Mehdi Adjeroud

Sophie Arnaud-Haond

Pim Bongaerts

Pierre Chevaldonné

Claude Miaud

Lorenzo Zane

Yannick Chancerelle

Pascal Ung

Gilles Siu

Benoit Espiau

Cécile Berthe

Christine Sidobre

Elina Burns

Aurélie Mariotti

Peter Esteve

Fabien Morat

Joaquim Claudet

Rita Sayoun

Laetitia Hedouin

Suzanne Mills

Ricardo Beldade

Maggy Nugues

Valeriano Parravicini

Gaël Lecellier

David Lecchini

Pierre Sasal

Bruno Delesalle

Catherine Gobin

René Galzin

Erwan Delrieu-Trottin

Valentina Neglia

! To

Océane Salles

Mélodie Dubois

Louis Bornancin

Lauric Thiault

Noa Nukamura

Antoine Puisay

USR Caroline E Dubé
email: caroline.dube.qc@gmail.com

Alexandre Mercière

Mark J A Vermeij

Serge Planes

Criobe

Emilie Boissin

Population Structure of the Hydrocoral Millepora platyphylla in Habitats Experiencing Different Flow Regimes in Moorea, French Polynesia

Keywords: Reproduction, Clonal dispersal, Genetic diversity, Morphology, Wave energy, Millepora Dispersal, Self-recruitment, Sibling aggregations, Clones, Microsatellites, Millepora Mosaicism, Chimerism, Microsatellites, Habitat, Reproductive strategies, Morphology

Emilie Boissin who taught me so much during the last three years. I would like to give her many thanks, not only for her availability

LIST OF FIGURES Fig. 1.1 Grime's triangle of life history strategies applied to reef corals from [START_REF] Darling | Evaluating life-history strategies of reef corals from species traits[END_REF] Principal Coordinates ordination of 143 coral species with four life history strategies (red: competitive, green: weedy, blue: stress-tolerant, grey: generalist). Arrows indicate trait loadings and traits are numbered from most important to least important in differentiating the life history strategies: (1) domed morphology (2) growth rate (3) brooding reproduction (4) fecundity (5) broadcast spawning reproduction (6) branching morphology (7) colony size (8) skeletal density (9) plating morphology (10) corallite diameter ( 11 Frequencies (%) for each size class were averaged by habitats with total population size (N in Table S2) and error bars show the standard error for transect replicates. .................................. 54 Fig. 3.5 Recruitment dynamics across the five surveyed habitats. Proportions of recruits (< 1 cm 2 ), juveniles (1-20 cm 2 ) and adults (> 20 cm 2 ) were averaged by habitats with total population size (N in Table S2) and error bars show the standard error for transect replicates. Similar data based on Spearman ranking, with each vector having lengths ≥ 0.4: density, cover, distribution index, mean neighborhood distance, mean height and size of adults, and proportion of recruits (< 1 cm 2 ), juveniles (1-20 cm 2 ) and adults (> 20 cm 2 ). The second transect of the fringing reef is shown as a single group mostly related to a small population size (i.e. 27 colonies, Table S2) S3. One full sib relationship was found for P1 and an unknown parent with a distance of and parentage assignments across the three surveyed habitats at Moorea. Number of colonies surveyed (# col), number of adults (# adu, > 20 cm 2 ) and number of juveniles (# juv, < 20 cm 2 ) are given. Percentages give the proportions of juveniles within that habitat that were i) offspring of parents sampled at the same habitat (SR = self-recruitment), ii) offspring of parents sampled at other habitats (HC = habitat connectivity), or iii) were not assigned to parents sampled within the entire area surveyed (UA = unassigned). ..................................... 127 Table 6.2 Summary results of parentage analysis in Millepora platyphylla within the entire reef area (9000 m 2 ). Characteristics of parents contributing to self-recruitment and comparisons between clonal and single genotype parents are given: number of potential parents surveyed in the study area; number of parents assigned to an offspring within the surveyed area with their mean colony size (cm²), standard error (SE) and median; total number of assigned offspring and mean number of assigned offspring to one single parent with standard error (SE), maximum and median. All values are presented at the genet level (i.e. without clonal replicates).

