainties on the estimates), such trans-Atlantic dispersal were retrieved 16 times in the recorded studies, including five direct dispersal events to Madagascar.

All inferred trans-Atlantic dispersal events would be under the influence of the southern Prevailing Westerly winds (also called West Wind Drift, however the name refers more to the oceanic current), which are circumaustral winds connecting southern continents like South America, Africa-Madagascar and Australia [START_REF] Sanmartín | West Wind Drift revisited: testing for directional dispersal in the Southern Hemisphere using event-based tree fitting[END_REF]. Moreover, modelling of the trajectory of spores from Brazil showed that an arrival in Madagascar via the South Atlantic Ocean is theoretically possible (Meza [START_REF] Torres | Distribution of Ophioglossum reticulatum L. in South America. A case of long-distance jump dispersal?[END_REF] and therefore supports the hypothesis of direct LDD from Neotropics to Madagascar.

EASTERN PALEOTROPICS

Comprising regions from the tropical continental Asia to Australasia and the Pacific, the Eastern Paleotropics cover areas renowned for their tropical biodiversity (Southeast Asia being one of the richest place of fern diversity, Introduction-Figure 8) that would be biogeographically linked to Western Paleotropics, notably Madagascar [START_REF] Warren | Why does the biota of the Madagascar region have such a strong Asiatic flavour?[END_REF][START_REF] Buerki | Spatio-temporal history of the endemic genera of Madagascar[END_REF]. Given the biogeographical affinities between Madagascar and Asia and the important biodiversity, the region was expected to be another important source pool for Madagascar. This was confirmed by data from the literature as well as my results, with 14 dispersal events to the Western Paleotropics, including six direct dispersal events to Madagascar (Tableau 1).

The available data were however too scarce to estimate the relative importance of regions like Southeast Asia, Melanesia or Australasia in the biogeographical history of Malagasy ferns, as they were not similarly coded in the surveyed studies. Some authors were indeed focused on the Eastern Paleotropics like [START_REF] Chao | Molecular phylogeny and biogeography of the fern genus Pteris (Pteridaceae)[END_REF], whereas Hennequin et al. (2010b) worked at a global scale and coded the entire region as only one area. However, continental and tropical Asia [START_REF] Chao | Molecular phylogeny and biogeography of the fern genus Pteris (Pteridaceae)[END_REF] or Australasia (Lindsaeaceae, Chapter III) were inferred as ancestral ranges, suggesting that different inclusive regions of the Eastern Paleotropics could act as species source pools for Madagascar. Dispersal to Madagascar could be explained by direct dispersal thanks to the Asian monsoons that blow from continental Asia to the WIO during winter. [START_REF] Warren | Why does the biota of the Madagascar region have such a strong Asiatic flavour?[END_REF] also suggested that islands could have been stepping stones for Asian dispersers, as well as the drifting Indian subcontinent after its separation from Madagascar 90 Ma [START_REF] Mcloughlin | The breakup history of Gondwana and its impact on pre-Cenozoic floristic provincialism[END_REF].

AFRICA

The Theory of Island Biogeography [START_REF] Macarthur | The theory of island biogeography[END_REF] predicts that the nearest continent would be the main species source pool of an island. For Madagascar, its geographic position in the WIO near Africa suggests that this continent should be the main source pool of dispersal. Floristic and biogeographical affinities were found between the continent and Madagascar in angiosperms and ferns (Introduction; e.g. [START_REF] Buerki | Spatio-temporal history of the endemic genera of Madagascar[END_REF][START_REF] Eiserhardt | Evidence for radiations of cheilanthoid ferns in the greater cape floristic region[END_REF] and some studies found Africa as a source for dispersal to Madagascar (Janssen et al., 2008;[START_REF] Labiak | Phylogeny and historical biogeography of the lastreopsid ferns (Dryopteridaceae)[END_REF][START_REF] Sessa | Into Africa: Molecular phylogenetics and historical biogeography of sub-Saharan African woodferns (Dryopteris)[END_REF]. However, the recorded biogeographical results from the literature and the present thesis showed the Neotropics and the Eastern Paleotropics at least as important as Africa, although these two regions are much farther away: respectively five and six direct dispersal from the Neotropics and the Eastern Paleotropics were inferred to Madagascar, against five from Africa (Table 1). Several studies unfortunately relied on incomplete samplings of the African flora that could bring bias in the ancestral area estimates (e.g. [START_REF] Chao | Molecular phylogeny and biogeography of the fern genus Pteris (Pteridaceae)[END_REF].

Several factors could also explain why Africa was not retrieved as the dominant source region compared to the Neotropics and the Eastern Paleotropics: the relative speciesrichness and size of the species source pools and ecological preferences of ferns for mountainous rainforests.

Species richness and size of the species source pools

The Neotropics, the Eastern Paleotropics (especially Southeast Asia) and Africa represent the most species-rich regions for ferns (Introduction-Figure 8). The Neotropics and Southeast Asia are however four to six times more species-rich than Africa, so they are the most species-rich pools among potential sources. Ferns are dependent on humid environments like rainforests which cover much more surface in the Neotropics and the Eastern Paleotropics than in Africa (Figure 2A). In Africa, rainforests are mostly reduced to an equatorial and subequatorial belt that extends from West Africa into the Congo basin (sensu Corlett & Primack, Figure 2A). The distance between Madagascar and the Neotropics or Southeast Asia could be counterbalanced by the abundance of ferns, the species-richness and the surface that would increase the probability of successful dispersal compared to Africa.

One of the most widely cited causes underlying the lower African species diversity is extinction [START_REF] Couvreur | Odd man out: why are there fewer plant species in African rain forests?[END_REF], and references therein) that occurred during the Cenozoic, due to climatic events. A global cooling after the Early Eocene climatic optimum and the closure of the Tethys Seaway would have resulted in the global decline of rainforests and Africa would have been more impacted than the other continents [START_REF] Pan | The fossil history of palms (Arecaceae) in Africa and new records from the Late Oligocene (28-27 Mya) of north-western Ethiopia[END_REF][START_REF] Morley | Cretaceous and tertiary climate change and the past distribution of megathermal rainforests[END_REF][START_REF] Couvreur | Odd man out: why are there fewer plant species in African rain forests?[END_REF]. A warmer and moister climate provided a time of diversification in Africa during the Early Pliocene, but another climate change during the Late Pliocene (3.6-2.6 Ma) triggered a new decrease of rainforests and species extinctions [START_REF] Morley | Origin and evolution of tropical rain forests[END_REF]. The decrease of tropical rainforests in Africa and extinction of numerous angiosperm lineages could have impacted the African ferns, by decrease and loss of their habitats.

Extinction of African fern lineages could have two consequences: i) less dispersal events to Madagascar, meaning a decrease of the importance of Africa in the biogeographical history of the Malagasy ferns, and ii) biases in biogeographical analyses, in which the African origins cannot be inferred because the parent lineage went extinct. Moreover, studies highlighted that some African fern lineages have originated from Neotropical or Asian ancestors [START_REF] Janssen | Origin and diversification of African ferns with special emphasis on Polypodiaceae[END_REF][START_REF] Labiak | Phylogeny and historical biogeography of the lastreopsid ferns (Dryopteridaceae)[END_REF][START_REF] Sessa | Into Africa: Molecular phylogenetics and historical biogeography of sub-Saharan African woodferns (Dryopteris)[END_REF], which could be erroneously inferred as parent of a Malagasy lineage that has originated from the extinct African lineage, reinforcing the apparent role of other tropical regions.

Ecological preferences

If African rainforests represent a relatively small and poor species source pool to Madagascar compare to the Neotropics and the Eastern Paleotropics, the effective African source pool could be even smaller, due to ecological preferences of ferns for mountainous regions [START_REF] Moran | Diversity, biogeography, and floristics[END_REF][START_REF] Kessler | Elevational diversity patterns as an example for evolutionary and ecological dynamics in ferns and lycophytes[END_REF], especially dealing with Malagasy ferns.

Among all the African regions, Malagasy ferns show the highest floristic affinities with the mountainous regions of East Africa [START_REF] Aldasoro | Diversity and distribution of ferns in sub-Saharan Africa, Madagascar and some islands of the South Atlantic[END_REF][START_REF] Liu | Exploring the pteridophyte flora of the Eastern Afromontane biodiversity hotspot[END_REF]. In ferns, dispersal events recorded in Table 1 from Africa also show connections with these regions: numerous Dryopteris species are distributed in East Africa, notably species found relatively close to the Malagasy endemic Dryopteris subcrenulata [START_REF] Sessa | Into Africa: Molecular phylogenetics and historical biogeography of sub-Saharan African woodferns (Dryopteris)[END_REF], and in Cyathea, the species found sister to the Malagasy lineages are endemic to the eastern African mountains [START_REF] Edwards | Cyatheaceae[END_REF][START_REF] Korall | Global biogeography of scaly tree ferns (Cyatheaceae): Evidence for Gondwanan vicariance and limited transoceanic dispersal[END_REF]. The affinities with these regions could be explained by the ecological disequilibrium of the Malagasy fern flora itself, as 85% of the Malagasy ferns occur in the elevated Central phytogeographic domain that covers mountainous regions (Rakotondrainibe, 2003b).

Moreover, the eastern African mountains represent a relatively small source pool compared to all the African tropical rainforests (Figure 2C) or compared to the mountainous regions in the Neotropics and the Eastern Paleotropics (Figure 2A,B), notably listed in the biodiversity hotspots [START_REF] Myers | Biodiversity hotspots for conservation priorities[END_REF].

THE WESTERN INDIAN OCEAN

A growing body of evidence show that islands are not the sink of biodiversity previously hypothesized, notably for spore-bearing plants [START_REF] Hutsemékers | Oceanic islands are not sinks of biodiversity in spore-producing plants[END_REF]. In the WIO, Madagascar seems to be a major source of species diversity for the other WIO islands, playing the role of a continental source in angiosperms (e.g. [START_REF] Strijk | In and out of Madagascar: Dispersal to peripheral islands, insular speciation and diversification of Indian Ocean daisy trees (Psiadia, Asteraceae)[END_REF] but also in ferns, e.g. in grammitid ferns (Chapter I) and in Ctenitis [START_REF] Hennequin | Global phylogeny and biogeography of the fern genus Ctenitis (Dryopteridaceae), with a focus on the Indian Ocean region[END_REF].

Surprisingly, a dispersal event from the small WIO islands to Madagascar was inferred in grammitid ferns over the last 1.2 Ma (Ceradenia comorensis, Chapter I). Mascarenes, Seychelles and Comoros were coded in a same range that was inferred as the range of origin of this dispersal event, so the island of origin remains unknown, but Ceradenia comorensis is only distributed in Madagascar and Comoros, suggesting a dispersal from this archipelago. Other dispersal from the small WIO island could be expected, especially from La Réunion with which Malagasy ferns show high floristic affinities (Introduction-Figure 9). 1. Dispersal events to a range including Madagascar, recorded from the literature and the present dissertation. The table summarizes a survey in the literature that recorded studies including ancestral areas estimates and dating, it was constructed as followed: 1) each Malagasy lineage that has originated from a dispersal event was recorded in a line of the table, 2) when the dispersal event was already named in the relevant study, the name was kept (e.g. Moranopteris: LDD10), if not, the lineage was named on the basis of the associated clade (e.g. Zygophlebia: Clade III), 3) when the source of the dispersal was clearly inferred to be Africa, the Neotropics or the Eastern Paleotropics, it was recorded in the relevant column, whereas dispersal events from unknown (?) or other sources were recorded in the last column. However, exception was done in case of uncertainties with other Western Paleotropical areas: the dispersal event was recorded in the relevant column and highlighted by an asterisk (e.g. Rumohra: LDD2*, from the Neotropics to Madagascar or Comoros; Phlegmariurus: LDD5*, from the Neotropics to Madagascar and other areas of the Western Paleotropics), 4) the age of dispersal was then recorded on the same line: a unique age stands for a lineage that has diverged into Madagascar (e.g. Phlegmariurus: LDD3), whereas a range of ages stands when the exact age of dispersal is unknown (e.g. Phlegmariurus: LDD2). A minimum age was recorded in case of important uncertainties in the biogeographical history of the Malagasy lineage. Dispersal events were graphically represented in a chronological framework in Figure 3 (except when the source was unknown).

CENOZOIC ORIGINS, WITH INTENSIFICATION OF ARRIVALS SINCE MIOCENE

Regarding all the source pools and events recorded in Table 1 and Figure 3, direct dispersal to Madagascar would have occurred over the last ca. 65 Ma to nowadays, highlighting the Cenozoic age of the Malagasy ferns. These relatively young ages compared to the old origin of ferns could be explained by the youth of the studied lineages themselves, combined to geologic or climatic events.

Indeed, a first observation is the relative young age of divergence of the genera recorded in Table 1, the older having diverged ca. 90 Ma (Nephrolepis, Hennequin et al., 2010b) and all of them having started their diversification in the last ca. 65 Ma (Figure 3). Moreover, most of these genera started to diversify in the Neotropics, tropical Asia or Africa, leading to a delay before a dispersal to Madagascar occurred, but this delay could also be explained by other limiting factors: the Cenozoic age of the Malagasy rainforest, the onset of some wind currents and the history of the biogeographical sources.

A CENOZOIC MALAGASY FOREST

It was only after the northward migration of India that humid winds from the Indian Ocean could have reached the eastern coast of Madagascar, allowing the onset of rainforests ca. 60 Ma. A real establishment of those rainforests would have started after a reinforcement of rainfalls ca. 35 Ma [START_REF] Wells | Geology and Soils[END_REF]. The Cenozoic age of the Malagasy rainforests could explain the Cenozoic age of the Malagasy fern flora, as the presence of rainforests (and so the presence of humid environments) in Madagascar is an important prerequisite to fern colonization. However, on the basis of the current data available on the Malagasy fern lineages (Figure 3), it seems that most of them have colonized Madagascar more recently. Out of the 15 direct LDD to Madagascar recorded, at least 11 would have occurred in the last ca. 10 Ma. This tendency was also retrieved for LDD events to Western Paleotropical ranges including Madagascar, with at least 17 out of 23 dispersal events being recorded for the last ca. 10 Ma.

MID-CENOZOIC WIND CURRENTS

The circumaustral wind current explaining eastward dispersal events (e.g. from the Neotropics to Madagascar) is considered to have started at the Eocene-Oligocene boundary ca. 35-30 Ma ago [START_REF] Sanmartín | West Wind Drift revisited: testing for directional dispersal in the Southern Hemisphere using event-based tree fitting[END_REF]. However, the onset of this circulation does not seem to coincide with most of the dispersal events from the Neotropics to Madagascar, which would be more recent (Figure 3). Indeed, despite their Neotropical origin that predates the establishment of a circumaustral circulation, the grammitid ferns, Lomariocycas (Blechnaceae) and Rumohra (Dryopteridaceae) colonized Madagascar only over the last 10 Ma, suggesting that other factors were limiting.

Considering tropical Asia, however, dispersal events to Western Paleotropics fully coincide with the onset of the Indian monsoons during mid-Miocene [START_REF] Jacques | Quantitative reconstruction of the Late Miocene monsoon climates of southwest China: A case study of the Lincang flora from Yunnan Province[END_REF][START_REF] Gupta | Evolution of the South Asian monsoon wind system since the late Middle Miocene[END_REF] and only the LDD recorded for Odontosoria is even much older (ca. 64-25 Ma). This latter could be explained by extinct wind currents generated by the past geologic and climatic configuration or/and by stepping stone dispersal by Indian during its Northward drifting in the Indian Ocean [START_REF] Warren | Why does the biota of the Madagascar region have such a strong Asiatic flavour?[END_REF].

BIOGEOGRAPHICAL HISTORY OF THE SOURCE POOLS: IMPORTANT DIVERSIFICATIONS STARTING DURING THE NEOGENE DUE TO GEOLOGICAL EVENTS

Understanding the biogeographical history of Malagasy ferns requires to know the history of the biogeographical sources. We saw that extinctions in Africa could have decreased the importance of the continent in the biogeographical history of the Malagasy ferns, but other events could also explain the sudden importance of the Neotropics and the Eastern Paleotropics starting from 10 Ma and even why dispersal from Africa occurred so recently.

When some prerequired elements to fern colonization to Madagascar were established, like the Malagasy rainforest and the circumaustral wind circulation (ca. 35-30 Ma;[START_REF] Wells | Geology and Soils[END_REF], the biogeographical source pools in their modern form did not yet exist, preventing numerous dispersal and colonization of Madagascar. Especially, the tropical mountains that provide rich place of species diversity sharing the same ecological preferences as the extant Malagasy ferns mostly appeared over the last 10 Ma.

In South America, many modern plants and animals have started their diversification with the Andes orogenesis during the Miocene [START_REF] Hoorn | Amazonia Through Time: Andean Uplift, Climate Change, Landscape Evolution, and Biodiversity[END_REF], like ferns in Polystichum [START_REF] Mchenry | Phylogeny and biogeography of exindusiate Andean Polystichum (Dryopteridaceae)[END_REF]. Diversification in grammitid ferns genera and Lomariocycas (Chapter I,III) also coincide with the orogenesis, as the first mountains appeared by the late Oligocene to early Miocene (ca. 23 Ma) with an intensification of the phenomenon during the late middle Miocene (ca. 12 Ma) and early Pliocene (ca. 4.5 Ma, Hoorn et al., 2010).

At the end of the Oligocene (ca. 25 Ma), the orogenesis of Southeast Asian mountains started, due to the collision of the Australian plate with the Pacific plate [START_REF] Hall | Southeast Asia's changing palaeogeography[END_REF]. However, numerous lands emerged later, with for example Sumatra, Java, Sulawesi and the Moluccas emerging since 5 Ma. Another example is the elevation of New Guinea that began only ca. 10 Ma, the present height being reached only ca. 5 Ma [START_REF] Hall | Southeast Asia's changing palaeogeography[END_REF]. The collision and the resultant uplifts have also impacted the regional climate, by holding the moisture from the warm Pacific Ocean. This, in turn, allowed the establishment of rainforests and an increase in diversity during the Miocene in the region [START_REF] Morley | A review of the Cenozoic palaeoclimate history of Southeast Asia[END_REF]. Diversification that predate dispersal to Madagascar notably coincide with these geological events in Lindsaea, grammitid ferns and Phlegmariurus.

Similarly, the mountains of East Africa are relatively young. Firstly, Eastern Arc Mountains blocks have been reactivated by the development of the East African Rift System the last seven million years to form the modern mountains found in Tanzania [START_REF] Griffiths | The geological evolution of East Africa[END_REF]. Secondly, numerous volcanoes of the region would have originated over the last eight million years [START_REF] Dawson | Neogene tectonics and volcanicity in the North Tanzania sector of the Gregory Rift Valley: contrasts with the Kenya sector[END_REF][START_REF] Griffiths | The geological evolution of East Africa[END_REF]. The highest summit of Africa, the Mount Kilimanjaro, notably appeared between 2.5 and 1.9 Ma [START_REF] Nonnotte | New K-Ar age determinations of Kilimanjaro volcano in the North Tanzanian diverging rift, East Africa[END_REF]. Here again, the emergence of mountains has attracted orographic precipitation and led to the formation of rainforests during the mid-Miocene, which coincides with the ages of tropicmontane and tropic-alpine angiosperms [START_REF] Linder | The evolution of African plant diversity[END_REF] and with dispersal events of ferns to Madagascar (Figure 3).

MADAGASCAR: AN IMPORTANT ROLE OF IN SITU DIVERSIFICATION

The number of endemic species, as well as the results recorded from the literature and the present thesis (Table 2) highlighted that in situ diversification have played a great role in the origin of Malagasy ferns, in addition to LDD. Madagascar is an island renowned for the diversification of its flora, thanks to the richness of bioclimates and ecosystems [START_REF] Yoder | Has Vicariance or Dispersal Has Vicariance Been the Predominant Force in Biogeographic Madagascar? Only Time Will Tell[END_REF]. Especially, the eastern mountains would have played a crucial role for the diversification of Malagasy ferns, as tropical mountains are known to be great places of diversification for these plants [START_REF] Kessler | Elevational diversity patterns as an example for evolutionary and ecological dynamics in ferns and lycophytes[END_REF].