Estimates of offspring dispersal within the study area are shown: mean distance between the parent and their assigned offspring with standard error (SE), minimum, maximum and median. Although coral reefs were formed only 230 million years ago [START_REF] Veron | Corals in space and time:the biogeography and evolution of the Scleractinia[END_REF] and are largely limited to warm shallow waters, they have succeeded in becoming one of the most productive and diverse ecosystem on Earth [START_REF] Hughes | Climate change, human impacts, and the resilience of coral reefs[END_REF]. Often called the rainforest of the sea due to their outstanding biodiversity, coral reefs only cover less than 0.1% of the ocean seafloor [START_REF] Spalding | New estimates of global and regional coral reef areas[END_REF][START_REF] Copper | Ancient reef ecosystem expansion and collapse[END_REF] or approximately 5% that of rainforest [START_REF] Ml | The global biodiversity of coral reefs: a comparison with rain forests[END_REF]. Coral reefs thrive under nutrient-poor and oligotrophic waters [START_REF] Odum | Trophic structure and productivity of a windward coral reef community on Eniwetok Atoll[END_REF][START_REF] Hatcher | Coral reef primary productivity. A hierarchy of pattern and process[END_REF][START_REF] Atkinson | Biogeochemistry of Marine Systems[END_REF], but yet harbor more than 25% of all marine species [START_REF] Mcallister | What is the status of the world's coral reef fishes?[END_REF][START_REF] Knowlton | Coral reef biodiversity[END_REF]. This paradoxal ecosystem is sustained through efficient nutrient recycling strategies developed by corals [START_REF] Wild | Coral mucus functions as an energy carrier and particle trap in the reef ecosystem[END_REF]) and algae [START_REF] Haas | Organic matter release by coral reef associated benthic algae in the Northern Red Sea[END_REF], the primary reef producers, and other key organisms, i.e. microbes [START_REF] Azam | The ecological role of water-column microbes in the sea[END_REF]) and sponges [START_REF] Goeij | Surviving in a marine desert: the sponge loop retains resources within coral reefs[END_REF].

In coral reef ecosystems, there are many calcifying benthic organisms that contribute to reef accretion and build the complex and massive tridimensional structure of reefs, among them scleractinian corals [START_REF] Bellwood | Regional-scale assembly rules and biodiversity of coral reefs[END_REF], hydrocorals [START_REF] Cairns | Worldwide distribution of the Stylasteridae (Cnidaria: Hydrozoa)[END_REF][START_REF] Lewis | Biology and ecology of the hydrocoral Millepora on coral reefs[END_REF]) and coralline algae [START_REF] Steneck | The ecology of coralline algal crusts: convergent patterns and adaptative strategies[END_REF]). These reef-building organisms are key components of coral reef health and biodiversity as they offer food and shelter for thousands of reef-dwelling organisms and fishes [START_REF] Bellwood | Coral bleaching, reef fish community phase shifts and the resilience of coral reefs[END_REF]). Nevertheless, coral reefs are increasingly threatened by chronic and acute stressors [START_REF] Bellwood | Confronting the coral reef crisis[END_REF]) and are expected to be highly vulnerable to future climate change due to rapidly increasing sea surface temperatures and ocean acidification [START_REF] Hoegh-Guldberg | Coral reefs under rapid climate change and ocean acidification[END_REF][START_REF] Pandolfi | Projecting coral reef futures under global warming and ocean acidification[END_REF]. Several reports on reef degradation and coral cover loss were related to their vulnerability to human impacts [START_REF] Gardner | Long-term region-wide declines in Caribbean corals[END_REF][START_REF] Bruno | Regional decline of coral cover in the Indo-Pacific: timing, extent, and subregional comparisons[END_REF][START_REF] De'ath | The 27-year decline of coral cover on the Great Barrier Reef and its causes[END_REF]. Human activities have altered both global (climate change associated with CO 2 emissions) and local reef health (e.g. poor water quality, over exploitation, destruction and invasive species) [START_REF] Lesser | Coral reef bleaching and global climate change: Can corals survive the next century[END_REF]. These antropogenic disturbances further change the biodiversity in coral reefs and hamper their capacity to deliver important sources of ecosystem services to more than 500 million people [START_REF] Wilkinson | Global Coral Reef Monitoring Network and Reef and Rainforest Research Center[END_REF][START_REF] Cardinale | Biodiversity loss and its impact on humanity[END_REF]. Because of the imminent disappearance of modern reefs, more information is needed to determine whether and how reef species can adapt and survive to such devastating disturbances.

Species' response to environmental changes

Because of the uncertainty on how coral reef ecosystems will respond to the inevitable increase of human activities and global change, evaluating life history of keystone species can benefit our ability to predict long-term consequences on community dynamics, a prerequisite for reef conservation [START_REF] Garrabou | A 20-year study on life-history traits of a harvested long-lived temperate coral in the NW Mediterranean: insights into conservation and management needs[END_REF][START_REF] Darling | Evaluating life-history strategies of reef corals from species traits[END_REF][START_REF] Darling | Life histories predict coral community disassembly under multiple stressors[END_REF]. Life history strategies describe the species traits in terms of their survival, growth and reproduction and define how they can interact with their surrounding environment [START_REF] Grime | The Evolutionary Strategies That Shape Ecosystems[END_REF]. Identifying species that may 'win' or 'lose' in the face of environmental changes remains a challenge. For instance, a recent trait-based classification approach has identified four life history strategies in scleractinian corals, the primary framework of coral reefs: competitive, weedy, stress tolerant and generalist, whereby colony morphology, growth rate and reproductive mode are the primary traits leading to these contrasting life histories (Darling et al. 2012, Fig. 1.1). Competitive species are dominant in productive environments, weedy species are found in recently disturbed environments and stress tolerant species can succeed in harsh environments. Such classification was based on interspecific variation in phenotypic traits at a global scale, although the combination of phenotypic and genetic data can provide additional information on species' life history strategies in response to local stress, e.g. growth, morphological plasticity, clonal propagation and dispersal patterns. Several important environmental gradient (temperature, light, wave and water quality condition) and disturbances (storms and eutrophication) occur over a relatively small spatial scale within reefs [START_REF] Glynn | Coral reef bleaching: facts, hypotheses and implications[END_REF][START_REF] Vermeij | How are coral populations structured by light? Marine light regimes and the distribution of Madracis[END_REF][START_REF] Nugues | Partial mortality in massive reef corals as an indicator of sediment stress on coral reefs[END_REF][START_REF] Fabricius | Effects of terrestrial runoff on the ecology of corals and coral reefs: review and synthesis[END_REF][START_REF] Monismith | Hydrodynamics of coral reefs[END_REF]). More information on species' life history traits in populations exposed to local environmental and/or anthropogenic stress is thus needed.

Overview of life history traits in colonial reef species

Reproductive strategies

Although only a few species are exclusively reproducing asexually, clonality has evolved repeatedly in many reef organisms [START_REF] Highsmith | Reproduction by fragmentation in corals[END_REF][START_REF] Jackson | Modes of dispersal of clonal benthic invertebrates: consequences for 4 species' distributions and genetic structure of local populations[END_REF][START_REF] Sherman | Asexual reproduction does not produce clonal populations of the brooding coral Pocillopora damicornis on the Great Barrier Reef, Australia[END_REF][START_REF] Foster | Hurricane-driven patterns of clonality in an ecosystem engineer: the Caribbean coral Montastraea annularis[END_REF]. In coral reef ecosystems, there are many organisms that can reproduce through both sexual and asexual reproduction, among which scleractinian corals [START_REF] Harrison | Sexual reproduction of scleractinian corals[END_REF]) and coralline algae [START_REF] Pearson | Patterns of reproduction, genetic diversity, and genetic differentiation in California populations of the geniculate coralline alga Lithothrix aspergillum (Rhodophyta)[END_REF] are the major reef-builders, in addition to sea anemones [START_REF] Sherman | Fine-scale adaptation in a clonal sea anemone[END_REF], gorgonians [START_REF] Kahng | Sexual reproduction in octocorals[END_REF]) and sponges [START_REF] Whalan | Mode of reproduction, recruitment, and genetic subdivision in the brooding sponge Haliclona sp[END_REF]. Asexual reproduction produces genetically identical offspring, often leading in local populations dominated by few adapted clones [START_REF] Miller | The role of sexual and asexual reproduction in structuring high latitude populations of the reef coral Pocillopora damicornis[END_REF][START_REF] Gorospe | Genetic relatedness does not retain spatial pattern across multiple spatial scales: dispersal and colonization in the coral, Pocillopora damicornis[END_REF][START_REF] Baums | Marginal coral populations: the densest known aggregation of Pocillopora in the Galapagos Archipelago is of asexual origin[END_REF]). In the contrary, sexual reproduction enables genetic recombination and production of genetically diverse propagules, thus generating the genotypic variation required for adaptation [START_REF] Rice | Sexual recombination and the power of natural selection[END_REF] and colonization of new habitats [START_REF] Williams | Sex and evolution[END_REF]. In many colonial reef organisms, asexual reproduction can occur through fragmentation, fission, budding, polyp expulsion or polyp bail-out [START_REF] Brazeau | Sexual reproduction and external brooding by the Caribbean gorgonian Briareum asbestinum[END_REF][START_REF] Ereskovsky | Asexual reproduction in homoscleromorph sponges (Porifera; Homoscleromorpha)[END_REF][START_REF] Reitzel | Comparison of developmental trajectories in the starlet sea anemone Nematostella vectensis: embryogenesis, regeneration, and two forms of asexual fission[END_REF][START_REF] Harrison | Sexual reproduction of scleractinian corals[END_REF].