Diversification of ferns in Madagascar is poorly understood and only one study focused on this issue. Based on the observation that tree ferns shared similar bioclimatic niches, Janssen et al. (2008) hypothesized that the impressive radiations of these ferns were influenced by climatic oscillations that have led to habitat fragmentation as well as shifts in altitudinal gradients. Grammitid genera, Lomaridium and Lomariocycas, are genera for which the colonization and the diversification in Madagascar were not followed by obvious change in their ecological preferences and in their morphology. Bioclimatic niche analyses would bring more evidences to understand if they could have diversified by following the same process as tree ferns, or if another process of diversification could be highlighted. Lindsaea and Phlegmariurus both showed signs of adaptive speciation, by the acquired epiphytism in Lindsaea species (especially with host specificity, Chapter IV) and by morphological convergences linked to ecological preferences in Phlegmariurus (Chapter V). These observations would suggest that diversification of ferns in Madagascar may have been under the influence of different factors and processes.

SCENARIO OF THE BIOGEOGRAPHICAL HISTORY OF THE MALAGASY FERNS: AN

ATTEMPT

Based on the current knowledge of the tectonic and climatic history of Madagascar and its species source pools, as well on the results from the present thesis and the literature, a biogeographical history is here proposed (Figure 4A-G). However, this scenario should be tested by more biogeographical analyses on Malagasy ferns.

A-Lower Cretaceous (145-100 Ma)

The break-up of Gondwana has already started, the Indo-Madagascar subcontinent forms an independent land from Africa and vicariance events could have occurred consequently to the separation from Africa [START_REF] Mcloughlin | The breakup history of Gondwana and its impact on pre-Cenozoic floristic provincialism[END_REF]. A connection with Antarctica could have persisted until the end of Cretaceous [START_REF] Yoder | Has Vicariance or Dispersal Has Vicariance Been the Predominant Force in Biogeographic Madagascar? Only Time Will Tell[END_REF], despite being contested [START_REF] Ali | Late Cretaceous bioconnections between Indo-Madagascar and Antarctica: refutation of the Gunnerus Ridge causeway hypothesis[END_REF]. Madagascar would be under the influence of a temperate climate [START_REF] Wells | Geology and Soils[END_REF] but some regions colonized by ferns would be warm, probably tropical and seasonally humid [START_REF] Appert | Die fossile Makroflora der Unterkreide (Hauterivian) von Manja in Südwest-Madagasckar. Farne und Schachtelhalme (Filicatae und Equisetatae)[END_REF].

B-Upper Cretaceous (100-66 Ma)

India and Madagascar separated ca. 90 Ma, but India still blocked the humidity from Indian Ocean and so prevented the establishment of a rainforest during this period in Madagascar. Moreover, the northern part of the island entered a subtropical arid zone due to its northward migration [START_REF] Wells | Geology and Soils[END_REF], leading to plausible extinction in Malagasy ferns.

The separation with India could have led to vicariant events. However, if Madagascar was under the influence of an arid climate at this time, few species would have been impacted by the separation of Madagascar from India, maybe drought-tolerant species that survived the climate change or species having found refuges. The plausible connection between Madagascar and Antarctica definitively ended [START_REF] Yoder | Has Vicariance or Dispersal Has Vicariance Been the Predominant Force in Biogeographic Madagascar? Only Time Will Tell[END_REF]. Starting from this point, vicariance linked to tectonic events is therefore not possible anymore.

C-Paleocene (66-56 Ma)

The gradual passage of Madagascar through an arid belt probably led to extinctions more to the South of the island and would explain the subsequent dominance of Cenozoic colonization and diversification in the biogeographical history of the Malagasy flora [START_REF] Wells | Geology and Soils[END_REF]. The subarid climate was progressively reduced to the extreme South of Madagascar.

Northward migration of India progressively exposed Madagascar to the humid winds from Indian Ocean, leading to rainfalls on the eastern coasts. The increasing humidity could have allowed the establishment of a humid or sub-humid climate and dispersal from Africa and the drifting India could have consequently occurred, as well as stepping stone dispersal from tropical Asia via India (e.g. Odontosoria?, Figure3). Species that would have survived the dry period in refuges during Upper Cretaceous could have started their spread on the island. However, the rainfalls could be not enough important to allow a real establishment of rainforests [START_REF] Wells | Geology and Soils[END_REF], so dispersal events probably remained scarce.

On a global scale, catastrophic events combining a meteor impact and intense volcanic activities ca. 65 Ma led to a major biological crisis and ecological changes (e.g. [START_REF] Vellekoop | Ecological response to collapse of the biological pump following the mass extinction at the Cretaceous-Paleogene boundary[END_REF]. These events could have deeply impacted the flora of Madagascar [START_REF] Agnarsson | The generation of a biodiversity hotspot: biogeography and phylogeography of the western Indian Ocean islands[END_REF].

D-Eocene (ca. 56-34 Ma)

Volcanism at Tsaratanana and Manongarivo was reported, forming new massifs in the Northern Madagascar [START_REF] Wells | Geology and Soils[END_REF], maybe leading to diversification of ferns in Madagascar. However, the tropical rainforests were probably not yet fully established [START_REF] Wells | Geology and Soils[END_REF], limiting the effect of these volcanoes on fern diversification.

India's rifting ended with its collision with Asia. Dispersal events from Indian seem unlikely as no event was reported (Figure 3) and as no wind current is known between India and Madagascar at this period.

Dispersal between Africa and Madagascar could have occurred, maybe reinforced from Africa during early and middle Eocene thanks to a globally warm temperature coinciding with rainforest expansion [START_REF] Couvreur | Odd man out: why are there fewer plant species in African rain forests?[END_REF]and references therein).

E-Oligocene (34-23 Ma)

The circumaustral wind circulation started ca. 30-35 Ma thanks to the opening of Drake Passage between South America and Antarctica [START_REF] Sanmartín | West Wind Drift revisited: testing for directional dispersal in the Southern Hemisphere using event-based tree fitting[END_REF], allowing the first dispersal events from the Neotropics to Madagascar (e.g. maybe in Phlegmariurus, Figure 3). It would also have reinforced the South Indian Ocean gyre and so the rainfalls on Eastern Malagasy coasts [START_REF] Wells | Geology and Soils[END_REF]. The Malagasy bioclimatic zones have probably reached their current areas, with a humid zone covering all the Eastern part of the island, including fully established tropical rainforests.

The establishment of rainforests would have resulted in intensification of fern colonisation in Madagascar, notably from African dispersal events, and diversification. However, the Eocene/Oligocene abrupt decrease of temperature resulted in the decline of rainforests and in extinctions in Africa [START_REF] Couvreur | Odd man out: why are there fewer plant species in African rain forests?[END_REF], reducing the dispersal potential from the continent.

Ankaratra volcanism began [START_REF] Wells | Geology and Soils[END_REF], leading to a new high peak in Madagascar with an altitude reaching more than 2600 meters (current height) and so to a new plausible place of fern diversification. PALEOMAP project, Scotese (2001). Each time frame was commented in the text. Malagasy mountains and volcanoes formation were not represented for the sake of clarity, but were mentioned in the text.

F-Miocene (23-5 Ma)

This period would be characterized by an intensification of dispersal to Madagascar, thanks to the formation of species-rich source pools combined to wind circulation.

Firstly, the establishment of Indian monsoons in the middle Miocene has allowed wind-driven dispersal events from Asia and Southeast Asia [START_REF] Jacques | Quantitative reconstruction of the Late Miocene monsoon climates of southwest China: A case study of the Lincang flora from Yunnan Province[END_REF][START_REF] Gupta | Evolution of the South Asian monsoon wind system since the late Middle Miocene[END_REF]. The northward migration of the Australian plate and its collision with the Pacific one have generated multiple volcanoes and the orogenesis of mountains, retaining humid winds from the Pacific [START_REF] Hall | Southeast Asia's changing palaeogeography[END_REF][START_REF] Morley | A review of the Cenozoic palaeoclimate history of Southeast Asia[END_REF]. A rapid uplift of the Tibetan plateau also occurred ca. 15-20 Ma but did not lead to the current high altitudes [START_REF] Royden | The Geological Evolution of the Tibetan Plateau[END_REF]. These events would have provided high elevated rainforests and ferns diversification in the source regions [START_REF] Wang | The rise of the Himalaya enforced the diversification of SE Asian ferns by altering the monsoon regimes[END_REF], and so species-rich source pools connected to Madagascar. Dispersal to the Western Paleotropics, especially to Madagascar, are documented (Figure 3).

Secondly, in the Neotropics, the Andes orogenesis provided mountain peaks [START_REF] Hoorn | Amazonia Through Time: Andean Uplift, Climate Change, Landscape Evolution, and Biodiversity[END_REF] and would be linked to the diversification of ferns [START_REF] Mchenry | Phylogeny and biogeography of exindusiate Andean Polystichum (Dryopteridaceae)[END_REF]. Dispersal events from this newly formed species-rich source pool occurred, especially for mountainous species, via circumaustral circulation (e.g. grammitid ferns, Chapter I).

The formation of volcanoes in East Africa the last ca. 8 Ma [START_REF] Dawson | Neogene tectonics and volcanicity in the North Tanzania sector of the Gregory Rift Valley: contrasts with the Kenya sector[END_REF][START_REF] Nonnotte | New K-Ar age determinations of Kilimanjaro volcano in the North Tanzanian diverging rift, East Africa[END_REF] have provided a new source pool of mountainous species for Madagascar, as it was highlighted by dispersal from this region to Madagascar, e.g. in tree ferns and Dryopteris (Figure 3).

In Madagascar, modern fern species have started their diversification (e.g. Lindsaea, Chapter IV), forming another species-rich source pool in the Southern Hemisphere. Dispersal to other regions would have started to Africa, newly formed archipelagos (Comoros from ca. 8 Ma and Mascarenes from ca. 10 Ma), French Southern and Antarctic Lands, and even the Neotropics (grammitid ferns, Chapter I). Thanks to summer monsoons, dispersal from Madagascar to tropical Asia should be expected either.

G-Pliocene to present (5-0 Ma)

Similar dispersal route and place of diversification are hypothesized during the Pliocene and the Pleistocene, however they were intensified in Asia and in the Neotropics due to last uplifts [START_REF] Li | A discussion on the period, amplitude and type of the uplift of the Qinghai-Xizang Tibetan Plateau[END_REF][START_REF] Zhou | A preliminary study on timing of the oldest Pleistocene glaciation in Qinghai-Tibetan Plateau[END_REF][START_REF] Hall | Southeast Asia's changing palaeogeography[END_REF][START_REF] Hoorn | Amazonia Through Time: Andean Uplift, Climate Change, Landscape Evolution, and Biodiversity[END_REF].

In Africa, a period of diversification was followed by a dry and cold climate leading to another extinction event [START_REF] Couvreur | Odd man out: why are there fewer plant species in African rain forests?[END_REF], which could have importantly decreased/blurred the importance of the African source pool for Madagascar. A part of the modern African diversity would be explained by dispersal from Madagascar, especially in Eastern Africa.

Human establishment in Madagascar has led to a drastic decrease of the rainforests, almost 40% of forest cover has been lost from the 1950s to ca. 2000 and 9.1% of species were estimated to have been committed to extinction due to deforestation [START_REF] Allnutt | A method for quantifying biodiversity loss and its application to a 50-year record of deforestation across Madagascar[END_REF].

Conclusion

The study of the biogeographical history Malagasy ferns supports the idea that despite the old isolation of Madagascar, the island was colonized recently mostly by dispersal post-dating the geologic isolation of the island. Reviews highlighted that dispersal events mostly originated from African ancestors in animals and angiosperms, the Neotropics and the Eastern Paleotropics playing a minor role in the biogeographical history of these Malagasy taxa. In ferns and lycophytes, the results from the present thesis and the literature so far rejected this tendency and showed equal roles of these source regions. Moreover, dispersal events were especially inferred from the Miocene (< 23 Ma).

Ferns and lycophytes are spore-bearing plants, renowned for their vagility by winddrifted dispersal. However, these plants are also dependent on humid environments (with rare exceptions). In Madagascar, ferns and lycophytes are mostly retrieved in elevated rainforests. These characteristics have probably influenced the biogeographical history of the Malagasy ferns. Indeed, all the dispersal events recorded coincide with or post-date the establishment of the Malagasy rainforests and wind-currents between Madagascar and its source regions. Dispersal events from Miocene would be linked to orogenesis shaping the source regions and leading to high elevated rainforests, where ferns with ecological preferences similar to the Malagasy species would have diversified.

The hypothesis of links between the establishment of ferns and lycophytes in Madagascar and the establishment of high elevated rainforests in source regions should be further tested. The biogeographical analyses should expand to more fern and lycophyte taxa, to observe if the ecological preference for high elevated rainforests whether or not has been mostly preserved from ancestors or acquired in Madagascar. This hypothesis would be supported if the ecological preferences for elevated rainforests have also driven the biogeographical history of other taxa, like angiosperms. A comparison with other taxa could also help to answer other questions, on the importance of the dispersal abilities for example. Do we observe the same biogeographical histories between highly-dispersive organisms, such as bryophytes, mushrooms, angiosperms with small seeds, lycophytes and ferns?

The present thesis also highlighted that diversifications in situ have generated numerous species in the studied taxa, with means of ca. 2 to 11 species generated by colonization event. Diversification of ferns in Madagascar is poorly understood and only one study focused on the issue so far. Some results have revealed patterns of diversification that should be studied, notably via bioclimatic niche analysis, to understand the factors and the processes underlying Malagasy in situ diversification.

Résumé long en français

La biodiversité est inégalement répartie à la surface de la planète : sur les 369,000 espèces de plantes aujourd'hui recensées, environ la moitié serait présente sur 2,3% de la surface terrestre dans des points chauds de diversité. Ces points chauds sont des écosystèmes menacés par les activités anthropiques et hébergeant une importante biodiversité endémique. Comment peut-on expliquer une telle concentration de biodiversité ? Quels sont les mécanismes évolutifs sous-jacents ?

Les îles ont joué un rôle crucial dans la compréhension des écosystèmes, des espèces et de leur évolution. Elles sont souvent comparées à des laboratoires naturels, fournissant des milieux plus simples à étudier par leur isolement. Madagascar est une île continentale au large de l'Afrique, dans l'Océan Indien, avec les autres îles de l'ouest de l'Océan Indien (OOI), elle est classée parmi les 35 points chauds de biodiversité.

Figure 1 .

 1 Figure 1. Map of the Western Indian Ocean islands and Eastern Africa. Areas resulting from the break-up of the paleo-continent Gondwana are illustrated in blue and oceanic islands in red, associated with their age of origin.

Figure 2 .

 2 Figure 2. A. Topographic map of Madagascar (source: Wikipédia). B. Bioclimates by[START_REF] Cornet | Essai de cartographie bioclimatique à Madagascar[END_REF], map modified from www.mobot.org/mobot/research/madagascar/gazetteer/. C. Phytogeographic domains from[START_REF] White | The vegetation of Africa[END_REF]. Pie charts represent in dark green the percent of the total diversity of pteridophytes found in the different domains, fromRakotondrainibe (2003a).

Figure 3 .

 3 Figure 3. A-D: Spatio-temporal history of the continents. Paleomaps modified from PALEOMAP project, Scotese (2001). E. Modern positions of the continents (source: Wikimedia), with age of Gondwana breakups between modern lands from McLoughlin (2001). Madagascar is indicated in red.

Figure 4 .

 4 Figure 4. Summary tracheophyte phylogeny modified from PPGI (2016), number of genera and species estimated by family. Families of the taxa studied in this thesis are highlighted by red boxes. Letters A to L, next to taxon names, refer to illustrations in Figure 5.

Figure 5 .

 5 Figure 5. Lycophytes and ferns diversity. A. Phlegmariurus pecten, B. Isoëtes engelmannii, C. Selaginella sp., D. Didymoglossum cuspidatum, E. Equisetum sp., F. Lygodium lanceolatum., G. Marsilea quadrifolia, H. Asplenium nidus, I. Monogramma graminea, J. Cyatheaceae, K. Elaphoglossum spatulatum, L. Platycerium sp. (Photos: L.Bauret : A, C, D, F-I, J, L ; Wikipedia Commons: B, E, J).

Figure 7 .

 7 Figure 7. Stages of spore shooting by a sporangium. (Modified from T. Moore's drawings).

Figure 8 .

 8 Figure 8. Ferns and lycophytes diversity in the world. Redrawn from Moran (2008).

Figure 9 .

 9 Figure 9. Distribution of the Malagasy ferns, lycophytes and angiosperms. Distribution of A. Malagasy ferns, based on a data retrieval of 579 accepted species from the Catalogue of the Plants of Madagascar (26 th June, 2017), B. Malagasy lycophytes, based on a data retrieval of 48 accepted species from the Catalogue of the Plants of Madagascar (26 th June, 2017), C. Malagasy angiosperms (10,319 spp.), modified from Callmander (2011), D. non-endemic Malagasy ferns shared only with the WIO islands (63 spp.), based on the same data retrieval as B., E. non-endemic Malagasy angiosperms shared only with the WIO islands (285 spp.), modified from Callmander (2011).

Figure 1 .

 1 Figure 1. Morphology and habit of the 11 genera distributed in Madagascar: (A) Alansmia elastica (Rouhan et al. 1138); (B) Ceradenia deltodon (Rouhan et al. 1350); (C) Ctenopterella zenkeri (Rouhan et al. 1347); (D) Enterosora sprucei (Rouhan et al. 1227); (E) Grammitis copelandii (Rouhan et al. 1190); (F) Leucotrichum madagascariense (Rakotondrainibe 6957); (G) Moranopteris sp. 1 (Bauret et al. 107); (H) Stenogrammitis hildebrandtii (Rouhan et al. 1375); (I) Melpomene flabelliformis (Bauret et al. 105); (J) Zygophlebia goodmanii (Rouhan et al. 1382); (K) Cochlidum serrulatum (Bauret et al. 7). Photos: G. Rouhan; except G, I, K: L. Bauret.

Figure 2 -

 2 Figure 2 -Majority rule consensus phylogram of grammitids recovered from the BI based on the combined dataset(atpB, rbcL, trnG-trnR, trnL-trnF and rps4-trnS), and figured as a summary phylogeny (infrageneric branches are shown in Appendix 1.2). Generic lineages are represented by triangles (whose heights are proportional to the numbers of samples included), with names of genera preceded by colored squares figuring their geographic distribution (see map) and followed by (number of species analyzed / number of samples included). Non-monophyletic genera are indicated in bold and their names are followed by symbols to show the distinct lineages of a given genus. The three grey-filled triangles are the three newly evidenced clades, and circled numbers (1 to 3) correspond to clades detailed in Figure3. Unless mentioned next to the nodes, support values were BS≥95 and PP≥0.95.

Figure 1 .

 1 Figure 1. Morphology of Rumohra spp. (A) R. adiantiformis lamina, Rouhan et al. 1148, Madagascar. (B) R. adiantiformis sori, left: young sori with indusia, right: mature sori with indusia either shrivelled or fallen, Bauret et al. 83, Madagascar. (C) R. adiantiformis rhizome, Bauret et al. 83, Madagascar. (D) R. linearisquamata rhizome, Rouhan et al. 1395, Madagascar. (E) R. lokohensis rhizome, Rouhan et al. 1167, Madagascar. (F) R. berteroana indument, left: rhizome scales, right: petiole scales, Gay s.n., Juan Fernández, Chile. (G) R. adiantiformis petiole scales, which are identical to those of the rhizome, Rouhan et al. 1148, Madagascar. (H) R. glandulosissima lamina glands: glandular hairs indicated by arrows, one shiny dot-like gland circled, Glaziou 11696, Brazil. (I) R. linearisquamata rhizome and petiole scales, Rakotondrainibe et al. 4068, Madagascar. (J) R. adiantiformis rhizome meristele, Bauret et al. 83, Madagascar. Photographs: L. Bauret, except A, D, E: G. Rouhan.

  stem nodes were modelled by normal prior distributions with means of 116.7 Mya (based on Sundue & Testo, 2016) or 67.0 Mya (based on Schuettpelz & Pryer, 2009; node284) for lastreopsids, and 52.5 Mya (based on Testo & Sundue, 2016) or 40.5 Mya (based on Schuettpelz & Pryer, 2009; node 288) for Rumohra. Standard deviations were set to 10% of the mean estimates.