Sexual reproduction often involved a wide range of reproductive strategies, i.e. gonochorism, hermaphroditism, internal (brooders) and external fertilization (spawners) [START_REF] Gutiérrez-Rodríguez | Reproductive biology, development, and planula behavior in the Caribbean gorgonian Pseudopterogorgia elisabethae[END_REF][START_REF] Harrison | Sexual reproduction of scleractinian corals[END_REF]. Because each reproductive mode confers different advantages under variable environmental conditions [START_REF] Williams | Sex and evolution[END_REF][START_REF] Eckert | The loss of sex in clonal plants[END_REF], determining the relative contribution from both sexual and asexual reproduction in natural populations can provide valuable insights to understand reef species' response to local stress.

Larval development

For most colonial reef species whose adults are sessile, their early life history includes a reproductive pelagic stage. These propagules represent the first step for successful recruitment and have profound implications for their population dynamics and renewal, which ultimately affect their evolutionary history [START_REF] Gaines | Avoiding current oversights in marine reserve design[END_REF][START_REF] Ayre | Climate change, genotypic diversity and gene flow in reef-building corals[END_REF]. Dispersal in colonial organisms is mostly mediated by the release of gametes and/or larvae during sexual reproduction events, together with the continuous supply in asexual propagules. In many reef species, the extent of dispersal is largely governed by the reproductive biology and early life history ecology. Molecular studies and oceanographic models have uncovered a wide range of dispersal patterns (i.e. dispersal kernels) in coral reefs, from populations primarily sustained by self-recruitment due to limited dispersal potential through ecologically significant gene flow and connectivity among adult populations [START_REF] Steneck | Staying connected in a turbulent world[END_REF]. For instance, brooded larvae settle and metamorphose rapidly after being released, which is most likely to enhance local dispersal patterns, while broadcast larvae require a planktonic development phase and settle further away from the parental source [START_REF] Harrison | Sexual reproduction of scleractinian corals[END_REF]. On the other hand, clonal propagation can allow populations to expand locally under unfavourable conditions. Such conditions include: fragmented [START_REF] Adjeroud | Genetic diversity, clonality and connectivity in the scleractinian coral Pocillopora damicornis: a multi-scale analysis in an insular, fragmented reef system[END_REF], marginal [START_REF] Baums | Marginal coral populations: the densest known aggregation of Pocillopora in the Galapagos Archipelago is of asexual origin[END_REF]) and highly disturbed habitats [START_REF] Foster | Hurricane-driven patterns of clonality in an ecosystem engineer: the Caribbean coral Montastraea annularis[END_REF], where clonal reproduction reinforce local adaptation process and population genetic heterogeneity due to restricted dispersal potential of asexual offspring [START_REF] Combosch | Population genetics of an ecosystem-defining reef coral Pocillopora damicornis in the Tropical Eastern Pacific[END_REF]Pinzόn et al. 2012). Uncovering the dispersal patterns of both sexual and asexual propagules is thus critical for understanding population replenishment and colonization of fragmented habitats, and how such populations can recover from local disturbances.

Modularity and growth

Modularity is a well established life history strategy among colonial reef invertebrates, i.e. corals, gorgonians, sea anemones, hydroids, hydrocorals, bryozoans and sponges [START_REF] Hughes | Lessons in modularity: the evolutionary ecology of colonial invertebrates[END_REF]. Modular organisms grow in size via the repeated, vegetative formation of genetically identical modules, referred as asexual budding, whereby all modules are derived from the same initial zygote to form a colony [START_REF] Jackson | Competition on marine hard substrata: the adaptive significance of solitary and colonial strategies[END_REF][START_REF] Jackson | Distribution and ecology of clonal and aclonal benthic invertebrates[END_REF]. Colony size often correlates with many fitness advantages in responses to both physical and biological stressors. For instance, larger colonies can survive better towards predation [START_REF] Hughes | Do corals lie about their age? Some demographic consequences of partial mortality, fission and fusion[END_REF] and competition [START_REF] Hughes | A Functional Biology of Clonal Animals[END_REF], and their fecundity is often increased due to the large number of polyps that contributes to sexual reproduction [START_REF] Hall | Reproductive strategies of modular organisms: comparative studies of reef-building corals[END_REF]. Modules usually remain physiologically interconnected, but may also separate from the colony through fission or fragmentation and persist as discrete units [START_REF] Wood | Reef Evolution[END_REF], thereafter reducing colony size. Some marine modular organisms, e.g. corals and ascidians, can grow larger and quicker via the fusion of distinct colonies that are isogeneic (same species, same genotype) or allogeneic (same species, different genotype) (Pineda-Krch and Lehtilä 2004).

Allogenic fusion results in genetically heterogeneous colony, also referred to as chimera, and usually occurs during early ontogeny due to a delay in maturation of the allorecognition system [START_REF] Frank | Alloimmune memory is absent in the Red Sea hydrocoral Millepora dichotoma[END_REF]. The occurrence of chimeras is more common in species with early life stages that settle and grow in close proximity (i.e. mainly brooding species) (Puill-Stephan et al. 2012a;[START_REF] Forsman | Growing coral larger and faster: microcolony-fusion as a strategy for accelerating coral cover[END_REF]. In addition to chimerism, somatic mutations may arise within a colony, which also results in intracolonial genotypic variability. In long-lived modular organisms, where germ cell differentiation occurs continuously from stem cells, these mutations can be passed on to the next sexual generation and asexual colony fragments and be spread in the population (van Oppen et al. 2011, Fig. 1.2). Both chimerism (fusion) and mosaicism (somatic mutation) are important source of genetic variation and raise questions on their implications regarding adaptive responses of reef-building species to environmental changes.

Morphological plasticity

Plastic developmental responses are often induced during ontogeny of modular organisms with persistent effect on adult phenotypes [START_REF] Pineda-Krch | Costs and benefits of genetic heterogeneity within organisms[END_REF]. These phenotypic responses can change independently from the genetic pool (acclimatization), but often rely on a genetic basis (adaptation) [START_REF] Agrawal | Phenotypic plasticity in the interactions and evolution of species[END_REF][START_REF] Beaman | Evolution of plasticity: mechanistic link between development and reversible acclimation[END_REF]. In coral reefs, some calcifying species, such as corals and hydrocorals, are known to have a high degree of morphological plasticity in response to hydrodynamic changes and light availability, which strongly influences their performance [START_REF] Muko | Morphological plasticity in the coral Porites sillimaniani and its adaptive significance[END_REF][START_REF] Todd | Morphological plasticity in scleractinian corals[END_REF][START_REF] Hennige | Acclimation and adaptation of scleractinian coral communities along environmental gradients within an Indonesian reef system[END_REF]. Branching and plating growth forms grow quickly into large arborescent colonies in shallow reef environments, where irradiance is high and water flow is low, which makes them effective competitors for space [START_REF] Denny | Biology and the mechanics of the wave-swept environment[END_REF][START_REF] Swierts | Competitive interactions between corals and turf algae depend on coral colony form[END_REF], light and food [START_REF] Baird | Competitive dominance by tabular corals: an experimental analysis of recruitment and survival of understorey assemblages[END_REF]. However, this growth strategy renders them extremely vulnerable to breakage when large waves and storm events occur, often resulting in fragmentation or coral mortality [START_REF] Madin | Mechanical limitations of reef corals during hydrodynamic disturbances[END_REF][START_REF] Madin | Mechanical vulnerability explains sizedependent mortality of reef corals[END_REF]) (see Fig. 1.3). Nonetheless, intraspecific morphological variation has been reported in many colonial reef organisms in response to environmental gradients, which ultimately affect their survival and growth [START_REF] Ayre | Population structure in the coral Pavona cactus: clonal genotypes show little phenotypic plasticity[END_REF]West et al. 1993: Bruno and[START_REF] Bruno | Clonal variation for phenotypic plasticity in the coral Madracis mirabilis[END_REF][START_REF] Hill | Morphological plasticity in the tropical sponge Anthosigmella varians: responses to predators and wave energy[END_REF]. Considering the unpredictability of the reef environment, phenotypic plasticity can provide another means of adaptation in reefbuilding organisms, and especially in population with lowered genetic diversity.