Figure 2 .

 2 Figure 2. Majority rule consensus tree for the genus Rumohra estimated by Bayesian inference on the combined plastid DNA dataset (cladogram on the left, phylogram on the right), with support values from the Bayesian inference and maximum likelihood method. Unless mentioned next to the nodes, support values are posterior probabilities (PP) ≥ 0.95 and bootstraps (BS) ≥ 95 (also highlighted by thick branches). A dash (-) indicates BS < 50 or a non-retrieved node. The samples of R. adiantiformis are highlighted by asterisks and the geographical lineages including specimens of R. adiantiformis are numbered and bordered with a dashed line on the insert map. Colours represent the areas coded in the biogeographical analysis: Neotropics (dark green); southern South America (light green); southern Africa (purple); Comoros (olive); Madagascar (red); Mascarenes and Seychelles (orange); southern Indian Ocean islands (blue); and Australasia (yellow). Top left corner: distribution map of the genus Rumohra. Colours represent the areas coded in the biogeographical analysis, while asterisks indicate R. adiantiformis sample localities and dashed lines and numbers correspond to the lineages of R. adiantiformis. Scale bar is for branch lengths of the phylogram (substitutions/site).

Figure 3 .

 3 Figure 3. Chronogram resulting from the BEAST analysis for the genus Rumohra, and ancestral areas estimated byBioGeoBEARS (DEC+j model) and biogeographical stochastic mapping (BSM). Horizontal blue bars correspond to 95% HPD intervals of the median ages. Coloured pies represent the ancestral areas estimated at nodes, with the following colour code: Neotropics (dark green); southern South America (light green); southern Africa (purple); Comoros (olive); Madagascar (red); Mascarenes and Seychelles (orange); southern Indian Ocean islands (blue); and Australasia (yellow). The area covering Madagascar, Mascarenes and Seychelles appears in dark red. For the stem and crown nodes of the genus and for the crown node of clade B, coloured squares around pie charts depict the most likely ancestral areas as inferred through the BSM realizations considering a Neotropical origin of Rumohra. White arrows on branches indicate the seven long-distance dispersal (LDD) events inferred in the biogeographical history of the genus. Top left corner: distribution map of the genus Rumohra. Colours represent the areas coded in the biogeographical analysis and asterisks indicate R. adiantiformis sample localities.

  Figure 5): to southern South America 11.2 Mya (LDD1); to Comoros or Madagascar 9.8 Mya (LDD2); and to southern Africa 9.4 Mya (LDD3). Later on, additional dispersal events must also have occurred: from south-ern South America to Australasia 5.3 Mya (LDD4); from the Comoros to Madagascar or from Madagascar to the Comoros 2.1 Mya (LDD5); from southern Africa to southern Indian Ocean islands 0.3 Mya (LDD6); and from Madagascar to Mascarenes/Seychelles (< 0.3 Mya; LDD7).

Figure 4 .

 4 Figure 4. Comparison of median ages (in My) obtained for the main nodes of the phylogenetic tree for Rumohra based oncalibration points taken from Testo & Sundue (2016; in white) and Schuettpelz & Pryer (2009; in black). Error bars represent the 95% HPD intervals. WIO, western Indian Ocean area.

Figure 5 .

 5 Figure 5. Circum-austral map showing the seven long-distance dispersal (LDD) events inferred in the biogeographical history of the genus Rumohra. Area colours and LDD numbers are the same as in Figures 2 and 3. For LDD4 and LDD5, dotted lines indicate alternative directions of dispersal.

Figure 1 .

 1 Figure 1. Diversity of Blechnoideae in Madagascar. (A) Blechnum australe, Rouhan et al. 1416: (B) Lomaridium xiphophyllum, no voucher; (C) Austroblechnum bakeri, Rouhan et al. 1625; (D) Lomaridium simillimum, Rouhan et al. 1370; (E) Lomaridium attenuatum, no voucher; (F) Lomariocycas longepetiolata, Bauret et al. 101; (G) Lomariocycas longipinna, Rouhan et al. 1585; (H) Blechnum punctulatum, Rouhan et al. 1405. Photos: G. Rouhan (A, D, H), L. Bauret (B, C, E-G).

Figure 2 .

 2 Figure 2. Majority rule consensus tree of Blechnaceae estimated by Bayesian inference on the combined chloroplast DNA dataset, with support values from the Bayesian inference and Maximum likelihood methods. Unless mentioned next to the nodes, support values were posterior probabilities (PP) ≥ 0.95 and bootstraps (BS) ≥ 95. A dash (-) stands for BS < 50 or a non-retrieved node. Blechnoideae Malagasy species are in bold. Black dots stand for genera crown nodes (at tip when the genus is monotypic). White squares are placed at the subfamily crown nodes, and a black square for the family crown node.

Four

  diversifications were estimated to have started in ranges including Madagascar, the Neotropics and other Paleotropical regions at nodes b, d (or e) and l. A diversification in Blechnum would have started in a range covering Madagascar and the Neotropics at node g (or h) and in Lomariocycas in a range covering the Neotropics, Africa and the WIO at node j. Diversification estimated in Madagascar alone were only found at Lomariocyas madagascariensis and L. longepetiolata-Bauret 101 stem nodes (Figure3B). DIVA analysis (not selected based on AIC) however retrieved Madagascar as the only area of diversification for two clades nesting Western Paleotropical species in Lomaridium (L. attenuatum-Rouhan1283-L. simillimum-Rouhan1370) and Lomariocycas (node j).

Figure 3 .

 3 Figure 3. A. Simplified chronogram resulting from the BEAST analysis on Blechnoideae and ancestral areas estimated by BioGeoBEARS (DEC model). Dot-lined squares indicate genera for which details are available in Figure 3B. Number of sampled species per genera is shown between square brackets at tips (size of the triangle proportional to the number of sampled species). Horizontal blue bars correspond to 95% HPD intervals of the median ages. Colored squares at tips represent the current distributions of the genera, with the following color code: (A) Madagascar (red); (B) Mascarenes-Comoros-Seychelles (orange); (C) Africa (purple); (D) Neotropics (green); (E) Asia (yellow); (F) Australasia (light blue); (G) North America and Europe (grey) and (H) southern temperate circumaustral regions (dark blue). For wide ranges (covering several coded areas), their composition is detailed by colored squares next to the corresponding pie section. For the sake of clarity, only the distribution of the most likely ranges were depicted, but details are available in Table4. Green arrows on branches indicate range expansions from Australasia to the Neotropics and white arrows show range expansions from/to wide ranges, not allowing clear inferences about the biogeographical history of the Malagasy lineages (see text). The stratigraphy follows the 2017 International Chronostratigraphic Chart, the global temperature and tectonic events were mapped following[START_REF] Zachos | Trends, rhythms, and aberrations in global climate 65 Ma to present[END_REF]: (I) Early Eocene Climatic Optimum, (II) Tasmania-Antarctic passage opens, (III) Drake passage opens. The vertical grey bar corresponds to the disconnection between South America and Australasia via Antarctica. B. Detailed chronograms and ancestral areas estimated for the five Malagasy lineages of Blechnoideae.

Figure 1 .

 1 Figure 1. Diversity of Lindsaea and Odontosoria species in Madagascar. (A) Lindsaea blotiana, Rouhan 1199; (B) Lindsaea marojejyensis sp. nov. ined., Rouhan 1191; (C) Lindsaea goudotiana, Rouhan 1156; (D) Odontosoria chinensis, Rouhan 1152; (E) Odontosoria melleri, Rouhan 1359, plus detail of a pinna. Photos: G. Rouhan.

Figure 3 .

 3 Figure 3.Chronogram resulting from the BEAST analysis on Lindsaea and Odontosoria, and ancestral areas estimated by BioGeoBEARS (DEC model). Horizontal blue bars correspond to 95% HPD intervals of the median ages. Doted branches indicate not-supported relationships (PP<50). Colored squares at tips represent the current distribution, with the following color code: (A) Madagascar (red), (B) Mascarenes-Comoros-Seychelles (orange), (C) Africa (purple), (D) Neotropics (green), (E) Asia-Southeast Asia (yellow), and (F) Australasia-Oceania (light blue, referred in the text as Australasia). For wide ranges (covering several coded areas), their composition is detailed by colored squares next to the corresponding pie section. For the sake of clarity, only the distribution of the most likely ranges were depicted, but details about nodes probabilities are available in Table4. Red arrows on branches indicate hypothesized dispersal events to Madagascar. The map represents the areas coded in the biogeographical analysis. The stratigraphy follows the 2017 International Chronostratigraphic Chart, the global temperature and tectonic events were mapped following[START_REF] Zachos | Trends, rhythms, and aberrations in global climate 65 Ma to present[END_REF], with (A) Tasmania-Antarctic passage opens and (B) Drake passage opens.

Figure 1 .

 1 Figure 1. A-F: habitat diversity of Phlegmariurus in Madagascar, (A) Phlegmariurus gnidioides; (B) Phlegmariurus lecomteanus; (C) Phlegmariurus megastachyus; (D) Phlegmariurus obtusifolius; (E) Phlegmariurus obtusifolius, (F) Phegmariurus ophioglossoides; G-I: diversity of microphyll shapes: (G) in Phlegmariurus obtusifolius, (H) Phlegmariurus lecomteanus and (I) Phlegmariurus pecten. Photos: G. Rouhan (D, E, F), L. Bauret (A-C, G-I).

Figure 2 .

 2 Figure 2. (A) Simplified tree of Lycopodiaceae, based on[START_REF] Field | Molecular phylogenetics and the morphology of the Lycopodiaceae subfamily Huperzioideae supports three genera: Huperzia, Phlegmariurus and Phylloglossum[END_REF]. (B) Majority rule consensus tree of Phlegmariurus estimated by Bayesian inference on the combined cpDNA dataset(rbcL, trnH-psbA, trnL/trnL-trnF), with support values from the Bayesian inference and Maximum likelihood methods at each node (BS/PP). A dash (-) stands for BS < 50 or a non-retrieved node. A color code indicates the region of sampling: green for the Neotropics, red for the Western Paleotropics, blue for the Eastern Paleotropics and black for other regions (temperate North Hemisphere or wide distribution covering several regions).

Figure 3 .

 3 Figure 3. Chronogram resulting from the BEAST analysis for Huperzioideae and ancestral areas estimated by BioGeoBEARS (DEC+j model). Horizontal blue bars correspond to 95% HPD intervals of the median ages.Next to terminals, colored squares depict biogeographical distribution considering eight areas: temperate Northern Hemisphere (grey), circumpolar (dark blue), Neotropics (green), continental and tropical Africa (violet), Madagascar (red), Mascarenes-Comoros-Seychelles islands (orange), tropical Asia (yellow), Australasia-Oceania (light-blue). Colored pies represent the ancestral areas estimated at nodes. When present next to pie charts, colored squares represent the combination of areas covered by a range. These combinations do not necessarily represent the most likely ancestral range estimated at a node. A reduced topology represents the entire BEAST chronogram, simplified in Huperzioideae, with black squares depicting the four fossil calibration points. The stratigraphy follows the 2017 International Chronostratigraphic Chart, the global temperature and the climatic events were mapped following[START_REF] Zachos | Trends, rhythms, and aberrations in global climate 65 Ma to present[END_REF].

Figure 2 .

 2 Figure 2. Tropical rainforests and mountains of the world, with a focus on Africa. A. Delimitation of tropical rainforests according to different authors, from Eiserhardt, Couvreur, & Baker (2017). Olson et al's definition often referred to tropical rainforest sensu lato, and includes non-tree rainforest vegetation like the Malagasy high plateau. TRF = tree rainforest. B. Topographic map, the relative altitude being coded by colors: green being the lowest altitudes, dark brown and grey the highest. (Source: pixabay.com). C. Mountainous rainforests of East Africa, around Lake Victoria, left: topographic map following the same color scheme as B, right: satellite view from Google Maps (19 th September, 2017), the rainforests being visible by dark green patches around the peaks and in Congo basin, 1: Mount Stanley (5109 m), 2: Mount Karisimbi (4507 m), 3: Mount Elgon (4321 m), 4: Mount Kenya (5199 m) and 5: Mount Kilimanjaro (5895 m).

Figure 3 .

 3 Figure3. Ages of dispersal events to Madagascar, as recorded in Table1from the literature and the present thesis, in relation to the area of origin and climatic and geologic events (at the bottom). One line represents one dispersal event to Madagascar. An asterisk stands for a LDD event to a range including Madagascar and at least another Western Paleotropical area, or when Western Paleotropical areas were found with similar probabilities as Madagascar. On the same line, a grey dot represents the age of divergence of the whole genus and a grey cross its age of diversification (ages of divergence older than 75 Ma were not represented). Climatic and geologic events references were given in the text (see part 2.3). Stratigraphy follows the International Chronostratigraphic Chart v.2017.02 and global temperature was redrawn from[START_REF] Zachos | Trends, rhythms, and aberrations in global climate 65 Ma to present[END_REF].

Figure 4 .

 4 Figure 4. Hypotheses on the biogeographical history of Malagasy ferns, paleomaps modified from PALEOMAP project,[START_REF] Scotese | Paleogeography, PALEOMAP Project[END_REF]. Each time frame was commented in the text. Malagasy mountains and volcanoes formation were not represented for the sake of clarity, but were mentioned in the text.

  ).

	Polystichum Dryopteridaceae	Unknown	< 20 Ma	No	Le Péchon et al. (2016)
	Deparia Athyriaceae	Unknown	< ca. 10 Ma Yes	Kuo et al. (2016)
	Ctenitis Dryopteridaceae	Neotropics and/or La Réunion	< ca. 10 Ma Yes	Hennequin et al. (2017)
	Dryopteris Dryopteridaceae	Africa unknown	< ca. 5 Ma	No	Sessa et al. (2017)
	Pyrrosia Polypodiaceae	Unknown	-	No	Zhou et al. (2017)
	Abrodictyum Hymenophyllaceae	Asia s.l.	-	Yes	Dubuisson et al. (in Press)
	Trichomanes Hymenophyllaceae	Unknown	-	Yes	Dubuisson et al. (in Press)

Table 1 .

 1 Area of origin and age (when available) of Malagasy fern lineages recorded from studies including Malagasy endemics (in chronological order of publication). A in situ diversification was recorded when at least two Malagasy endemics were retrieved sister species.

Table 2 .

 2 Worlwide and Malagasy diversity of the studied taxa and worldwide phylogeny of reference.

References: 1 Perrie & Parris (2012), 2 Rakotondrainibe (2010b), Sundue, Hirai, & Prado (2013), 3 de Gasper et al. (2016b), 4 Lehtonen et al. (2010), 5 PPGI, (2016).

  This work is published in Molecular Phylogenetic and Evolution:Bauret L, Gaudeul M, Sundue MA, Parris BS, Ranker TA, Rakotondrainibe F, Hennequin S, Ranaivo J, Selosse MA, Rouhan G. 2017. Madagascar sheds new light on the molecular systematics and biogeography of grammitid ferns: New unexpected lineages and numerous long-distance dispersal events. Molecular Phylogenetics and Evolution 111: 1-17.

Table 1 .

 1 Grammitid

		Worldwide	Number of	Number	Comments (at the
		estimated	species	of species	worldwide scale)
		diversity	recorded in the	recorded
		(number	WIO region	in Africa
		of species)	[and in
			Madagascar
			only]
	Alansmia	26	1 [1]	1
	Ceradenia	73	5 [2]	2
	Cochlidium	18	1 [1]	1
	Ctenopterella	24	3 [3]	2	monophyly never tested
	Enterosora	11	2 [2]	2	monophyletic but nested in
					Zygophlebia
	Grammitis	26	12 [10]	7	polyphyletic, and Grammitis
					s.s.	paraphyletic	with
					respect to Cochlidium
	Leucotrichum 6	1 [1]	0
	Melpomene	29	1 [1]	1
	*Moranopteris 30	0	0	monophyly to be tested
					given the newly discovered
					species in Madagascar
	Stenogrammitis 31	3 [3]	7
	Zygophlebia	20	7 [7]	3	paraphyletic with respect
					to Enterosora

genera occurring in the Western Indian Ocean (WIO, incl. Madagascar) and Africa, based on

[START_REF] Roux | Synopsis of the Lycopodiophyta and Pteridophyta of Africa, Madagascar and neighbouring islands[END_REF]

updated with more recent genera recognized, and corrected for distributions of some species. *Only known from the Neotropics to date, but a new species was recently discovered in Madagascar.

Table 2 .

 2 PCR primers sequences and thermal cycling conditions; primers used as internal primers for sequencing only are marked with an asterisk (*)

Table 3 .

 3 Statistics on the five separate plastid DNA regions and the combined datasetFigure 3 -Detailed phylograms of clades 1 to 3. Unless mentioned next to the nodes, support values were BS≥95 and PP≥0.95, thick branches indicate BS≥95 and PP≥0.95. Polyphyletic species are indicated in color. Vouchers are indicated when several samples of the same species were sequenced, and localities specified are discussed in the text.

3.2. DIVERGENCE TIME AND ANCESTRAL AREAS ESTIMATIONS 3.2.1. Divergence time estimation

	Molecular dating showed that grammitid ferns diverged from other Polypodiaceae about
	39.3 Ma (stem age; 95% Highest Posterior Density (HPD) interval: 31.2-50.6) and started
	to diversify at least 34.1 Ma (crown age; 95% HPD: 28.3-40.2) at the end of the Eocene
	(Figure

Table 4 .

 4 Taxonomic issues at the species level for African and WIO grammitid fern taxa, raised by the molecular phylogenetic results; taxonomic novelties accommodating these results are suggested whenever possible. Non-monophyletic species are indicated in color (same colors as in Figure

Table 1 .

 1 Distribution of the seven Rumohra spp.

		Western
		Indian Ocean	America	Australasia	Other
		-Africa
	R. adiantiformis	Madagascar, Mascarenes, Comoros, Seychelles, Southern Africa	Neotropics, Galapagos*, Southern South America, Falkland Islands, West Indies	Australia, Papua Guinea, New New Zealand (type locality)	Tristan Cunha, South da Indian Ocean Islands, Bermuda*
	R. berteroana	-	Juan Fernández Islands	-	-
			Neotropics	-
	R. glandulosissima -	(Brazilian Atlantic		-
			Rainforest)
	R. linearisquamata Madagascar	-	-	-
	R. lokohensis	Madagascar	-	-	-
	R. madagascarica Madagascar	-	-	-
			Neotropics	-
	R. quadrangularis -	(Brazilian Atlantic		-
			Rainforest)

*Unsampled localities for the widely distributed R. adiantiformis.

Table 2 .

 2 PCR primers sequences and thermal cycling conditions.

	DNA region	Primer name	Literature reference	Primer sequence (5' to 3')	Thermal cycling conditions
	atpA	ESTRNR46F	Schuettpelz, Korall, & Pryer (2006)	GTA TAG GTT CRA RTC CTA TTG GAC G	5 min 94°C / 40 × (30 s 94°C / 1
		ESATPA535F	Schuettpelz, Korall, & Pryer (2006)	ACA GCA GTA GCT ACA GAT AC	min 50°C / 2 min 72°C) / 10 min
					72°C
		ESATPA856F*	Schuettpelz, Korall, & Pryer (2006)	CGA GAA GCA TAT CCG GGA GAT G
		ESATPA877R*	Schuettpelz, Korall, & Pryer (2006)	CAT CTC CCG GAT ATG CTT CTC G
	atpB	ESATPB172F	Schuettpelz & Pryer (2007)	AAT GTT ACT TGT GAA GTW CAA CAA T	5 min 94°C / 40 × (30 s 94°C / 1
		ESATPE45R	Schuettpelz & Pryer (2007)	ATT CCA AAC WAT TCG ATT WGG AG	min 50°C / 2 min 72°C) / 10 min
					72°C
		atpB 1163F*	Wolf (1997)	ATG GCA GAA TRT TTC CGA GAT RTY A
		ATPB910R*	Pryer et al. (2004)	TTC CTG YAR AGA NCC CAT TTC TGT
	rbcL	ESRBCL1F	Schuettpelz & Pryer (2007)	ATG TCA CCA CAA ACG GAG ACT AAA GC	5 min 94°C / 40 × (30 s 94°C / 45 s
		ESRBCL1361R	Schuettpelz & Pryer (2007)	TCA GGA CTC CAC TTA CTA GCT TCA CG	50°C / 2.5 min 72°C) / 10 min 72°C
		ESRBCL628F*	Schuettpelz & Pryer (2007)	CCA TTY ATG CGT TGG AGA GAT CG
		ESRBCL654R*	Schuettpelz & Pryer (2007)	GAA RCG ATC TCT CCA ACG CAT
	atpB-rbcL	atpB 672F	Wolf (1997)	ACA CTW AGA GGR GCT CCC GTA TCA A

Table 3 .