Millepora hydrocorals

To date, the vast majority of studies on species' life history traits in coral reefs have mainly focused on scleractinian corals due to their key role in providing much of the habitat framework and structural complexity of reefs [START_REF] Hughes | Recruitment failure, life histories, and long-term decline of Caribbean corals[END_REF][START_REF] Garrabou | A 20-year study on life-history traits of a harvested long-lived temperate coral in the NW Mediterranean: insights into conservation and management needs[END_REF][START_REF] Vermeij | Early life-history dynamics of Caribbean coral species on artificial substratum: the importance of competition, growth and variation in life-history strategy[END_REF][START_REF] Darling | Evaluating life-history strategies of reef corals from species traits[END_REF][START_REF] Darling | Life histories predict coral community disassembly under multiple stressors[END_REF][START_REF] Kayal | Searching for the best bet in life-strategy: a quantitative approach to individual performance and population dynamics in reef-building corals[END_REF]. Although the extent to which other nonscleractinian reef-building organisms might rescue reef populations in response to environmental changes is largely unknown, more information on how these organisms can survive and adapt is still needed. Millepora hydrocorals, also called fire corals, are an important component of reefs communities worldwide where they, similar to scleractinian corals, contribute to reef accretion and community dynamics [START_REF] Nagelkerken | Loss of coral cover and biodiversity on shallow Acropora and Millepora reefs after 31 years on Curaçao, Netherlands Antilles[END_REF]. Millepora species are hydrozoans and, similar to hermatypic corals (anthanzoans), belong to the phylum Cnidaria (Fig. 1.4), while their life cycle includes both polyp and medusa stages (Fig. 1.5). Fire corals are abundant in many Indo-Pacific reefs, where they can dominate shallow water communities in some coral reef ecosystems [START_REF] Andréfouët | A monospecific Millepora reef in Marquesas Island, French Polynesia[END_REF]. Like scleractinian corals, hydrocorals feed heterotrophically on a variety of resources [START_REF] Lewis | Heterotrophy in corals: zooplankton predation by the hydrocoral Millepora complanata[END_REF][START_REF] Lewis | Biology and ecology of the hydrocoral Millepora on coral reefs[END_REF]) and rely on a mutualistic symbiosis with Symbiodinium algae for autotrophic nutrition and calcification [START_REF] Banaszak | The distribution of mycosporine-like amino acids (MAAs) and the phylogenetic identity of symbiotic dinoflagellates in cnidarian hosts from the Mexican Caribbean[END_REF]). Many studies have described these hydrocorals as opportunistic species that show rapid growth rates, with high fecundity and the ability for clonal propagation through fragmentation (reviewed in [START_REF] Lewis | Biology and ecology of the hydrocoral Millepora on coral reefs[END_REF]. Although fire corals compete with other corals, they also contribute to coral survival during Acanthaster outbreaks, highlighting their key ecological role in reef resilience [START_REF] Kayal | Colonies of the fire coral Millepora platyphylla constitute scleractinian survival oases during Acanthaster outbreaks in French Polynesia[END_REF]. Despite their major importance for reef conservation, fire corals have been relatively understudied and not much is known with respect to their reproduction and dispersal patterns. Millepora hydrocorals are gonochoric broadcast spawners that reproduces sexually by producing medusoids and planula larvae. In hydrozoans, medusoids are formed via asexual budding from the lateral wall of polyps and undergo sexual reproduction. Medusoids produce the gametes and release them in the water column in one hour post-spawning for external fertilization. The larvae sink and move epibenthically (i.e. crawling not swimming) on the reef substratum and metamorphose into a new calcifying polyp in one day post-spawning [START_REF] Bourmaud | Mass spawning events, seasonality and reproductive features in Milleporids (Cnidaria, Hydrozoa) from Reunion Island[END_REF], suggesting some limited dispersal abilities (Fig. 1.5). Although milleporids rely on [START_REF] Edmunds | The role of colony morphology and substratum inclination in the success of Millepora alcicornis on shallow coral reefs[END_REF][START_REF] Lewis | Biology and ecology of the hydrocoral Millepora on coral reefs[END_REF], the production of asexual larvae has never been documented within this genus. Fire corals are also known for their extensive morphological variability and vulnerability to fragmentation varies greatly among their morphologies [START_REF] Edmunds | The role of colony morphology and substratum inclination in the success of Millepora alcicornis on shallow coral reefs[END_REF][START_REF] Lewis | Biology and ecology of the hydrocoral Millepora on coral reefs[END_REF]. While the corallivorous predator Acanthaster planci tend to avoid Millepora species [START_REF] Glynn | Feeding ecology of selected coral-reef macroconsumers: Patterns and effects on coral reef community structure[END_REF]), these zooxanthellate hydrocorals are extremely sensitive to coral bleaching [START_REF] Marshall | Bleaching of corals on the Great Barrier Reef: differential susceptibilities among taxa[END_REF], i.e. the functional loss of their endosymbiotic algae [START_REF] Glynn | Coral reef bleaching: facts, hypotheses and implications[END_REF], and can be threatened by future climate change. All these life history traits suggest that fire corals are competitive species and typically efficient at using local resources in productive environments [START_REF] Grime | The Evolutionary Strategies That Shape Ecosystems[END_REF][START_REF] Darling | Evaluating life-history strategies of reef corals from species traits[END_REF].

The present thesis focuses on Millepora platyphylla, which is the only species of fire corals found in French Polynesia, where it thrives in a wide range of reef environments [START_REF] Bosserelle | Guide d'identification des coraux de Moorea[END_REF].

Studying its reproduction and dispersal patterns, along with its morphological variation across various reef habitats in Moorea, will provide more information to determine whether and how this important reef-building species respond to local environmental stress.