 3 (3) South Africa; and (4) South Africa and Amsterdam Island, the two latter subclades including only R. adiantiformis samples. Clade B (BS = 100; PP = 1) encompassed a southern South American subclade (with R. adiantiformis and R. berteroana samples) and an Australasian subclade (with R. adiantiformis samples only; both subclades with BS = 100; PP = 1). Statistics on the eight plastid DNA regions and combined dataset obtained for Rumohra.

		Number of sequences	Aligned length (in base pairs)	Percent of variable characters	Percent of informative characters
	atpA	33	948	1.8	1.7
	atpB	36	1275	1.9	1.6
	atpB-rbcL	36	629	3.5	3.2
	rbcL	47	1308	18.8	10.9
	rps4-trnS	47	548	40.5	26.8
	trnG-trnR	41	961	27.3	17.8
	trnH-psbA	36	437	3.4	3.2
	trnL/trnL-trnF	46	820	20.7	12.1
	Combined dataset 58	6926	14.1	9.1

was divided into two supported clades. In clade A (BS = 90; PP = 1), four strongly sup-ported geographical subclades (forming a polytomy) grouped samples from: (1) the western Indian Ocean [WIO, including R. adiantiformis, R. linearisquamata Rakotondr., R. lokohensis Tardieu and R. madagascarica (Bonap.) Tardieu]; (2) the Neotropics [R. quadrangularis (Fée) Brade, R. glandulosissima Sundue & J.Prado and R. adiantiformis];

  . Applying the latest classification of Blechnoideae, the 15 Malagasy species belong to five genera: Austroblechnum Gasper & V.A.O.Dittrich, Blechnum L., Lomaridium C.Presl, Lomariocycas (J.Sm.) Gasper & A.R. Sm. and Parablechnum C.Presl. (Table1). Only five out of the 15 Malagasy species were included in the study ofde Gasper et al. (2016a): Lomaridium biforme, Blechnum punctulatum, Blechnum australe, Lomariocycas tabularis and Parablechnum marginatum, so the genus assignations of the other ten species remain to be tested by molecular data.

Lomariocycas longipinna (Rakotondr.) Gasper & A.R.Sm.

  Gasper et al. (2016a) with additional specimens; 2) to test the monophyly of Malagasy species; 3) to estimate the age of Malagasy lineages, and 4) to infer the biogeographical origins of the Malagasy lineages in the global framework of the Blechnoideae biogeographical history.

	Species	Distribution	Notes
	Austroblechnum bakeri		Combination in
	(C.Chr.) Gasper &	WIO, Africa	Cranfillia? (see
	V.A.O.Dittrich		Results)
	Austroblechnum integrifrons		Combination in
	(Bonap. ex Rakotondr.) Gasper	Endemic to Madagascar	Lomaridium? (see
	& V.A.O.Dittrich		Results)
	Blechnum australe L.	WIO, Neotropics, Tristan da Cunha archipelago
	Blechnum punctulatum Sw.	WIO, Africa
	Lomaria inflexa Kunze	Endemic to Africa
	Lomaridium attenuatum (Sw.)	WIO (excluding Madagascar),
	Gasper & V.A.O.Dittrich	Africa
	Lomaridium biforme (Baker) Gasper & V.A.O.Dittrich	Endemic to Madagascar
	Lomaridium bonapartei
	(Rakotondr.) Gasper &	Endemic to Madagascar
	V.A.O.Dittrich*
	Lomaridium simillimum		Combination
	(Baker) Gasper &	WIO	confirmed by this
	V.A.O.Dittrich		study
	Lomaridium xiphophyllum		Combination
	(Baker) Gasper &	Endemic to Madagascar	confirmed by this
	V.A.O.Dittrich		study
	Lomariocycas decrescens (Rakotondr.) Gasper & A.R.Sm.	Endemic to Madagascar
	Lomariocycas longepetiolata (Tardieu) Gasper & A.R.Sm.	Endemic to Madagascar	Combination confirmed by this study
			Combination
		Endemic to Madagascar	confirmed by this
			study
	Lomariocycas		Combination
	madagascariensis (Tardieu)	Endemic to Madagascar	confirmed by this
	Gasper & A.R.Sm.		study
	Lomariocycas tabularis (Thunb.) Gasper & A.R.Sm.	WIO, Africa, Neotropics
	Parablechnum capense (Burm.f.) Gasper & Salino	Africa (records from Asia or the Pacific region refer most probably to P. vestitum)
			Combination of the
	Parablechnum marginatum (Kuhn) Gasper & Salino	WIO	Malagasy variety confirmed by this
			study

Table 1 .

 1 Blechnoideae

species occurring in tropical Africa and Western Indian Ocean (including Madagascar), distribution based on

[START_REF] Roux | Synopsis of the Lycopodiophyta and Pteridophyta of Africa, Madagascar and neighbouring islands[END_REF]

and

[START_REF] Rakotondrainibe | Révision synoptique du genre Blechnum L. (Blechnaceae) à Madagascar[END_REF]

and taxonomic notes on the basis of my results. Sampled species are in bold.

Table 2 .

 2 Matrix statistics.At species level, the results showed that the Blechnoideae species from Madagascar were nested in five genera: Blechnum, Cranfillia, Lomaridium, Lomariocycas and Parablechnum, but none of them belong to Austroblechnum s.s. (Austroblechnum andinum-Austroblechnum doodioides clade; Figure

		of sequences (on the total number of samples)	Aligned length (base pairs)	Percent of variable characters	Percent of informative characters
	rbcL	194 (96%)	1252	29.6	23.5
	rps4	177 (88%)	570	45.4	31.4
	rps4-trnS	175 (87%)	542	62.0	48.3
	trnL/trnL-trnF	176 (87%)	1129	55.4	42.6
	Combined dataset 202 (100%)	3493	45.5	34.8

Table 3 .

 3 Biogeographical models tested, with log-likelihoods and AIC values, and the p-value of the LRT between nested models. Models selected for estimating the biogeographical history are in bold.

		LnL	AIC	LRT p-value
	DEC DEC+J	-278.8 -278.7	561.6 563.4	0.69
	DIVALIKE DIVALIKE+J	-305.4 -305	614.8 616.1	0.40
	BAYAREALIKE BAYAREALIKE+J	-357.5 -319	719 643.9	1.6e-18

afra (K.U. Kramer) J.P.Roux Endemic to Africa Odontosoria africana F.Ballard Endemic to Africa Odontosoria chinensis (L) J.Sm. WIO

  , 2) to estimate the age of the Malagasy lineages, and 3) to infer the biogeographical history of the Malagasy species of Lindsaea and Odontosoria.

	Species	Distribution	Synonymy to test
	Lindsaea blotiana K.U.Kramer	Endemic to Madagascar
	Lindsaea decaryana (C.Chr.)	Endemic to Madagascar
	Tardieu
	Lindsaea ensifolia Sw.	WIO, Southeast Asia,
		Australasia-Oceania
	Lindsaea flabellifolia (Baker)	Endemic to Madagascar	= L. millefolia syn. nov.
	Kuhn		(Rakotondrainibe,
			com. pers.)
	Lindsaea goudotiana (Kunze)	Endemic to Madagascar	= L. subtilis syn. nov.
	Mett. ex Kuhn		(Rakotondrainibe,
			com. pers.)
	Lindsaea grandiareolata	Endemic to Madagascar
	(Bonap.) K.U.Kramer
	Lindsaea heterophylla Dryand. WIO, Southeast Asia
	Lindsaea humbertii Tardieu	Endemic to Madagascar
	Lindsaea leptophylla Baker	Endemic to Madagascar	= L. coursii syn. nov.
			(Rakotondrainibe,
			com. pers.)
	Lindsaea madagascariensis	Endemic to Madagascar
	Baker
	Lindsaea marojejyensis	Endemic to Madagascar
	Rakotondr. sp. nov. ined.
	Lindsaea odontolabia (Baker)	Endemic to Madagascar
	K.U.Kramer
	Lindsaea oxyphylla Baker	Endemic to Madagascar
	Lindsaea plicata Baker	Endemic to Madagascar
	Odontosoria , Africa, Southeast
		Asia, Australasia-Oceania

Odontosoria melleri (Flook. ex Baker) C.Chr.

Table 2 .

 2 were transposed on Figure 2, to facilitate comparison with their retrieved topology. Matrix statisticsThe two Malagasy species of Odontosoria were retrieved in two clades (Figure2A), with O. chinensis sister-group to the Asian-Australasian O. biflora (BS=100; PP=1), and O. melleri sister-group to the Asian clade formed by O. angustifolia and O. deltoidea, however with weak support (BS=62; PP=0.81). Within Lindsaea, the Malagasy species were nested in two clades: in clade II, with the endemic L. plicata sister-group to a clade Majority rule consensus tree of Lindsaea and Odontosoria estimated by Bayesian inference on the combined chloroplast DNA dataset, with support values from the Bayesian inference and Maximum likelihood methods. Unless mentioned next to the nodes, support values were posterior probabilities (PP) ≥ 0.95 and bootstraps (BS) ≥ 95. A dash (-) stands for BS < 50 or a non-retrieved node. The Malagasy species are in bold and Malagasy species retrieved polyphyletic are colored (but not all the nonmonophyletic species).

		Number	of
	DNA region	sequences (on the total number of	Aligned length (base pairs)	Percent of variable characters	Percent informative characters	of
		sequences)
	rpoC1	117 (66%)		732	28.8	21.6
	rps4	90 (51%)		577	43.8	26.5
	rps4-trnS	89 (50%)		502	37.1	25.5
	trnH-psbA	166 (93%)		674	45.3	28.2
	trnL/trnL-trnF	175 (98%)		829	51.5	40.4
	Combined dataset 178 (100%)		3314	41.7	29.1

PP=1), and sister-group to the L. flabellifolia-L. blotiana clade (BS=1; PP=1). Lindsaea leptophylla, L. madagascariensis and L. marojejyensis specimens were all included in the same clade but with low support (BS=60; PP=0.81) and the three species were not monophyletic. A similar result was observed in the clade nesting L. heterophylla, L. grandiareolata and L. oxyphylla (BS<50; PP=0.79). Lindsaea heterophylla was polyphyletic, with a sample forming a clade with L. grandiareolata and L. oxyphylla (BS<50; PP=0.88) and another sample forming a clade with two L. ensifolia samples (BS=60; PP=0.99). The polyphyly of L. heterophylla was however poorly or not supported in ML (BS≤60). Figure 2.

Table 1 .

 1 African and Western Indian Ocean Huperzioideae considered in this study, their distribution and systematic notes. Species sampled are in bold, with an asterisk for the sampled localities in our molecular study.

	Continental Africa	Notes

Table 2 .

 2 PCR primers sequences and thermal cycling conditions; primers only used as internal primers for sequencing are marked with an asterisk (*)

Table 3 .

 3 Calibrated nodes for the dating analysis with BEAST

	Node calibrated	Uniform prior values (Ma)	Fossils	Stratigraphic occurrence age (Ma)
	Tree height	382.7-410.8	Earliest lycophytes fossils	Lower Devonian, Pragian, 407.6-410.8
	Isoetes-Selaginella divergence	382.7-410.8	Yuguangia ordinata Hao et al. (2007)	Middle Devonian, Givetian, 382.7-387.7
	Selaginella crown node	330.9-410.8	Selaginella resimus Rowe (1988)	Carboniferous, Visean, 330.9-346.7
	Lycopodielloideae-Lycopodioideae divergence	190.8-410.8	Retitriletes spp. Bomfleur et al. (2014)	Lower Jurassic, Sinemurian, 190.8-199.3

  Philippines and Indonesian islands West of Lydekker's line); Melanesia-Australasia-Oceania (later referred as Australasia). Each sample was coded following the distribution of the species (except for geographic polyphyletic lineages of Phlegmariurus squarrosus), based on type citations, herbarium occurrences observed in the herbaria AAU, B, BHCB, BONN, BR, BRI, CANB, CNS, HO, JCT, KLU, P, PR, PRC, QRS, SING, TUD and US (herbarium codes following The Index Herbarium, Thiers) as well as flora and personal observations (A

	): a
	large and mostly temperate Northern hemisphere area, including North America, Iceland,
	Europe, Macaronesian Islands and temperate Asia (up to 25°N); a temperate to boreal
	circumpolar area above 40°S, including Southern South America, Tristan da Cunha

archipelago, French Southern and Antarctic Lands (Crozet, Kerguelen, Amsterdam) and Macquarie Island; the Neotropics (30°N to 40°S); continental and tropical Africa; Madagascar; Mascarenes, Comoros and Seychelles archipelagos; tropical Asia, including the continental part (up to 25°N), plus Sri Lanka, Taiwan and Southeast Asia (Malaysia,

Table 4 .

 4 Statistics on the three separate plastid DNA regions and the combined dataset.

	Percent of variable characters	Percent of informative characters

  1 Ma (95% Highest Posterior Density (HPD): 390.7-410.8), and to have started to diversify during the Permian at 273.6 Ma (HPD: 213.6-344.2) when Huperzioideae diverged from a lineage including Lycopodielloideae and Lycopodioideae. Phylloglossum would have diverged from Phlegmariurus-Huperzia 102.6 Ma (HPD: 59.8-160.3) in the Lower Cretaceous, when Phlegmariurus would be estimated to diverge from Huperzia during the Upper Cretaceous 79.1 Ma (HPD: 46.2-122; Figure

  Table

		Neotropics Neotropics Neotropics	Age Age Age	Eastern Paleotropics Eastern Paleotropics Eastern Paleotropics	Age Age Age	Africa Africa Africa	Age Age Age	Other Other Other	Age Age Age
	Athyriaceae Moranopteris	LDD12	10.7-0.6	P. catoptera -P.	ca. 5.0
	Deparia Chapter I			sp2 clade				n.a. (?)	≤ 6.7
	Kuo et al. (2016) Stenogrammitis	LDD10	15.1-14.6	P. friesii*	ca. 8.0
	Blechnaceae Pteris Chapter I			P. pteridioides*	≤ ca. 8.0			LDD11 (?)	≤2.4
	Lomaridium Chao et al. (2014) Zygophlebia Chapter I Chapter III Cranfillia Chapter III Blechnum Chapter III Lomariocycas Parablechnum Alsophila Janssen et al. (2008) Cyathea Janssen et al. (2008) Ctenitis Hennequin et al. (2017) Dryopteris Chapter I Cochlidium Chapter I Ceradenia Chapter I Alansmia Dryopteridaceae Polypodiaceae Korall & Pryer (2014) Hennequin et al. (2010b) Nephrolepis Korall & Pryer (2014) Nephrolepidaceae Chapter IV Cyatheaceae Odontosoria Chapter III Chapter IV Lindsaea Chapter III Rumohra Chapter II Lindsaeaceae Chapter V Phlegmariurus Lycopodiaceae	Clade III* C. cirrhosa -LDD2* (?) LDD7* C. sieberiana clade* LDD6* LDD6* LDD4 LDD2* LDD5*	12.9-6.7 10.3-0.0 12.2-7.4 10.4-6.1 5.9-0.0 38.5-12.3 9.6 25.3-5.7 9.8	P. vittata* N. cordifolia* N. abrupta* N. acutifolia* N. biserrata* O2 L2 LDD4 LDD3	ca. 13.0-0.0 ca. 2.0-0.0 ca. 22-0.0 ca. 3.0-0.0 ca. 5.0-0.0 64.4-25.0 9.9-8.6 19.8-4.4 1.0	D. subcrenulata D. comorensis* D. manniana* C. andohahelensis clade A. acutula clade A. lastii clade LDD2*	ca. 5.0-0.0 ca. 5.0-0.0 ca. 5.0 ca. 10 ca. 5.0 ca. 8.0 2.0-0.0	LDD1 (?) P. biaurita (?) LDD2 (?) LDD3 (?) Blechnum australe (polyphyly) Ceradenia comorensis (WIO) O1 ( ?) LDD5 (?) L1 ( ?) P. cretica (?) B2 ( ?) P. tripartita (?) LDD1 (?)	50.9-19.7 ca. 1.0-0.0 ≤ 34.0 n.a. 1.2-0.0 64.4-36.5 29.0-12.1 45.8-35.8 ≤ 35.8 ca. 1.0-0.0 ca. 7 ca. 3-0.0 29.6-19.1
	Sessa et al. (2017) Enterosora	LDD1*	3.7-0.0					D. pentheri (polyphyly)	n.a.
	Chapter I							D. squamiseta (?)	≤ ca. 5.0
	Grammitis s.s.	LDD3	3.7-3.0					D. antarctica (polyphyly)	n.a.
	Chapter I	LDD4*	19.1-10.2			P. barterianum -	ca. 23.0-7.0
	Parapolystichum Genus nov.			LDD13	23.7-23.5	P. vogelii clade
	Labiak et al. (2014) (inc. Ctenopterella and					(Lastreopsis s.l.)
	Grammitis species)
	Chapter I			P. ammifolium -	≤ 20.0
	Polystichum Leucotrichum	LDD5	8.0-5.1	P. maevaranense	(precise age
	Le Péchon et al. (2016) Chapter I			clade*	not shown)
	Melpomene	LDD9*	1.7-0.0
	Chapter I

  Table1from the literature and the present thesis, in relation to the area of origin and climatic and geologic events (at the bottom). One line represents one dispersal event to Madagascar. An asterisk stands for a LDD event to a range including Madagascar and at least another Western Paleotropical area, or when Western Paleotropical areas were found with similar probabilities as Madagascar. On the same line, a grey dot represents the age of divergence of the whole genus and a grey cross its age of diversification (ages of divergence older than 75 Ma were not represented).

	Climatic and geologic events references were given in the text (see part 2.3). Stratigraphy follows the
	International Chronostratigraphic Chart v.2017.02 and global temperature was redrawn from Zachos (2001).

Table 2 .

 2 Number of dispersal events to Madagascar and mean number of Malagasy species per event recorded in ferns and lycophytes, from the present thesis and in studies coding Madagascar as a single area.

  Herbarium vouchers and GenBank accession numbers (Blechnoideae).Herbarium vouchers and GenBank accession numbers (Lindsaeaceae).Herbarium vouchers and GenBank accession numbers (Phlegmariurus).Phlegmariurus gnidioides (L. fil.) A.R.Field & Bostock Comoros Rouhan et al. 749 (P) to submit to submit to submit Phlegmariurus gnidioides (L. fil.) A.R.Field & Bostock Madagascar Janssen 2454 (P) to submit to submit to submit Phlegmariurus gnidioides (L. fil.) A.R.Field & Bostock Madagascar Janssen 2917 (P) to submit to submit to submit Phlegmariurus gnidioides (L. fil.) A.R.Phlegmariurus ophioglossoides (Lam.) A.R. Field & Bostock Comoros Pignal 3352 (P) to submit to submit to submit Phlegmariurus ophioglossoides (Lam.) A.R. Field & Bostock Madagascar Rakotondrainibe 6955 (P) to submit to submit to submit Phlegmariurus ophioglossoides (Lam.) A.R. Field & Bostock Madagascar Rasolohery 130 (P) to submit to submit to submit Phlegmariurus ophioglossoides (Lam.) A.R. Field & Bostock Madagascar Janssen 2898 (P) to submit to submit to submit Phlegmariurus ophioglossoides (Lam.) A.R. Field & Bostock Madagascar Rouhan et al. 1244 (P) to submit to submit to submit Phlegmariurus ophioglossoides (Lam.) A.R. Field & Bostock Madagascar Rouhan et al. 1400 (P) to submit to submit to submit Phlegmariurus ophioglossoides (Lam.) A.R. Field & Bostock Tanzania Phlegmariurus parksii (Copel.) A.R.Field & Bostock Vanuatu Rouhan et al. 606 (P) to submit to submit to submit Phlegmariurus pecten (Bak.) A.R.Field & Bostock Madagascar Rakotondrainibe 6329 (P) to submit to submit to submit Phlegmariurus pecten (Bak.) A.R.Field & Bostock Madagascar Janssen 2470 (P) to submit to submit to submit Phlegmariurus pecten (Bak.) A.R.Phlegmariurus staudtii (Nessel) A.R.Field & Bostock Gabon Hallé 835 (P) to submit to submit to submit Phlegmariurus strictus (Baker) A.R.Field & Bostock Madagascar Bauret et al. 175 (P) to submit to submit to submit Phlegmariurus strictus (Baker) A.R.Phlegmariurus tardieuae (Herter) A.R.Field & Testo Comoros Rouhan et al. 892 (P) to to submit to submit Phlegmariurus tardieuae (Herter) A.R.Field & Testo Madagascar Janssen 2435 (P) to submit to submit to submit Phlegmariurus tardieuae (Herter) A.R.Field & Testo Madagascar Rouhan et al. 372 (P) to submit to submit to submit Phlegmariurus tardieuae (Herter) A.R.Field & Testo Madagascar Rouhan et al. 386 (P) to submit to submit to submit Phlegmariurus tardieuae (Herter) A.R.Field & Testo Tanzania Rouhan et al. 509 (P) to submit to submit to submit Phlegmariurus tardieuae (Herter) A.R.Field & Testo Phlegmariurus verticillatus (L.f.) A.R. Field & Testo Madagascar Rasolohery 132 (P) to submit to submit to submit Phlegmariurus verticillatus (L.f.) A.R. Field & Testo Comoros Pignal 3406 (P) to submit to submit to submit Phlegmariurus verticillatus (L.f.) A.R. Field & Testo