Reef habitats in Moorea, French Polynesia

Recent genetic studies have uncovered that geographically isolated populations, such as those of Moorea, appear to be more dependent on self-recruitment for local replenishment and sustainability [START_REF] D'aloia | Self-recruitment in a Caribbean reef fish: a method for approximating dispersal kernels accounting for seascape[END_REF][START_REF] Cuif | Monthly variability of self-recruitment for a coral reef damselfish[END_REF], highlighting the importance of studying local patterns of life history traits in keystone species. Moorea is a high volcanic island surrounded by a barrier reef with extensive fringing reefs and lagoon systems [START_REF] Galzin | Moorea Island, Society Archipelago[END_REF]. Lagoons and deep interrupted channels separate the fore reefs from the island, and the lagoon is connected to the oceanic waters via deep passes through the barrier reef. Such linear barrier reef provides us with the opportunity to gain insights on M. platyphylla life history traits across various reef habitats, where they experienced contrasting environmental conditions.

To determine whether and how the environment affects its life history, five habitats where M. platyphylla are found were selected on the north shore of Moorea; two on the fore reef: the mid slope (13 m depth) and upper slope (6 m depth) and three in the lagoon (< 1 m depth): the back reef, fringing reef and patch reef. These habitats greatly differ in terms of water flow and solar irradiance. The fore reef experiences strong wave action from incoming waves that break on the reef crest with a decrease in swell exposure and irradiance towards deeper waters [START_REF] Lesser | Depth-dependent photoacclimatization to solar ultraviolet radiation in the Caribbean coral Montastraea faveolata[END_REF]Monismith 2007, see Fig. 1.6). Variations in temperature are small in the fore reef environment due to continuous waves that break on the reef crest, which fills the lagoon with oceanic water. Inside lagoons, internal waves and flows drive circulation and water exchange with the surrounding ocean via deep passes [START_REF] Hench | Episodic circulation and exchange in a wave-driven coral reef and lagoon system[END_REF][START_REF] Leichter | Biological and physical interactions on a tropical island coral reef: Transport and retention processes on Moorea, French Polynesia[END_REF]. In lagoonal environments, the wave energy and oceanic influence decrease from the reef crest towards nearshore fringing reefs [START_REF] Monismith | Hydrodynamics of coral reefs[END_REF][START_REF] Ferrario | The effectiveness of coral reefs for coastal hazard risk reduction and adaptation[END_REF]. Consequently, wave energy is higher on the back reef, near the reef crest compared to the fringing reef, a nearshore reef experiencing great variations in temperature and high irradiance (Fig. 1.6). Although the patch reef is located in a nearshore narrow channel, the wave energy there is also higher than on the fringing reef due to its proximity to the reef crest and to the currents that run on either side of the channel (pass circulation). Despite their proximity (< 1 km to 15 km), these habitats offer a large variety of environmental settings, in which M. platyphylla can be found. Furthermore, coral reefs surrounding Moorea Island in French Polynesia have undergone a massive decline in coral cover from a recent outbreak of Acanthaster planci and cyclone Oli [START_REF] Kayal | Predator crown-of-thorns starfish (Acanthaster planci) outbreak, mass mortality of corals, and cascading effects on reef fish and benthic communities[END_REF], which provides a unique perspective from which to comprehend how fire corals can survive and recover to such disturbances. Wave energy dispersal on a barrier reef modified from [START_REF] Monismith | Hydrodynamics of coral reefs[END_REF][START_REF] Ferrario | The effectiveness of coral reefs for coastal hazard risk reduction and adaptation[END_REF]. The fore reef experiences strong wave action from incoming waves that break on the reef crest, near the upper slope, with a significant decrease in swell exposure towards deeper waters. The reef crest dissipates ~70% of the incident swell wave energy with gradual wave attenuation from the back reef to nearshore fringing reefs.

Insight from population genetic approaches

Evaluating life history traits in natural populations, such as reproductive strategies and dispersal patterns, is one of the greatest challenges in marine ecology and conservation biology (reviewed in [START_REF] Jones | Larval retention and connectivity among populations of corals and reef fishes: history, advances and challenges[END_REF]). Clonality appears to be a ubiquitous feature of colonial reef organisms, which has prompted many issues for population genetic studies due to the difficulty in discriminating genetically distinct individuals and clonal replicates [START_REF] Hey | The study of structured populations -New hope for a difficult and divided science[END_REF]. Because gametes and larvae of most colonial reef organisms are relatively small and difficult to track in the pelagic environment, many studies investigating their dispersal have relied on virtual simulations of hydrodynamics rather than empirical estimates [START_REF] Treml | Modeling population connectivity by ocean currents, a graph-theoretic approach for marine conservation[END_REF][START_REF] Andutta | Sticky water'enables the retention of larvae in a reef mosaic[END_REF][START_REF] Wood | Modelling dispersal and connectivity of broadcast spawning corals at the global scale[END_REF]. Improvement in genetic analysis and genotyping techniques using microsatellite markers has overcome these problems. Many microsatellite loci show high mutation rates (10 -2 -10 -6 mutation per locus per generation), resulting in high allelic diversity [START_REF] Selkoe | Microsatellites for ecologists: a practical guide to using and evaluating microsatellite markers[END_REF]. Genetic studies based on individual multilocus genotype using a combination of many microsatellites loci allow the characterization of each individual within a population (Reviewed in [START_REF] Sunnucks | Efficient genetic markers for population biology[END_REF].