	Mycopteris subtilis Mycopteris taxifolia (L.) Sundue Niphidium crassifolium (L.) Lellinger Niphidium crassifolium Notogrammitis cf. angustifolia (Jacq.) Parris Notogrammitis angustifolia Notogrammitis angustifolia Notogrammitis angustifolia Notogrammitis billardierei (Willd.) Parris Notogrammitis billardierei Notogrammitis billardierei Notogrammitis ciliata (Colenso) Parris Notogrammitis ciliata Notogrammitis ciliata Notogrammitis crassior (Kirk) Parris Notogrammitis crassior Notogrammitis crassior Notogrammitis crassior Notogrammitis crassior Notogrammitis crassior Notogrammitis givenii (Parris) Parris Notogrammitis heterophylla (Labill.) Parris Notogrammitis patagonica (C. Chr.) Parris Notogrammitis pseudociliata (Parris) Parris Notogrammitis rawlingsii (Parris) Parris Notogrammitis rigida (Hombron) Parris Oreogrammitis adspersa (Blume) Parris Oreogrammitis congener (Blume) Parris Oreogrammitis congener Scleroglossum wooroonooran (F. M. Bailey) C. Chr. Scleroglossum wooroonooran Scleroglossum wooroonooran Serpocaulon fraxinifolium (Jacq.) A. R. Sm. Serpocaulon triseriale (Sw.) A. R. Sm. Stenogrammitis hartii (Jenman) Labiak Stenogrammitis hellwigii (Mickel & Beitel) Labiak Stenogrammitis hildebrandtii (Hieron.) Labiak Stenogrammitis hildebrandtii Stenogrammitis jamesonii (Hook.) Labiak Stenogrammitis limula (Christ) Labiak Stenogrammitis myosuroides (Sw.) Labiak Stenogrammitis oosora (Baker) Labiak Stenogrammitis oosora Stenogrammitis oosora Stenogrammitis oosora Stenogrammitis prionodes (Mickel & Beitel) Labiak Stenogrammitis pumila (Labiak) Labiak Stenogrammitis saffordii (Maxon) Labiak Stenogrammitis sp. 1 Stenogrammitis sp. 1 APPENDIX 3 Species name Anchistea virginica (L.) C.Presl Austroblechnum ×aggregatum (Colenso) Gasper & V.A.O.Dittrich x Sundue 1140 (NY) x Labiak 4018 (NY) x Kreier s.n. (GOET)* x Schuettpelz 209 (DUKE)* Jolinon 1089 (P) Lendemer 30006 (NY) Parris 12423 (AK) Jolinon 1089 (P) Brownsey P022138 (WELT) Australia Ecuador Brazil cultivated Ecuador Amsterdam Island, France Australia New Zealand Amsterdam Island, France x Parris 12421 (AK) New Zealand Sundue s.n. (VT) Australia Jane s.n. (AK) New Zealand Parris 12360 (AK) New Zealand Parris 12657 (AK) New Zealand Boulangeat 11 (P) Kerguelen Islands, France Boulangeat 19 (P) Kerguelen Islands, France Corner 333 (P) Malouines, UK Huntley 721 (P) Prince Edward Isl., South-Africa Perrie 3742 (WELT) New Zealand Quetel & Chambrin 2 (P) Kerguelen Islands, France Perrie 3842 (WELT) New Zealand x Parris 12419 (AK) New Zealand Perrie 4760 (WELT) New Zealand Perrie 4088 (WELT) New Zealand Young s.n. (AK296949) (AK) New Zealand Perrie 4857 (WELT) New Zealand Sundue 2233 (VT) Sabah, Malaysia Parris 12782 (AK) Peninsular Malaysia Ranker 2126 & Klimas (COLO) Sabah, Malaysia Kessler 14289 (VT) Australia Kessler 14304 (VT) Australia Mackee 18207 (P) New Caledonia, France x Jimenez 3302 (UC) Bolivia x Smith 2902 (UC) Brazil x Lellinger 455 (US) Dominican Republic x Mickel & Leonard 4636 (NY) Mexico x Rouhan et al. 1213 (P) Madagascar Rouhan et al. 1375 (P) Madagascar x Sundue 1149 (NY) Ecuador x Sundue 1736 (NY) Costa Rica x Liogier 4 (NY) Guatemala Cable 77 (K) Cameroon x Rakotondrainibe 6929 (P) Madagascar x Rouhan et al. 1188 (P) Madagascar Rouhan et al. 1246 (P) Madagascar x Mickel & Beitel 6567 (NY) Mexico x Labiak 4015 (UPCB) Brazil x Ranker 1892 (COLO) Hawaii, USA Jolinon 912 (P) Amsterdam Island, France x Noël 35 (P) Amsterdam Island, France Voucher Cranfill s.n. (RBC 606) (UC) USA KY711743 KY711916 KY712244 KY712085 KY711569 GU476800 GU476914 KM106167 KM106009 GU476699 --EU250358 -EU250359 EF463503 EF463254 ---KY711907 KY712075 KY712400 KY712234 KY711735 KM218824 KM218770 KM106168 KM106010 KM106074 JX499252 JQ904083 --JQ904113 ----KY711736 JX499250, JQ904096 --JQ904103 AY459469 JQ904094 KM106169 KM106011 JQ904102 -KM218755 KM106170 KM106012 KM106075 JX499249 JQ904097 --JQ904105 JX499247 JQ904078 --JQ904104 JX499248 JQ904095 --JQ904106 KY711810 KY711985 KY712307 KY712149 KY711634 KY711811 KY711986 KY712308 KY712150 KY711635 ----KY711734 ----KY711733 JX499241 JQ904077 --JQ904115 KY711744 KY711918 KY712246 KY712086 KY711571 JX499242 JQ904079 --JQ904110 AY459462 AY460629 --JQ904100 JX499246 JQ904088 ---JX499245 JQ904080 --JQ904117 -JQ904085 --JQ904119 -JQ904082 --JQ904121 -KM218808 KM106171 KM106013 KM106076 KM218845 KM218762 KM106172 KM106014 KY711570 -EF178617 -KY712081 -KM218835 KM218809 KM106189 KM106031 KM106091 KM218836 KM218810 KM106190 KM106032 KM106092 --KY712386 -KY711714 -EF551071 EF551096 -EF551134 --EF551118 -EF551157 GU376583 GU386985 GU387057 GU387143 GU387225 GU376584 GU386990 GU387058 GU387144 GU387226 KY711844 KY712020 KY712336 KY712184 KY711669 KY711845 KY712021 KY712337 KY712185 KY711670 GU376596 GU386999 GU387074 GU387160 GU387237 GU476765 GU476903 GU387066 GU387152 GU476651 GU376599 GU386988 GU387077 GU387163 GU387240 GU376600 GU386972 GU387078 GU387164 GU387241 KY711848 KY712024 KY712340 KY712188 KY711673 KY711846 KY712022 KY712338 KY712186 KY711671 KY711847 KY712023 KY712339 KY712187 KY711672 GU376605 GU386991 GU387086 GU387170 GU387249 GU376608 GU387022 GU387089 GU387173 GU387252 EF178645 EF178628 KM106191 -EF178662 KY711905 KY712073 KY712398 -KY711731 KY711906 KY712074 KY712399 -KY711732 Locality rbcL rps4/rps4-trnS trnL/trnL-trnF AY137660 AF533857 n.a. Wilson 68 (MELU) Australia KJ170817 KJ170790 KJ170844 Austroblechnum andinum (Baker) Gasper & V.A.O.Dittrich Salino s.n. (BHCB) Brazil KU898604 KU898550 KU925243 Austroblechnum bakeri (C.Chr.) Gasper & V.A.O.Dittrich Rouhan et al. 1625 (P) Madagascar to submit to submit to submit Austroblechnum bakeri (C.Chr.) Gasper & V.A.O.Dittrich Rouhan et al. 1401 (P) Madagascar to submit to submit to submit Austroblechnum bakeri (C.Chr.) Gasper & V.A.O.Dittrich Janssen 2424 (P) Madagascar to submit to submit to submit Austroblechnum bakeri (C.Chr.) Gasper & V.A.O.Dittrich Janssen 2665 (P) Tanzania to submit to submit to submit Austroblechnum colensoi (Hook.f.) Gasper & V.A.O.Dittrich Perrie 3572 (WELT) New Zealand KF975783 KF975739 DQ683379 Austroblechnum divergens (Kunze) Gasper & V.A.O.Dittrich Funez 1000 (FURB) Brazil KU898605 KU898548 KU898664 Austroblechnum doodioides (Brack.) Gasper & V.A.O.Dittrich Rouhan et al. 634 (P) Vanuatu to submit to submit to submit Austroblechnum durum (T.Moore) Gasper & V.A.O.Dittrich Perrie 4023 (WELT) New Zealand KF975788 KF975744 DQ683383 Austroblechnum integrifons (Bonap. ex Rakotondr.) Gasper & V.A.O.Dittrich Rakotondrainibe 4412 (P) Madagascar n.a. to submit to submit Austroblechnum lechleri (T.Moore) Gasper & V.A.O.Dittrich Larsen 252 (SI) Chile KU898608 KU898553 KU898667 Austroblechnum lehmannii (Hieron.) Gasper & V.A.O.Dittrich Almeida 3374 (BHCB) Brazil KU898606 KU898551 KU898665 Austroblechnum leyboldtianum (Phil.) Gasper & V.A.O.Dittrich Perrie 3295 (WELT) New Zealand KF975780 KF975736 DQ683374 Austroblechnum melanocaulon (Brack.) Gasper & V.A.O.Dittrich Perrie & Brownsey FJ2011182 (WELT) Fiji KF975794 KF975750 KF975720 Austroblechnum membranaceum (Colenso ex Hook.) Gasper & V.A.O.Dittrich Perrie 3475 (WELT) New Zealand KF975795 KF975751 DQ683391 Austroblechnum microphyllum (Goldm.) Gasper & V.A.O.Dittrich Biganzoli 2141 (SI) Argentina KU898607 KU898552 KU898666 Austroblechnum norfolkianum (Heward) Gasper & V.A.O.Dittrich Parris 12358 (WELT) New Zealand KF975801 KF975757 DQ683401 Austroblechnum patersonii (R.Br.) Gasper & V.A.O.Dittrich subsp. patersonii Gasper & V.A.O.Dittrich Wilson 70 (MELU) Australia KJ170822 KJ170795 KJ170849 Austroblechnum patersonii (R.Br.) Gasper & V.A.O.Dittrich subsp. queenslandicum (T.C.Chambers & P.A.Farrant) Gasper & V.A.O.Dittrich Ohlsen BB144 (BRI) Australia KJ170823 KJ170796 KJ170850 Austroblechnum penna-marina (Poir.) Gasper & V.A.O.Dittrich Gasper 3039 (FURB) Brazil KU898609 KU898554 KU898668 Austroblechnum squamipes (Hieron.) Gasper & V.A.O.Dittrich Salino 14737 (BHCB) Brazil KU898610 KU898555 KU898669 Austroblechnum stoloniferum (Mett. ex E.Fourn.) Gasper & V.A.O.Dittrich Campos Salas 12 (MEXU) Mexico KU898611 KU898556 KU898670 Austroblechnum vieillardii (Mett.) Gasper & V.A.O.Dittrich Perrie NC 2012 227 (WELT) New Caledonia KF975814 n.a. KF975730 Austroblechnum wardiae (Mickel & Beitel) Gasper & V.A.O.Dittrich Salino 15367 (BHCB) Panama KU898612 KU898557 KU898671 Blechnidium melanopus (Hook.) T.Moore Knapp 3355 (P) Taiwan KU898627 n.a. n.a. Blechnopsis orientalis (L.) C.Presl Brownsey & Perrie FJ201190 (WELT) Australia KF975806 KF975762 KF975726 Blechnum appendiculatum Willd. Salino 15454 (BHCB) Panama KU898613 KU898558 KU898672 Blechnum areolatum V.A.O.Dittrich & Salino Salino 15184 (BHCB) Brazil KU898614 KU898559 KU898673 Blechnum asplenioides Sw. Salino 14449 (BHCB) Brazil KU898615 KU898560 KU898674 Blechnum auriculatum Cav. Funez 2162 (FURB) Brazil KU898616 KU898561 KU898675 Blechnum australe L. Unknown / Prada s.n. (Unknown / MA) Argentina / Unknown AB040557 n.a. JQ907366 Blechnum australe L. Rouhan et al. 1416 (P) Madagascar to submit to submit to submit Blechnum australe L. Janssen 2588 (P) Madagascar to submit to submit to submit Blechnum australe L. Hennequin 286 (P) La Réunion to submit to submit to submit Blechnum austrobrasilianum de la Sota Almeida 3372 (BHCB) Brazil KU898617 KU898562 KU898676 Blechunm ×caudatum Cav. Almeida 3371 (BHCB) Brazil KU898618 KU898563 KU898677 Blechnum ×confluens Schltdl. & Cham. Kessler 13457 (LPB) Bolivia KU898625 KU898569 KU898682 Blechnum gracile Kaulf. Jiménez I. 1051 (LPB) Bolivia KU898620 KU898565 KU898678 Blechnum gracilipes (Rosenst.) M.Kessler & A.R.Sm. Jiménez I. 1485 (LPB) Bolivia n.a. n.a. KU898679 Blechnum hastatum Kaulf. Zuloaga 11322 (SI) Argentina KU898619 KU898564 n.a. Blechnum laevigatum Cav. Canestraro 527 (MBM) Brazil KU898621 KU898566 n.a. Blechnum lanceola Sw. Laurent 275 (BHCB) Brazil KU898622 KU898567 KU898680 Blechnum longipilosum V.A.O.Dittrich & Salino Salino 15570 (BHCB) Brazil KU898626 KU898570 KU898683 Blechnum occidentale L. Funez 548 (FURB) Brazil KU898623 KU898568 KU898681 Blechnum polypodioides Raddi Salino 15334 (BHCB) Panama KU898624 KU925241 KU925244 Blechnum punctulatum Sw. Parris 12683 (WELT) cult. KF975811 KF975767 DQ683412 Blechnum punctulatum Sw. Rouhan et al. 1652 (P) Madagascar to submit to submit to submit Blechnum punctulatum Sw. Rouhan et al. 1405 (P) Madagascar to submit to submit to submit Blechnum punctulatum Sw. Janssen 2660 (P) Tanzania to submit to submit to submit Brainea insignis (Hook.) J.Sm. Averyanov 2702 (P) Vietnam KU898628 KU898571 KU898684 Cleistoblechnum eburneum (Christ) Gasper & Salino LU/Z1 (PYU) China JN168003 JN168071 n.a. Cranfillia fluviatilis (R.Br.) Gasper & V.A.O.Dittrich Wilson 64 (MELU) Australia KJ170818 KJ170791 KJ170845 Cranfillia hirsuta (Rosenst.) Gasper & V.A.O.Dittrich Perrie NC 2012 196 (WELT) New Caledonia KF975792 KF975748 KF975718 Cranfillia nigra (Colenso) Gasper & V.A.O.Dittrich Perrie 3454 (WELT) New Zealand KF975800 KF975756 DQ683399 Cranfillia opaca (Mett.) Gasper & V.A.O.Dittrich Perrie NC 2012 167 (WELT) New Caledonia KF975805 KF975761 KF975725 Cranfillia pilosa (Brack.) Gasper & V.A.O.Dittrich Perrie & Brownsey FJ2011181 (WELT) Fiji KF975809 KF975765 KF975728 Cranfillia sampaioana (Brade) Gasper & V.A.O.Dittrich Salino 13818 (BHCB) Brazil KU898629 KU898572 KU898685 Cranfillia sprucei (C.Chr) Gasper & V.A.O.Dittrich Jiménez 1743 (LPB) Bolivia KU898630 KU898573 KU898686 Cranfillia vulcanica (Blume) Gasper & V.A.O.Dittrich Perrie 3461 (WELT) Australia KF975816 KF975771 DQ683416 Diploblechnum acuminatum (C.T.White & Goy) Gasper & V.A.O.Dittrich Field et al. s.n. (CNS) Australia KJ170839 KJ170812 KJ170866 Diploblechnum diversifolium (Mett.) Gasper & V.A.O.Dittrich Perrie NC 2012 157 (WELT) New Caledonia KF975787 KF975743 KF975716 Diploblechnum fraseri (A.Cunn.) De Vol Perrie 3434 (WELT) New Zealand KF975790 KF975746 DQ683390 Diploblechnum lenormandii (Baker) Gasper & V.A.O.Dittrich Perrie NC 2012 169 (WELT) New Caledonia KF975793 KF975749 KF975719 Diploblechnum neglectum (F.M.Bailey) Gasper & V.A.O.Dittrich van der Werff 17045 (MO) Australia KU898631 KU898574 KU898687 Doodia aspera R.Br. Perrie and Ohlsen BB113 (MELU) Australia KJ170836 KJ170809 KJ170863 Doodia australis Parris Ohlsen BB151 (MELU) Australia KJ170837 KJ170810 KJ170864 Doodia brackenridgei Carruth. ex Seem. Perrie & al. FJ2011123 (WELT) Fiji KF975818 KF975773 KF975732 Doodia caudata (Cav.) R.Br. Perrie and Ohlsen BB88 (MELU) Australia KJ170838 KJ170811 KJ170865 Doodia dives Kunze Perrie et al. BB24 (BRI) Australia KJ170831 KJ170804 KJ170858 Doodia kunthiana Gaudich. Unknown / WELT P21219 USA AB040578 n.a. DQ683424 Doodia linearis J.Sm. Ohlsen BB147 (MELU) Australia KJ170833 KJ170806 KJ170860 Doodia media R.Br. Perrie NC 2012 120 (WELT) Australia KF975819 KF975774 KF975733 Doodia milnei Carruth. Parris 12689 (WELT) New Zealand KF975820 KF975775 DQ683425 Doodia mollis Parris Parris 12688 (WELT) New Zealand KF975821 KF975776 DQ683427 Doodia paschalis C.Chr. Christenhusz 5047 (P) Chile (Easter Island) n.a. n.a. KU925245 Doodia squarrosa Colenso Perrie 3517 (WELT) New Zealand KF975822 KF975777 DQ683429 Icarus filiformis (A.Cunn.) Gasper & Salino Perrie 3459 (WELT) New Zealand KF975789 KF975745 DQ683385 Lomaria nuda (Labill.) Willd. Wilson 69 (MELU) Australia KJ170821 KJ170794 KJ170848 Lomaria oceanica (Rosenst.) Gasper & V.A.O.Dittrich Perrie NC 2012 105 (WELT) New Caledonia KF975804 KF975760 KF975724 Lomaria raymondii Gasper & V.A.O.Dittrich Perrie 4015 (WELT) New Zealand KF975786 KF975742 DQ683382 Lomaria spannagelii (Rosenst.) Gasper & V.A.O.Dittrich Almeida 3387 (BHCB) Brazil KU898643 KU898584 KU898698 Lomaridium acutum (Desv.) Gasper & V.A.O.Dittrich van der Werff 16799 (MO) Peru KU898638 KU925242 KU925246 Lomaridium attenuatum (Sw.) Gasper & V.A.O.Dittrich Pignal 3409 (P) Comoros to submit to submit to submit Lomaridium attenuatum (Sw.) Gasper & V.A.O.Dittrich Pignal 3486 (P) Comoros to submit to submit to submit Lomaridium attenuatum (Sw.) Gasper & V.A.O.Dittrich Bauret et al. 111 (P) Madagascar to submit to submit to submit Lomaridium attenuatum (Sw.) Gasper & V.A.O.Dittrich Rouhan et al. 1231 (P) Madagascar to submit to submit to submit UC Botanical Garden 55.0076 (UC) Philippines AF425104 AF425157 n.a. Stenochlaena palustris (Burm.f.) Bedd. Ohlsen and Bayly BB197 (MELU) Australia KJ170829 KJ170802 KJ170856 Stenochlaena tenuifolia (Desv.) T.Moore Schuettpelz 504 (DUKE) cultivated EF463163 n.a. n.a. Struthiopteris castanea (Makino & Nemoto) Nakai Ohashi 49965 (LPB) Japan KU898661 n.a. KU898715 Struthiopteris spicant (L.) F.W.Weiss Windham 3395 / cultivated (DUKE / AK) cultivated JF832059 n.a. DQ683413 Telmatoblechnum indicum (Burm.f.) Perrie Perrie and Ohlsen BB107 (MELU) Australia KJ170830 KJ170803 KJ170857 Telmatoblechnum serrulatum (Rich.) Perrie Funez 487 (FURB) Brazil KU898662 KU898602 KU898716 Woodwardia auriculata Blume Cranfill s.n. (RBC 650) (UC) Malaysia AY137661 n.a. n.a. Woodwardia fimbriata Sm. Unknown (Unknown) Japan AB040597 AF533859 n.a. Woodwardia harlandii Hook. Unknown (Unknown) Japan AB040598 AF533860 n.a. Woodwardia japonica (L.f.) Sm. Cranfill 21 / Cranfill 21 / P21222 (UC / UC / WELT) Japan AY137664 AF533861 DQ683432 Woodwardia kempii Copel Cranfill s.n. (RBC 023) (UC) Taiwan/Chi na KM60699 2 KM606992 n.a. Woodwardia martinezii Maxon ex Weath. Cerón 420 (MEXU) Mexico KU898663 n.a. n.a. Woodwardia prolifera Hook. & Arn. Cranfill s.n. (RBC 010) / Cranfill s.n. (RBC 010) / P21332 (UC / UC / WELT) cultivated AY137666 AF533864 DQ683433 Woodwardia radicans (L.) Sm. Cranfill 163 / Cranfill 163 / (UC; UC; WELT) Spain AY137667 AF533865 DQ683434 Woodwardia spinulosa M.Martens & Galeotti Salino 15746 (BHCB) Mexico n.a. KU898603 KU898718 APPENDIX 4 Species Voucher Locality trnL/trnL-trnF trnH-psbA rpoC1 rps4 rps4-trnS Cystodium sorbifolium (Sm.) J.Sm. Hoogland 4617 (BM) Papua New Guinea GU478726 n.a. n.a. n.a. n.a. Lindsaea annamensis K.U.Kramer Averyanov VH2540 (AAU) Vietnam GU478804 GU478501 GU478612 n.a. n.a. Lindsaea apoensis Copel. in Perkins Elmer 11565 (U) Mindanao GU478865 GU478563 n.a. n.a. n.a. Lindsaea arcuata Kunze Maas 5032 (U) Costa Rica GU478788 GU478506 GU478615 GU478657 GU478359 Lindsaea austrosinica Ching Averyanov VH4816 (AAU) Vietnam GU478801 GU478486 n.a. n.a. n.a. Lindsaea azurea Christ Cheesman 165 (U) Papua New Guinea GU478852 GU478536 n.a. n.a. n.a. Lindsaea bifida (Kaulf.) Mett. ex Kuhn Lehtonen 552 (TUR) Brazil GU478799 GU478485 GU478608 n.a. n.a. Lindsaea blanda Mett. ex Kuhn Palmer 747 (U) Java GU478806 GU478525 n.a. n.a. n.a. Lindsaea blotiana K.U.Kramer Rakotondrainibe 4327 (MO) Madagascar GU478814 GU478511 n.a. n.a. n.a. Lindsaea blotiana K.U.Kramer Rakotondrainibe 6350 (P) Madagascar GU478813 GU478510 GU478633 GU478679 GU478381 Lindsaea blotiana K.U.Kramer Rouhan et al. 1253 (P) Madagascar to submit to submit to submit to submit to submit Lindsaea blotiana K.U.Kramer Rouhan et al. 1591 (P) Madagascar to submit to submit to submit n.a. n.a. Lindsaea blotiana K.U.Kramer Rouhan et al. 1155 (P) Madagascar n.a. to submit to submit to submit to submit Lindsaea bolivarensis V.Marcano Tuomisto 14478 (TUR) Peru FJ360992 FJ360902 FJ360947 GU478652 GU478354 Lindsaea borneensis Hook. Wong 2 (AAU) Brunei GU478866 GU478538 n.a. n.a. n.a. Lindsaea botrychioides A.St.-Hil. Windisch 4987 (AAU) Brazil FJ360994 FJ360904 FJ360949 GU478714 GU478416 Lindsaea bouillodii Christ Nielsen 592 (AAU) Sarawak FJ360993 FJ360903 FJ360948 GU478716 GU478418 Lindsaea brachypoda (Baker) Salomon Balgooy 1529 (L) Australia GU478848 GU478553 n.a. n.a. n.a. Lindsaea brevipes Copel. Braithwaite 4029 (MO) Guadalcanal GU478809 GU478541 GU478627 n.a. n.a. Lindsaea carvifolia K.U.Kramer Mjöberg 9 (BM) Borneo GU478860 GU478562 n.a. n.a. n.a. Lindsaea cf. cambodgensis Christ Iwatsuki 14505 (AAU) Thailand GU478840 GU478502 n.a. n.a. n.a. Lindsaea cf. fissa Copel. Tolentino HAL-049 (U) Mindoro Island GU478857 GU478557 n.a. n.a. n.a. Lindsaea chienii Ching Kramer 7554 (U) Taiwan FJ360995 FJ360905 FJ360950 n.a. n.a. Lindsaea chrysolepis K.U.Kramer Croft 216 (L) New Ireland GU478850 GU478552 n.a. GU478709 GU478411 Lindsaea coarctata K.U.Kramer Tuomisto 14500 (TUR) Peru FJ360996 FJ360906 FJ360951 GU478656 GU478358 Lindsaea crispa Baker Parris 11469 (L) Borneo GU478834 GU478526 n.a. n.a. n.a. Lindsaea cubensis Underw. & Maxon Morton 10035 (BM) Cuba GU478795 GU478494 n.a. GU478687 GU478389 Lindsaea cultrata (Willd.) Sw. Poulsen 128 (AAU) Borneo GU478859 GU478554 n.a. GU478668 GU478370 Lindsaea cyclophylla K.U.Kramer Liesner 23788 (MO) Venezuela GU478776 GU478483 n.a. n.a. n.a. Lindsaea digitata Lehtonen & Tuomisto Tuomisto 14470 (TUR) Peru EU146057 EU146041 EU146051 GU478698 GU478400 Lindsaea diplosora Alderw. Nielsen 815 (AAU) Sarawak GU478833 GU478535 GU478598 GU478722 GU478424 Lindsaea dissectiformis Ching Averyanov VH2557 (AAU) Vietnam FJ360997 FJ360907 FJ360952 n.a. n.a. Lindsaea divaricata Klotzsch Tuomisto 14553 (TUR) Peru EU146052 EU146040 EU146042 GU478697 GU478399 Lindsaea divergens Wall. ex Hook. & Grev. Abdullah 228 (U) Malaysia GU478765 GU478465 n.a. n.a. n.a. Lindsaea doryphora K.U.Kramer Poulsen 341 (AAU) Borneo GU478868 GU478539 GU478636 GU478683 GU478385 Lindsaea dubia Spreng. Christenhusz 2312 (TUR) French Guiana GU478779 GU478493 GU478623 GU478701 GU478403 Lindsaea ensifolia Sw. Larsen 42363 (AAU) Thailand GU478853 GU478522 n.a. n.a. n.a. Lindsaea ensifolia Sw. Kessler 13597 (GOET) La Réunion n.a. GU478521 GU478606 GU478678 GU478380 Lindsaea falcata (Dryand.) Rosenst. Tuomisto 14925 (TUR) Peru FJ361005 FJ360914 FJ360960 GU478702 GU478404 Lindsaea feei C.Chr. van der Werff 3418 (U) Venezuela FJ361004 FJ360913 FJ360959 GU478689 GU478391 Lindsaea flabellifolia (Bak.) C. Chr Rouhan et al. 1327 (P) Madagascar to submit to submit to submit to submit to submit Lindsaea flabellifolia (Bak.) C. Chr Rouhan et al. 334 (P) Madagascar to submit to submit to submit to submit to submit Lindsaea flabellifolia (Bak.) C. Chr Rouhan et al. 1129 (P) Madagascar to submit to submit to submit to submit to submit Lindsaea flabellifolia (millefolia) (Bak.) C. Chr Lan 5065 (L) Madagascar GU478812 GU478513 n.a. n.a. n.a. Lindsaea flabellifolia (millefolia) (Bak.) C. Chr Guillaumet 4206 (P) Madagascar GU478811 n.a. n.a. n.a. n.a. Lindsaea fraseri Hook. Streimann 8951 (L) Australia FJ360998 FJ360908 FJ360953 GU478719 GU478421 Lindsaea gomphophylla Baker Hotta 12856 (U) Brunei GU478820 GU478497 n.a. n.a. n.a. Lindsaea goudotiana (Kunze) Mett. ex Kuhn Deroin 112 (P) Madagascar GU478818 n.a. n.a. n.a. n.a. Lindsaea goudotiana (Kunze) Mett. ex Kuhn Rouhan et al. 1252 (P) Madagascar to submit to submit to submit to submit to submit Lindsaea goudotiana (Kunze) Mett. ex Kuhn Janssen 2475 (P) Madagascar to submit to submit to submit to submit to submit Lindsaea goudotiana (Kunze) Mett. ex Kuhn Rouhan et al. 1156 (P) Madagascar to submit to submit to submit to submit to submit Lindsaea goudotiana (subtilis) (Kunze) Mett. ex Kuhn van der Werff 12855 (MO) Madagascar GU478817 GU478514 GU478595 n.a. n.a. Lindsaea grandiareolata (Bonap.) Kramer Gautier 5315 (P) Madagascar to submit n.a. to submit n.a. n.a. Lindsaea grandiareolata (Bonap.) Kramer Nusbaumer 2950 (P) Madagascar to submit n.a. to submit n.a. to submit Lindsaea grandiareolata (Bonap.) Kramer CJR (Reeb) 115 (-) Madagascar to submit n.a. to submit n.a. n.a. Lindsaea gueriniana (Gaudich.) Desv. Stone 2506 (US) Solomon Islands GU478766 GU478467 GU478594 n.a. n.a. Lindsaea guianensis (Aubl.) Dryand. Tuomisto 14927 (TUR) Peru FJ360999 FJ360944 FJ360954 GU478700 GU478402 Lindsaea hainaniana (K.U.Kramer) Lehtonen & Tuomisto Wuzhishan fern survey 533 (MO) Hainan GU478807 GU478555 GU478604 GU478671 GU478373 Lindsaea harveyi Carrière Brownlie 978 (TUR) Fiji FJ361000 FJ360909 FJ360955 GU478673 GU478375 Lindsaea hemiglossa K.U.Kramer Tuomisto 12742 (TUR) Peru FJ361001 FJ360910 FJ360956 GU478660 GU478362 Lindsaea hemiptera K.U.Kramer Tuomisto 13049 (TUR) Peru FJ374265 FJ374263 FJ374264 GU478717 GU478419 Lindsaea heterophylla Dryand. Charoenphol 5081 (AAU) Thailand GU478855 n.a. GU478607 n.a. n.a. Lindsaea heterophylla Dryand. Ammann 253 (P) Madagascar to submit n.a. to submit n.a. n.a. Lindsaea imrayana (Hook.) Perez Christenhusz 2826 (TUR) Dominica GU478772 GU478435 GU478592 GU478649 GU478351 Lindsaea incisa Prent. Blake 21210 (MO) Australia GU478856 GU478520 n.a. GU478682 GU478384 Lindsaea integra Holttum Poulsen 72 (AAU) Borneo GU478821 GU478531 n.a. GU478670 GU478372 Lindsaea jamesonioides Baker Clemens 30733 (BM) Borneo GU478764 GU478466 n.a. GU478711 GU478413 Lindsaea javanensis Blume Hennipman 3937 (U) Thailand FJ361002 FJ360911 FJ360957 n.a. n.a. Lindsaea javitensis Humb. & Bonpl. ex Willd. Prance 15677 (U) Brazil GU478792 GU478490 n.a. n.a. n.a. Lindsaea kawabatae Kurata Saiki 1093 (Z) Japan GU478803 GU478499 GU478596 n.a. n.a. Lindsaea kingii Copel. Braithwaite 4304 (U) Solomon Islands GU478831 n.a. GU478629 GU478681 GU478383 Lindsaea lancea (L.) Bedd. var. lancea Tuomisto 14466 (TUR) Peru FJ361006 FJ360915 FJ360961 GU478651 GU478353 Lindsaea lapeyrousei (Hook.) Baker Brownlie 1575 (U) Fiji FJ361007 FJ360916 FJ360962 GU478680 GU478382 Lindsaea leptophylla Baker Raharimalala 2017 (MO) Madagascar GU478819 GU478509 n.a. n.a. n.a. Lindsaea leptophylla Baker Rouhan et al. 1144 (P) Madagascar n.a. to submit to submit to submit to submit Lindsaea leptophylla Baker Rouhan et al. 1163 (P) Madagascar to submit to submit to submit to submit to submit Lindsaea leptophylla Baker Rouhan et al. 1195 (P) Madagascar n.a. to submit to submit n.a. n.a. Lindsaea lherminieri Fée Bernard 4775 (P) Guadeloupe GU478784 GU478505 n.a. GU478718 GU478420 Lindsaea linearis Sw. Braggins 589 (AAU) New Zealand FJ361008 FJ360917 FJ360963 GU478721 GU478423 Lindsaea lobata Poir. in Lam. Alston 16699 (U) North Moluccas FJ361009 FJ360918 FJ360964 GU478674 GU478376 Lindsaea longifolia Copel. Elmer 16151 (U) Luzon GU478837 GU478527 n.a. n.a. n.a. Lindsaea lucida Blume Charoenphol 4999 (AAU) Thailand GU478808 GU478542 GU478628 n.a. n.a. Lindsaea madagascariensis Baker Rakotondrainibe 6349 (P) Madagascar GU478815 GU478512 GU478634 n.a. n.a. Lindsaea madagascariensis Baker Rouhan et al. 1256 (P) Madagascar to submit to submit to submit to submit to submit Lindsaea madagascariensis Baker Rouhan et al. 1320 (P) Madagascar to submit to submit to submit to submit to submit Lindsaea madagascariensis Baker Bauret et al. 132 (P) Madagascar to submit to submit to submit to submit to submit Lindsaea madagascariensis Baker Bauret et al. 139 (P) Madagascar to submit to submit to submit n.a. n.a. Lindsaea madagascariensis Baker Rouhan et al. 1623 (P) Madagascar to submit to submit to submit to submit to submit Lindsaea malayensis Holttum Schneider 222 (Z) Malaysia GU478858 GU478530 GU478602 GU478672 GU478374 Lindsaea marojejyense sp. nov. Bauret et al. 94 (P) Madagascar to submit to submit to submit n.a. n.a. Lindsaea marojejyense sp. nov. Rouhan et al. 1604 (P) Madagascar to submit to submit to submit to submit to submit Lindsaea media R.Br. van der Werff 11655 (MO) Australia GU478843 GU478516 GU478597 n.a. n.a. Lindsaea meifolia (Kunth) Mett. ex Kuhn Liesner 7062 (MO) Venezuela GU478783 GU478478 n.a. n.a. n.a. Lindsaea merrillii Copel. ssp. yaeyamensis (Tagawa) K.U.Kramer Kramer 8005 (U) Taiwan GU478863 GU478559 n.a. n.a. n.a. Lindsaea microphylla Sw. Everist 8062 (AAU) Thailand FJ361010 FJ360919 FJ360965 n.a. n.a. Lindsaea monocarpa Rosenst. in C.Chr. Edwards 4414A (L) Papua New Guinea FJ361011 FJ360920 FJ360966 n.a. n.a. Lindsaea multisora Alderw. Cicuzza 104 (GOET) Sulawesi GU478849 GU478534 GU478631 GU478676 GU478378 Lindsaea nervosa Mett. McKee 2617 (U) New Caledonia GU478829 n.a. n.a. n.a. n.a. Lindsaea oblanceolata Alderw. Larsen 42928 (U) Thailand FJ361012 FJ360921 FJ360967 GU478685 GU478387 Lindsaea obtusa J.Sm. ex Hook. Kramer 8004 (U) Taiwan GU478823 GU478547 GU478599 n.a. n.a. Lindsaea orbiculata (Lam.) Mett. ex Kuhn Averyanov VH4814 (AAU) Vietnam FJ361013 FJ360922 FJ360968 n.a. n.a. Lindsaea ovoidea Fée Hatschbach 7083 (L) Brazil FJ361014 FJ360923 FJ360969 GU478713 GU478415 Lindsaea oxyphylla Baker Gautier 2662 (P) Madagascar GU478816 GU478508 n.a. n.a. n.a. Lindsaea oxyphylla Baker Janssen 2387 (P) Madagascar to submit to submit to submit n.a. n.a. Lindsaea pacifica K.U.Kramer Brownlie 979 (U) Fiji FJ361015 FJ360924 FJ360970 GU478663 GU478365 Lindsaea pallida Klotzsch Christenhusz 2518 (TUR) French Guiana GU478778 GU478479 GU478624 GU478705 GU478407 Lindsaea parallelogramma Alderw. Poulsen 342 (AAU) Borneo GU478851 GU478533 n.a. GU478675 GU478377 Lindsaea parasitica (Roxb. ex Griffith) Hieron. Larsen 42927 (AAU) Thailand FJ361016 FJ360925 FJ360971 GU478684 GU478386 Lindsaea parkeri (Hook.) Kuhn Boudrie 4254 (TUR) French Guiana GU478775 GU478492 GU478622 GU478695 GU478397 Lindsaea pectinata Blume Nielsen 816 (AAU) Australia FJ361021 FJ360930 FJ360976 GU478686 GU478388 Lindsaea pellaeiformis Christ Kjellberg 3561 (BM) Celebes GU478767 GU478468 n.a. n.a. n.a. Lindsaea pendula Klotzsch Kramer 2891 (U) Suriname GU478782 GU478477 n.a. n.a. n.a. Lindsaea phassa K.U.Kramer Tuomisto 14940 (TUR) Peru FJ361017 FJ360926 FJ360972 GU478659 GU478361 Lindsaea pickeringii (Brack.) Mett. ex. Kuhn Brownlie 996 (U) Fiji FJ361018 FJ360927 FJ360973 GU478666 GU478368 Lindsaea plicata Baker Callmander 291 (P) Madagascar GU478768 GU478471 GU478593 GU478661 GU478363 Lindsaea polyctena K.U.Kramer Price 2789 (Z) Mindanao GU478838 GU478544 n.a. n.a. n.a. Lindsaea portoricensis Desv. Christenhusz 3384 (TUR) Jamaica FJ361019 FJ360928 FJ360974 n.a. n.a. Lindsaea portoricensis Desv. Tuomisto 13045 (TUR) Peru FJ361028 FJ360937 FJ360983 GU478692 GU478394 Lindsaea pratensis Maxon Croat 90913 (MO) Ecuador GU478771 GU478469 n.a. n.a. n.a. Lindsaea prolongata E.Fourn. Mackee 6609 (P) New Caledonia GU478830 GU478519 n.a. n.a. n.a. Lindsaea propinqua Hook. in Night. Wood 10051 (BISH) Marquesas GU478825 GU478537 GU478601 GU478662 GU478364 Lindsaea pseudohemiptera (Alderw.) Lehtonen & Tuomisto Hou 245 (U) Borneo GU478861 GU478560 n.a. n.a. n.a. Lindsaea pulchella (J.Sm.) Mett. ex Kuhn Alston 16692 (U) North Moluccas GU478805 GU478528 n.a. GU478723 GU478425 Lindsaea pulchra (Brack.) Carrière ex Seem. Brousilie 1049 (U) Fiji GU478826 GU478551 n.a. GU478665 GU478367 Lindsaea quadrangularis Raddi ssp. antillensis K.U.Kramer Christenhusz 3588 (TUR) Puerto Rico FJ361020 FJ360929 FJ360975 GU478653 GU478355 Lindsaea regularis Rosenst. Jaag 1730 (Z) Flores GU478847 GU478564 n.a. n.a. n.a. Lindsaea reniformis Dryand. Boudrie 4250 (TUR) French Guiana GU478777 GU478482 GU478618 GU478704 GU478406 Lindsaea rigida J.Sm. Tolentino HAL-026 (U) Mindoro Island GU478832 GU478549 GU478600 GU478710 GU478412 Lindsaea rigidiuscula Lindm. Poole 2060 (Z) Brazil GU478794 GU478476 GU478621 GU478691 GU478393 Lindsaea rosenstockii Brause Hoogland 10860 (L) Papua New Guinea FJ361023 FJ360932 FJ360978 n.a. n.a. Lindsaea rufa K.U.Kramer Munzinger 1254 (P) New Caledonia GU478828 GU478518 n.a. n.a. n.a. Lindsaea rufa K.U.Kramer Tronchet 532 (P) New Caledonia to submit to submit to submit n.a. n.a. Lindsaea sagittata Dryand. Christenhusz 2618 (TUR) Suriname FJ361024 FJ360933 FJ360979 GU478688 GU478390 Lindsaea schizophylla (Baker) Christ Sledge 613 (Z) Sri Lanka GU478802 GU478498 n.a. n.a. n.a. Lindsaea schomburgkii Klotzsch Tuomisto 13044 (TUR) Peru FJ361026 FJ360935 FJ360981 GU478694 GU478396 Lindsaea seemannii J.Sm. in Seem. Hammel 3369 (AAU) Panama GU478770 GU478470 n.a. n.a. n.a. Lindsaea semilunata (C.Chr.) C.Chr. Renz 14307 (U) Guyana GU478797 GU478489 GU478619 GU478693 GU478395 Lindsaea sessilis Copel. Koster 13846 (U) Papua New Guinea GU478862 GU478561 n.a. n.a. n.a. Lindsaea sphenomeridopsis K.U.Kramer Renz 14184 (U) Guyana FJ361027 FJ360936 FJ360982 GU478708 GU478410 Lindsaea spruceana Mett. ex Kuhn Quipuscoa 878 (AAU) Peru GU478787 n.a. n.a. n.a. n.a. Lindsaea stolonifera Mett. ex Kuhn Braithwaite 4283 (U) Solomon Islands GU478827 GU478524 n.a. n.a. n.a. Lindsaea stricta (Sw.) Dryand. var. jamesoniiformis K.U.Kramer Maas 6460 (U) Puerto Rico GU478790 GU478473 GU478611 GU478696 GU478398 Lindsaea stricta (Sw.) Dryand. var. parvula (Fée) K.U.Kramer Boudrie 4253 (TUR) French Guiana GU478789 GU478474 GU478625 GU478690 GU478392 Lindsaea stricta (Sw.) Dryand. var. stricta Boudrie 4246 (TUR) French Guiana GU478791 GU478472 GU478610 GU478650 GU478352 Lindsaea surinamensis Posth. Granville 15461 (CAY) French Guiana GU478785 GU478495 GU478630 GU478703 GU478405 Lindsaea taeniata K.U.Kramer Tuomisto 14170 (TUR) Peru FJ361029 FJ360938 FJ360984 GU478655 GU478357 Lindsaea tenuifolia Blume Hartley 12334 (AAU) Papua New Guinea FJ361030 FJ360939 FJ360985 GU478677 GU478379 Lindsaea tenuis Klotzch Maguine 53824 (U) Venezuela GU478798 GU478491 n.a. GU478715 GU478417 Lindsaea tetragona K.U.Kramer Kato 14212 (MO) Seram GU478839 GU478543 GU478603 n.a. n.a. Lindsaea tetraptera K.U.Kramer Tuomisto 13048 (TUR) Peru FJ361031 FJ360940 FJ360986 GU478699 GU478401 Lindsaea trichomanoides Dryand. Cameron s.n. (AAU) New Zealand FJ361032 FJ360941 FJ360987 n.a. n.a. Lindsaea ulei Hieron. ex Christ Tuomisto 13002 (TUR) Peru GU478796 GU478488 GU478616 GU478658 GU478360 Lindsaea venusta Kaulf. ex Kuhn Sledge 1377 (U) Sri Lanka GU478835 GU478550 n.a. GU478720 GU478422 Lindsaea vieillardii Mett. McKee 5304 (U) New Caledonia GU478844 GU478496 n.a. n.a. n.a. Lindsaea virescens Sw. Lehtonen 621 (TUR) Brazil GU478800 GU478484 GU478609 GU478712 GU478414 Lindsaea viridis Col. Crookes s.n. (U) New Zealand GU478769 GU478503 n.a. n.a. n.a. Lindsaea vitiensis K.U.Kramer Smith 5918 (U) Fiji GU478845 GU478529 n.a. n.a. n.a. Lindsaea walkerae Hook. Bostock 638 (Z) Australia GU478841 GU478517 n.a. n.a. n.a. Lindsaea werneri Rosenst. Alston 16860 (U) North Moluccas FJ361034 FJ360943 FJ360989 GU478667 GU478369 Lonchitis hirsuta L. Christenhusz 3508 (TUR) Puerto Rico GU478725 GU478429 GU478567 GU478640 n.a. Nesolindsaea caudata (Hook.) Lehtonen & Christenh. Ballard 1390 (US) Sri Lanka GU478757 GU478446 GU478570 n.a. n.a. Nesolindsaea kirkii (Hook. ex Baker) Lehtonen & Christenh. Kramer 11073 (MO) Seychelles GU478758 GU478447 n.a. n.a. n.a. Odontosoria aculeata (L.) J.Sm. Christenhusz 4242 (TUR) Puerto Rico GU478740 GU478463 GU478580 n.a. n.a. Odontosoria afra (K.U.Kramer) J.P.Roux Hess-Wyss s.n. (Z) Angola GU478738 GU478454 GU478578 n.a. n.a. Odontosoria africana F.Ballard Lewate 5959 (P) Burundi GU478739 GU478455 n.a. n.a. n.a. Odontosoria angustifolia (Bernh.) C.Chr. Sarasin 65 (Z) New Caledonia GU478736 GU478451 n.a. n.a. n.a. Odontosoria biflora (Kaulf.) C.Chr. Raulerson 5549 (BISH) Guam GU478732 GU478453 GU478586 n.a. n.a. Odontosoria chinensis (L.) J. Sm. Bauret et al. 11 (P) Madagascar to submit to submit to submit n.a. n.a. Odontosoria deltoidea (Copel.) Lehtonen & Tuomisto Mackee 19315 (P) New Caledonia GU478733 n.a. n.a. n.a. n.a. Odontosoria melleri (Hook.) C. Chr. Bauret et al. 6 (P) Madagascar to submit to submit to submit n.a. n.a. Odontosoria retusa (Cav.) J.Sm. Fallen 620 (MO) Papua New Guinea GU478735 GU478450 n.a. n.a. n.a. Odontosoria schlechtendalii (C.Presl.) C.Chr. Nee 24879 (Z) Mexico GU478745 GU478457 GU478585 n.a. n.a. Osmolindsaea japonica (Baker) Lehtonen & Christenh. Huang 329 (MO) Taiwan GU478761 GU478433 GU478590 GU478644 GU478346 Osmolindsaea odorata (Roxb.) Lehtonen & Christenh. Averyanov VH3287 (AAU) Vietnam GU478760 GU478431 GU478589 GU478646 GU478348 Saccoloma inaequale (Kunze) Mett. Tuomisto 14409 (TUR) Peru GU478727 GU478428 GU478568 GU478638 n.a. Sphenomeris clavata (L.) Maxon 1 Christenhusz 4218 (TUR) Puerto Rico GU478729 GU478448 GU478587 n.a. n.a. Tapeinidium amboynense (Hook.) C.Chr. Dayton 26238 (BISH) Babeldaob, Palau GU478753 GU478441 GU478573 GU478642 GU478344 Tapeinidium moorei (Hook.) Hieron. Mackee 196 (AAU) New Caledonia GU478756 GU478445 n.a. n.a. n.a. APPENDIX 5 Taxon Locality Collector (Herbarium) rbcL trnL-trnL/F trnH-psbA Diphasium jussiaei (Desv. ex Poir.) Rothm. Ecuador Øllgaard 100615 (AAU) AJ133256 AJ133264 n.a. Diphasium jussiaei (Desv. ex Poir.) Rothm. Ecuador Rothfels 3601 (DUKE, QCA) n.a. n.a. KT749943 Huperzia appressa (Desv.) Á. Löve & D. Löve China Pan WJ0409048 (SHMU) DQ464220 n.a. DQ464203 Huperzia arctica (Tolm.) Sipliv. Norway -(-) n.a. GQ245031 n.a. Huperzia australiana (Herter) Holub Australia Field 1041 (BRI) JQ513908 JQ679088 JQ520368 Huperzia crispata (Ching) Ching China Pan WJ0509023 (SHMU) DQ464221 n.a. DQ464204 Huperzia emeiensis (Ching & H.S. Kung) Ching & H.S. Kung China Pan WJ409023 (SHMU) DQ464222 n.a. DQ464205 Huperzia fuegiana (Roiv.) Holub Chile Larrain 36361 (NY) n.a. n.a. KT749932 Huperzia haleakalae (Brack.) Holub Norway -(-) n.a. GQ245032 n.a. Huperzia lucidula (Michx.) Trevis. Canada Gerrath & A. Porr JAG607 (-) HQ590135 n.a. HQ596728 Huperzia lucidula (Michx.) Trevis. USA Eriksson 664 (GH) n.a. AJ224591 n.a. Huperzia miyoshiana (Makino) Ching Canada Rothfels 4483 (DUKE) DQ464225 n.a. n.a. Huperzia nanchuanensis (Ching & H.S. Kung) Ching & H.S. Kung China Pan WJ409101 (SHMU) DQ464226 n.a. DQ464209 Huperzia quasipolytrichoides (Hayata) Ching Papua New Guinea Sundue 3692 (BISH, NY) n.a. n.a. KT749933 Huperzia selago (L.) Bernh Norway Rouhan 1114 (P) to submit n.a. to submit Huperzia serrata (Thunb. ex Murray) Trevis. China Pan WJ409041 (SHMU) DQ464228 n.a. n.a. Huperzia somae (Hayata) Ching Taiwan TNS:776522 AB574640 n.a. AB575316 Huperzia suberecta (Lowe) Tard. Portugal Rouhan 1043 (P) to submit n.a. to submit Huperzia sutchueniana (Herter) Ching China Pan JSG0504192 n.a. n.a. DQ464212 Isoetes flaccida Shuttlew. USA -(WTU) GU191333 n.a. n.a. Lycopodiella inundata (L.) Holub Sweden Waantorp & N. Wikstrom s.n. (S) Y07938 AJ224605 AB575308 Phlegmariurus ambrensis (Rakotondr.) A.R.Field & Bauret comb. ined. Madagascar Janssen 2469 (P) to submit to submit to submit Phlegmariurus attenuatus (Spring) B. Øllg. Costa Rica Testo 167 (VT) KT634232 n.a. KT749924 Phlegmariurus balansae (Herter) A.R. Field & Bostock New Caledonia Wikstrom 243 (S) n.a. AJ224553 n.a. Phlegmariurus bampsianus (Pichi-Serm.) A. R.Field & Bostock Rwanda Bamps 2964 (P) n.a. n.a. Phlegmariurus lockyeri (D. Jones & B. Gray) A.R. Field & Australia Field 1025 (BRI) n.a. Phlegmariurus squarrosus (G. Forst.) Á. Löve & D. Löve China Pan WJ207111 (SHMU) DQ464235 n.a. n.a. Phlegmariurus varius (R. Br.) A.R. Field & Bostock New Zealand Wikstrom 259 (S) to submit to submit n.a. AJ224551 JQ663828 Bostock to submit Phlegmariurus brassii (Copel.) A.R. Field & Bostock Papua New Guinea Field 89 ex Rawlins, O. s.n. (CNS) n.a. n.a. JQ520372 Phlegmariurus campianus (B. Øllg.) B. Øllg. Ecuador Øllgaard 100612 (AAU) X98282 AJ224586 n.a. Phlegmariurus capellae (Herter) B. Øllg. Ecuador Øllgaard 100835 (AAU) n.a. AJ224570 n.a. Phlegmariurus carinatus (Desv.) Ching Australia Field 969 (BRI) DQ464229 JQ679090 JQ520363 Phlegmariurus cavifolius (C.Chr.) A.R.Field & Bostock Madagascar Janssen 2528 (P) to submit to submit to submit Phlegmariurus cf. obtusifolius (P. Beauv.) A.R.Field & Bostock Madagascar Bauret et al. 153 (P) to submit to submit to submit Phlegmariurus cf. phlegmaria (L.) T. Sen & U. Sen Papua New Guinea Field 700 ex Mason, M. s.n. (CNS) n.a. n.a. to submit Phlegmariurus compactus (Hook) B. Øllg. Ecuador Wikstrom 271 (S) n.a. AJ224571 n.a. Phlegmariurus crassus (Humb. & Bonpl. ex Willd.) B. Øllg. Ecuador Øllgaard 100832 (AAU) n.a. AJ224572 n.a. Phlegmariurus cryptomerinus (Maxim.) Satou Japan --(TNS) AB574628 n.a. AB575305 Phlegmariurus cumingii (Nessel) B. Øllg. Ecuador Øllgaard 100836 (AAU) Y07930 AJ224578 n.a. Phlegmariurus dacrydioides (Baker) A.R. Field & Bostock Tanzania Mantelow 91452 (S) n.a. AJ224562 n.a. Phlegmariurus dalhousieanus (Spring) A.R. Field & Bostock Australia Field 766 (BRI) n.a. n.a. JQ520367 Phlegmariurus dentatus (Herter) Arana Portugal Rouhan et al. 1032 (P) to submit to submit to submit Phlegmariurus dichaeoides (Maxon) B. Øllg. Panama Sundue 3229 (COL, NY, VT) n.a. KT634236 n.a. Phlegmariurus dichotomus (Jacq.) W.H. Wagner Mexico Eliasson 538 (S) n.a. AJ224567 n.a. Phlegmariurus elmeri (Herter) A.R. Field & Bostock Philippines Field 816 ex Rawlins, O. s.n. (CNS) n.a. n.a. Phlegmariurus ericifolius (C. Presl) B. Øllg. Ecuador Wikstrom 286 (S) n.a. AJ224587 n.a. Phlegmariurus eversus (Poir.) B. Øllg. Ecuador Øllgaard 100620 (AAU) n.a. AJ224579 Phlegmariurus fargesii (Herter) Ching Japan Yahara et al. 398 (TNS) AB574629 n.a. Phlegmariurus foliosus (Copel.) A.R. Field & Bostock Fiji Field 19 ex Rawlins s.n. (CNS) n.a. n.a. Phlegmariurus fordii (Baker) Ching Japan --(TNS) Phlegmariurus funiformis (Cham. ex Spring) B. Øllg. Panama Asplund 19290 (S) n.a. AJ224560 n.a. Mantelow 91135 (S) n.a. AJ224590 n.a. Phlegmariurus sp1 "ulicifolius" Comoros Pignal 3396 (P) to submit to submit to submit Phlegmariurus varius (R. Br.) A.R. Field & Bostock Australia Field 1043 (BRI) JQ679089 JQ672503 JQ663831 AB574630 AJ224548 AB575307 Phlegmariurus linifolius (L.) B. Øllg. Ecuador Werff 19390 (MO) Y07932 AJ224569 n.a. Phlegmariurus sp1 "ulicifolius" Comoros Bidault 107 (P) to submit to submit to submit Phlegmariurus unguiculatus (B. Øllg.) B. Øllg. Ecuador Wikstrom 264 (S) n.a. AJ224582 n.a. JQ663817 Phlegmariurus lindenii (Spring) B. Øllg. Ecuador Øllgaard 100831 (AAU) n.a. AJ224585 n.a. Congo Phlegmariurus trigonus (C.Chr.) A.R.Field & Bostock Madagascar Janssen 2458 (P) to submit to submit to submit AB575306 Phlegmariurus lehnertii Testo Burma Field 851 ex Liddle s.n. (CNS) n.a. n.a. JQ663840 Phlegmariurus sooianus LawaIrée Republic of the Léonard 718 (P) n.a. n.a. to submit Phlegmariurus trifoliatus (Copel.) A.R.Field & Bostock Vanuatu Rouhan et al. 660 (P) to submit to submit to submit n.a. Phlegmariurus lecomteanus (Nessel) A.R.Field & Bostock Madagascar Rouhan et al. 1643 (P) Phlegmariurus ledermannii (Herter) A.R. Field & Bostock Australia Field 1001 (BRI) n.a. n.a. JQ663816 Phlegmariurus sieboldii (Miq.) Ching Japan Yahara et al. 176 (TNS) AB574638 to submit AJ224549 Democratic Phlegmariurus tetrastichus (Kunze) A.R. Field & Bostock Papua_New_Gui nea Field 815 ex Stocker s.n. (CNS) n.a. 613 (116 indels) n.a. to submit to submit to submit JQ663836 Field & Bostock Madagascar Rouhan et al. 454 (P) to submit n.a. to submit Phlegmariurus goebelii (Nessel) A.R. Field & Bostock Malaysia Field 2742 (CNS) n.a. n.a. JQ663822 Phlegmariurus heteroclitus (Desv. ex Poir.) B. Øllg. Ecuador Lenhert 1851 (VT) KT634230 n.a. KT749920 Phlegmariurus hippurideus (Christ) B. Øllg. Ecuador Øllgaard 100619 (AAU) Y07931 AJ224566 n.a. Phlegmariurus hippuris (Desv. ex Poiret) A.R. Field & Testo Indonesia Wikstrom et al. 157 (S) AJ133895 AJ224550 n.a. Phlegmariurus holstii (Hieron.) A.R. Field & Bostock Tanzania Mantelow 91163 (S) n.a. AJ224563 n.a. Phlegmariurus horizontalis (Nessel) A.R. Field & Bostock Indonesia Waantorp s.n. (S) n.a. AJ224559 n.a. Phlegmariurus humbertii (Nessel) A.R.Field & Bostock Madagascar Bauret et al. 180 (P) to submit to submit to submit Phlegmariurus humbertii (Nessel) A.R.Field & Bostock Madagascar Bauret et al. 180b (P) to submit to submit to submit Phlegmariurus humbertii (Nessel) A.R.Field & Bostock Madagascar Rakotondrainibe 3806 (P) to submit n.a. to submit Phlegmariurus humbertii-henrici (Herter) A.R.Field & Bostock Madagascar Razafitsalama 671 (P) to submit n.a. to submit Phlegmariurus hystrix (Herter) B. Øllg. Ecuador Wikstrom 294 (S) n.a. AJ224574 n.a. Phlegmariurus ignambiensis (Compton) A.R.Field & Testo Papua New Guinea Field 714 ex Clements s.n. (CANBG) n.a. n.a. to submit Phlegmariurus jaegeri (Herter) A.R.Field & Bostock Guinea Schnell 5614 (P) n.a. n.a. to submit Phlegmariurus jaegeri (Herter) A.R.Field & Bostock Liberia Jaeger 9642 (P) to submit to submit to submit Phlegmariurus lauterbachii (E. Pritz. ex K. Schum. & Lauterb.) A.R. Field & Bostock Papua New Guinea Field 770 ex Kenning s.n. (CNS) n.a. n.a. JQ663820 Phlegmariurus lecomteanus (Nessel) A.R.Field & Bostock Madagascar Rouhan et al. 1578 (P) to submit to submit to submit Phlegmariurus marsupiiformis (D. Jones & B. Gray) A.R. Field & Bostock Australia Field 1023 (BRI) n.a. to submit JQ663811 Phlegmariurus megastachyus (Bak.) A.R.Field & Bostock Madagascar Rakotondrainibe 6333 (P) Field & Bostock Madagascar Rouhan et al. 1201 (P) to submit to submit to submit Field & Bostock Madagascar Janssen 2780 (P) to submit to submit to submit Madagascar Janssen 2459 (P) to submit to submit to submit to submit to submit to submit Phlegmariurus megastachyus (Bak.) A.R.Field & Bostock Madagascar Janssen 2468 (P) Phlegmariurus perrierianus (Tard.) A.R.Field & Bostock Madagascar Rakotomalala 238 (P) n.a. n.a. to submit Phlegmariurus strictus (Baker) A.R.Field & Bostock Madagascar Rouhan et al. 1396 (P) to submit n.a. to submit Phlegmariurus verticillatus (L.f.) A.R. Field & Testo Reunion Hennequin 263 (P) to submit to submit to submit to submit to submit to submit Phlegmariurus megastachyus (Bak.) A.R.Field & Bostock Madagascar Janssen 2621 (P) to submit to submit to submit Phlegmariurus megastachyus (Bak.) A.R.Field & Bostock Madagascar Rouhan et al. 1229 (P) Phlegmariurus petiolatus (C. B. Clarke) H. S. Kung & Li Bing Zhang China Pan WJ107181 (SHMU) DQ464233 n.a. DQ464217 Phlegmariurus subtrifoliatus (Brownlie) A.R.Field & Bostock Vanuatu Rouhan et al. 595 (P) Phlegmariurus verticillatus (L.f.) A.R. Field & Testo Indonesia Wikstrom N. et al. 156 (S) AJ133897 AJ224561 n.a. to submit to submit to submit Phlegmariurus wilsonii (Underw. & F.E. Lloyd) B. Øllg. Ecuador Øllgaard, B. 1700 (AAU) Y07933 AJ224565 n.a. to submit to submit to submit Phlegmariurus phlegmaria (L.) T. Sen & U. Sen Australia Field 22 (CNS) n.a. n.a. to submit Phlegmariurus subulatus (Desv. ex Poir.) B. Øllg. Ecuador Øllgaard 100618 (AAU) n.a. AJ224589 n.a. Phylloglossum drummondii Australia Waycott & Calladine s.n. (AD) Y07939 AJ224593 to submit Phlegmariurus megastachyus (Bak.) A.R.Field & Bostock "curiosus-like" Madagascar Rouhan et al. 1558 (P) to submit to submit to submit Phlegmariurus megastachyus (Bak.) A.R.Field & Bostock "curiosus-like" Madagascar Rouhan et al. 1559 (P) Phlegmariurus mingcheensis Ching China Pan WJ112127 (SHMU) DQ464232 n.a. Phlegmariurus mirabilis (Willd.) A.R.Field & Testo Australia Field 717 (BRI) n.a. n.a. Phlegmariurus nummulariifolius (Blume) Ching Phlegmariurus obtusifolius (P. Beauv.) A.R.Field & Bostock Madagascar Bauret et al. 163 (P) to submit to submit to submit Phlegmariurus obtusifolius (P. Beauv.) A.R.Field & Bostock Madagascar Rouhan et al. 1577 (P) to submit to submit to submit Phlegmariurus obtusifolius (P. Beauv.) A.R.Field & Bostock Madagascar Bauret et al. 158 (P) to submit n.a. to submit Phlegmariurus obtusifolius (P. Beauv.) A.R.Field & Bostock Madagascar Rouhan et al. 1580 (P) to submit n.a. to submit Phlegmariurus obtusifolius (P. Beauv.) A.R.Field & Bostock Madagascar Janssen 2471 (P) to submit to submit to submit Phlegmariurus obtusifolius (P. Beauv.) A.R.Field & Bostock Madagascar Janssen 2876 (P) to submit to submit to submit Phlegmariurus obtusifolius (P. Beauv.) A.R.Field & Bostock Madagascar Rouhan et al. 1399 (P) to submit n.a. Phlegmariurus saururus (Lam.) B. Øllg. Kerguelen Chambrin 4 (P) to submit to submit to submit Phlegmariurus schlechteri (E. Pritz.) A.R. Field & Bostock New Zealand Field 658 ex Ziesing 63 (CANBG) n.a. n.a. JQ663823 A.R.Field & Bostock Australia Field 822 (BRI) n.a. n.a. to submit Phlegmariurus tetrastichoides (A.R.Field & Bostock) to submit Phlegmariurus pseudophlegmaria (Nessel) A.R. Field & Testo Fiji Field 632 ex Hilder, R. s.n. (CNS) n.a. n.a. Phlegmariurus reflexus (Lam.) B. Øllg. Mexico Sundue 3089 (AAU) KT634233 n.a. Phlegmariurus rosenstockianus (Herter) B. Øllg. Ecuador Branbyge 42178 (S) n.a. AJ224583 Phlegmariurus rufescens (Hook.) B. Øllg. Ecuador Øllgaard 100833 (AAU) n.a. AJ224576 Phlegmariurus salvinioides (Hert.) Ching Malaysia Field 51 ex Rawlins s.n. (CNS) n.a. n.a. Phlegmariurus sarmentosus (Spring) B. Øllg. Ecuador Øllgaard 100816 (AAU) n.a. AJ224584 n.a. Phlegmariurus tetragonus (Hook. & Grev.) B. Øllg. ECUADOR Ecuador Wikstrom, N. 301 (S) n.a. AJ224577 n.a. JQ663819 Phlegmariurus tenuis (Humb. & Bonpl. Ex Willd.) B. Øllg. Ecuador Øllgaard 100817 (AAU) n.a. AJ224568 n.a. n.a. Phlegmariurus tauri (Herter) A.R. Field & Testo Indonesia Wikstrom N. et al. 151 (S) n.a. AJ224556 n.a. n.a. Phlegmariurus tardieuae (Herter) A.R.Field & Testo Comoros Viscardi 195 (P) to submit to submit to submit KT749925 Phlegmariurus tardieuae (Herter) A.R.Field & Testo Madagascar Rouhan et al. 1302 (P) to submit to submit to submit JQ663837 Maurice Hennequin 341 (P) to submit to submit to submit inea Forster & Liddle s.n. (BRI) n.a. n.a. JQ663824 Phlegmariurus proliferus (Bl.) A.R.Field & Bostock Vanuatu Rouhan et al. 607 (P) to submit to submit to submit Indonesia_PNGu Phlegmariurus polydactylus (B. Øllg.) B. Øllg. Ecuador Øllgaard 100834 (AAU) n.a. AJ224575 n.a. to submit Phlegmariurus piscius comb. Ined. Australia Field 2690 (BRI) n.a. n.a. to submit DQ464216 Phlegmariurus pichianus (Tard.) A.R.Field & Bostock Madagascar Janssen 2451 (P) to submit to submit to submit to submit to submit to submit Phlegmariurus phlegmaria (L.) T. Sen & U. Sen Japan --(TNS) AB574635 n.a. AB575311 Phlegmariurus phlegmarioides (Gaudich.) A.R. Field & Bostock New Caledonia Wikstrom 238 (S) AJ133896 AJ224554 Phlegmariurus talamancanus (B. Øllg.) B. Øllg. Costa Rica Testo 171 (AAU) KT634231 KT634234 KT749921 Phlegmariurus tardieuae (Herter) A.R.Field & Testo Comoros Loup 628 (P) to submit to submit to submit Selaginella moellendorffii Hieron. --(-) HM17308 n.a. n.a. 0 n.a. Selaginella selaginoides (L.) P. Beauv. ex Mart. & Schrank Canada Therrien s.n. (KANU) AF419048 n.a. n.a.

Madagascar apporte de nouveaux éléments à la systématique et la biogéographie des fougères grammitides : découverte de nouvelles lignées, et inférence de nombreux évènements de dispersion à longue distance.

  Plus de 12 000 espèces de plantes vasculaires y sont recensées, dont plus de 10 000 espèces d'angiospermes et environ 600 espèces de fougères, caractérisées par un endémisme d'environ 45%. L'exceptionnelle biodiversité de Madagascar est notamment expliquée par la diversité de ses écosystèmes, favorisée par un gradient d'humidité augmentant d'ouest en est et généré par les pluies d'origine orographique sur la côte est. Les forêts tropicales humides ne se forment ainsi que le long de la côte est.Madagascar est d'origine gondwanienne, et s'est séparée de l'Afrique il y a 165 millions d'années (Ma) puis de l'Inde il y a 90 Ma. Pourtant, la flore la faune semblent être majoritairement plus récentes et issues de dispersions durant le Cénozoïque (ces 66 derniers millions d'années), majoritairement en provenance du continent africain. L'étude de la flore s'étant cependant fondée majoritairement sur les angiospermes, les origines biogéographiques d'autres groupes, comme les fougères, restent mal connues.Malgré leur origine ancienne de plus de 300 millions d'années, les données disponibles sur les fougères actuelles semblent montrer une colonization récente de Madagascar, après sa séparation de l'Afrique et de l'Inde. Trois sources de dispersion ont été mises en évidence : les néotropiques, l'Afrique et l'Asie tropicale (au sens large, incluant l'Asie continentale et le sud-est asiatique jusqu'en Australasie), mais sans dominance de l'Afrique par rapport aux autres sources. Cependant, relativement peu de données sont disponibles pour confirmer cette tendance. Quelles sont les sources de dispersion et leur importance relative ? Quel est l'âge des lignées malgaches ? Peut-on corréler les évènements de dispersion avec des évènements climatiques et géologiques ayant eu lieu à Madagascar et dans d'autres régions du monde ?Pour répondre à ces questions, quatre groupes de fougères ont fait l'objet d'une étude biogéographique : les sous-familles de fougères grammitides et blechnoides, les genres Rumohra et Lindsaea-Odontosoria, ainsi qu'un genre de lycophytes Phlegmariurus qui fournit un réplica phylogénétique dans une autre lignée de plantes vasculaires à spores. L'histoire biogéographique des lignées malgaches au sein de ces groupes a été reconstruite, à partir de phylogénies moléculaires mondiales dont l'échantillonnage a été amélioré par l'ajout des espèces malgaches, de datations moléculaires, ainsi que de l'estimation des aires ancestrales. Les résultats concernant chaque groupe ont été développé dans cinq chapitres qui sont ici brièvement résumés. Trois nouveaux clades incluant des espèces des genres Grammitis s.l., Ctenopterella et Enterosora ont été observés. Les résultats montrent que Grammitis s.s. est monophylétique et que Ctenopterella et Enterosora sont polyphylétiques. Le genre néotropical Moranopteris est désormais connu à Madagascar par la découverte d'une nouvelle espèce sur l'île. Les résultats mettent en évidence plusieurs lignées cryptiques, probablement expliquées par homoplasie morphologique. Les résultats permettent d'identifier au moins 12 dispersions vers la région Afrique-OOI durant les 20 derniers millions d'années, principalement depuis les néotropiques. L'Asie tropicale s.l. n'aurait joué qu'un rôle mineur via une dispersion à la fin de l'Oligocène. De nombreuses dispersions depuis Madagascar vers d'autres régions (en particulier vers l'Afrique et d'autres îles de l'Océan Indien) et des diversifications in situ sont également à noter.

	Chapitre I -Chapitre II -

Des données moléculaires, basées sur un échantillonnage exhaustif des fougères Rumohra (Dryopteridaceae), révèlent une histoire biogéographique marquée par des dispersions à longue distance et plusieurs espèces cryptiques au sein de Rumohra adiantiformis.

  Rumohra adiantiformis, à large répartition au sein de l'hémisphère sud, est hautement polyphylétique. L'absence de caractères morphologiques distinctifs entre les lignées suggère un complexe d'espèces cryptiques. De telles divergences moléculaires non retrouvées sur le plan morphologique peuvent être expliquées par hybridation, convergence morphologique ou (plus probablement ici) par stase morphologique.Le genre Rumohra aurait divergé de Megalastrum dans les néotropiques il y a environ 46 Ma et se serait diversifié il y a 11 Ma environ. Sept dispersions à longue distance expliqueraient la répartition actuelle du groupe dans l'hémisphère sud dont trois depuis les Néotropiques vers l'Afrique, Madagascar et la région australe de l'Amérique du Sud. Les trois espèces endémiques de Madagascar seraient issues d'une diversification in situ durant les deux derniers millions d'années.

	Chapitre III -

Histoire biogéographique des Blechnoideae à Madagascar : mise en évidence de connexions avec les régions tropicales de l'hémisphère sud et de deux diversifications in situ.

  Le placement phylogénétique des espèces malgaches confirment leur récente classification dans les genres Blechnum, Lomaridium, Lomariocycas et Parablechnum, mais pas Austroblechnum. La polyphylie de Lomaridum attenuatum, avec une lignée composée uniquement de spécimens des Mascareignes, suggère la présence d'espèces cryptiques.

L'origine biogéographique des lignées malgaches est rendue confuse par d'importantes connexions biogéographiques entre les régions tropicales de l'hémisphère sud.

Oreogrammitis forbesiana (W. H.

Madagascar est une île continentale de l'Océan Indien, au large de l'Afrique. C'est également un point chaud de biodiversité, hébergeant plus de 12 000 espèces de plantes vasculaires, dont plus de 600 espèces de fougères caractérisées par un endémisme dépassant les 45%. L'Afrique continentale n'héberge en comparaison que 800 espèces. Comment peut-on expliquer une telle concentration de biodiversité à Madagascar ? Quelles sont les origines biogéographiques des fougères malgaches ? L'apport de nouvelles données et la littérature préexistante permettent de proposer ici des hypothèses sur l'histoire biogéographique des fougères de Madagascar. Quatre groupes de fougères ont fait l'objet d'une étude biogéographique : les sous-familles de fougères grammitides et blechnoides, les genres Rumohra et Lindsaea-Odontosoria, ainsi qu'un genre de lycophytes, Phlegmariurus, représentant un réplica dans une autre lignée de plantes vasculaires à spores. L'histoire biogéographique des lignées malgaches au sein de ces groupes a été reconstruite, à partir de phylogénies moléculaires mondiales complétées par les espèces malgaches, de datations moléculaires, ainsi que de l'estimation des aires ancestrales. Bien que Madagascar soit d'origine ancienne, gondwanienne, les résultats des analyses biogéographiques montrent que les fougères et les lycophytes auraient colonisé Madagascar après son isolement, durant le Cénozoïque (< 66 Ma), depuis les néotropiques (Amérique du Sud) l'Afrique et l'Asie tropicale (au sens large, incluant l'Asie continentale et le sud-est asiatique jusqu'en Australasie). En particulier, de nombreuses dispersions ont été observées à partir du Miocène (< 23 Ma). Ces résultats seraient expliqués par une combinaison d'événements au Cénozoïque (formation des forêts tropicales humides Malgaches, formation de courants éoliens permettant la dispersion par spores) et des préférences écologiques des fougères et des lycophytes pour les forêts tropicales humides d'altitude, s'étant formées à partir du Miocène dans les régions sources.

Acknowledgments

We thank Drs. B. Senterre, D. Middleton and S. Lindsay for providing leaf material; T. Cheminel and I. Fabre for their help in the lab; and Dr. M. S. Vorontsova and another, anonymous reviewer for their valuable comments on an earlier version of the manuscript.

ACKNOWLEDGMENTS

We thank P. Danton, M. Kessler, N. Rendell, E. Santiago Valentin, A. Stanworth, J.M. Tamon, and H. Väre for providing leaf material. We thank the Editor and two anonymous reviewers for helpful comments on an earlier version of the manuscript. Collecting permits in Madagascar were granted by Madagascar National Parks and the Ministère de l'Environnement, de l'Ecologie et des Forêts. We are also grateful, for field assistance, to CNRE-Madagascar, MBG-Madagascar and CNDRS-Comoros (especially Y. Ibrahim). We acknowledge funding from the ATM MNHN 'Emergence des clades, des biotes et des cultures', ATM MNHN 'Taxonomie moléculaire, DNA Barcode & gestion durable des collections' and the FRB project 'Connaître pour conserver : le patrimoine naturel caché des Comores'. This project was also supported by the 'Service de Systématique Moléculaire' (UMS2700 MNHN/CNRS), and the network 'Bibliothèque du Vivant' funded by the CNRS, the MNHN, the INRA and the CEA (Centre National de Séquençage). All molecular work was performed at the BoEM laboratory of the MNHN.

Chapter V -First insights on the biogeographical history of Phlegmariurus (Lycopodiaceae), with a focus on Madagascar

Lucie Bauret a,b,* , Ashley R. Field c,* , Myriam Gaudeul a , Marc-André Selosse Fully detailed majority rule consensus phylogram of grammitids recovered from the BI based on the combined dataset (atpB, rbcL, trnG-trnR, trnL-trnF and rps4-trnS). Unless mentioned next to the nodes, support values were BS≥95 and PP≥0.95. Non-monophyletic species are highlighted in bold and color. Vouchers are indicated when several samples were included for the same species. Genera names are on the right, followed by (number of species analyzed / number of samples included), as in Fig. 1.

Available online:

http://www.sciencedirect.com/science/article/pii/S1055790317301860?via%3Dihub

APPENDIX 2

Herbarium vouchers and GenBank accession numbers (Rumohra). Newly generated sequences are indicated with an asterisk.

Species

Abstract

Madagascar is a continental island in the Indian Ocean, near African coasts. It is also a biodiversity hotspot, comprising more than 12,000 species of vascular plants and including more than 600 fern species with an endemism reaching the 45%. Comparatively, continental Africa comprises only 800 species. How can such a diversity be explained in Madagascar? What are the biogeographical origins of the Malagasy ferns? Thanks to new data combined to the literature, hypotheses on the biogeographical history of Malagasy ferns are here proposed. Four fern taxa were newly investigated: grammitid and blechnoid subfamilies, Rumohra and Lindsaea-Odontosoria, as well as Phlegmariurus, a genus of lycophytes considered as a phylogenetic replicate in another vascular spore-bearing plant lineage. The biogeographical history of the Malagasy lineages was inferred, based on worldwide molecular phylogenies completed by Malagasy species, molecular dating and ancestral area estimates. Despite its Gondwanian origin, ferns and lycophytes would have colonized Madagascar after its isolation, during the Cenozoic (< 66 Ma), from the Neotropics (South America), Africa and tropical Asia s.l. (meaning from continental Asia to Southeast Asia and Australasia). Dispersal events were especially inferred from the Miocene (< 23 Ma). These results could be explained by the combination of events during the Cenozoic (establishment of the Malagasy rainforests, onset of wind currents allowing spore dispersal) and ecological preferences of ferns and lycophytes for elevated tropical rainforests that have established from the Miocene in the source regions.

Résumé