Such ability to discriminate each individual creates new opportunities to investigate life history strategies in natural populations of colonial reef species, such as evaluating the level of clonality through the identification of repeated genotypes and estimating dispersal patterns using parentage analysis of georeferenced colonies. To assist conservation management, molecular data are often used to determine the levels of genotypic diversity and potential for adaptation. Such conservation studies rely on the concept of individuality, where each individual represents the unit on which selection pressures occur [START_REF] Williams | Adaptation and Natural Selection[END_REF]. However, recent studies have shown the occurrence of genetically heterogeneous colonies in some modular reef species [START_REF] Maier | Intracolonial genetic variation in the scleractinian coral Seriatopora hystrix[END_REF][START_REF] Schweinsberg | More than one genotype: How common is intracolonial genetic variability in scleractinian corals?[END_REF]. More studies considering intracolonial genetic variability are needed to fully understand the evolutionary consequences of both chimerism and mosaicism in threatened species such as reef-building corals. While our understanding of population genetics and life history of scleractinian corals has improved considerably over the last decade [START_REF] Van Oppen | Genetic traces of recent longdistance dispersal in a predominantly self-recruiting coral[END_REF][START_REF] Noreen | Genetic diversity and connectivity in a brooding reef coral at the limit of its distribution[END_REF][START_REF] Darling | Evaluating life-history strategies of reef corals from species traits[END_REF][START_REF] Darling | Life histories predict coral community disassembly under multiple stressors[END_REF][START_REF] Warner | Sperm dispersal distances estimated by parentage analysis in a brooding scleractinian coral[END_REF], such information remains very scarce and unavailable for Millepora hydrocorals, despite their significant contribution to the accretion of reefs. This gap is mostly related to the lack of highly variable genetic markers for this genus until very recently [START_REF] Ruiz-Ramos | Microsatellite abundance across the Anthozoa and Hydrozoa in the phylum Cnidaria[END_REF][START_REF] Heckenhauer | Isolation, characterization and cross amplification of eleven novel microsatellite loci for the hydrozoan coral Millepora[END_REF]. Gathering geographic, phenotypic and genotypic data from extensive field surveys in natural populations, in addition to applying several genetic population approaches, provide valuable insights to understand reef species' response to local environmental stress. Studies based on such sampling design in natural populations of a single species exposed to different local environmental settings have, to our knowledge, never been performed. This approach will increase our knowledge on life history strategies in reef-building corals and how such populations can persist and survive to environmental changes.

Thesis aims and outline

The overall aim of this study is to improve our understanding of life history strategies and the renewal mechanisms in populations of the fire coral M. platyphylla in response to local stress and to determine whether this species may 'win' or 'lose' under expected environmental changes. To ensure accurate evaluation of its life history, an exhaustive sampling of georeferenced colonies of fire corals were performed and the subsequent phenotypic and genotypic datasets were gathered and analyzed to answer the following key questions:

Chapter 2: Do Millepora hydrocorals have growth strategies that make them effective competitors for space on coral reefs? Stolonal expansion of encrusting bases and fast linear growth of branches in milleporids have been described in the 1980s as aggressive strategies to preempt substratum space [START_REF] Wahle | Detection, pursuit, and overgrowth of tropical gorgonians by milleporid hydrocorals: Perseus and Medusa revisited[END_REF][START_REF] Müller | Histocompatability reactions in the hydrocoral Millepora dichotoma[END_REF]). Here, we investigated whether this opportunistic spread of Millepora platyphylla in Moorea, where a massive decline in coral cover was reported, may become an important component for their recovery.

Chapter 3: How do different reef habitats with contrasting water regimes affect the population structure of Millepora platyphylla? Diversity in species' life history traits plays a key role in structuring populations exposed to different local environmental conditions. Given the difficulties in quantifying key demographic parameters, such as growth rates, longevity and recruitment, valuable insights into life histories of reef-building organisms are often inferred from individual traits based on their size [START_REF] Hughes | Population dynamics based on size rather than age: a general model with a reef coral example[END_REF].

Here, we investigated the colony size distribution, morphological variation and recruitment dynamics to assess to what degree the variability in the population structure of M. platyphylla among reef habitats can be attributed to different flow regimes. Such information is needed to unveil the processes underlying their colonization success.

Chapter 4: Are microsatellite markers useful to infer patterns of genetic diversity and differentiation in Millepora hydrocorals?

The development of new molecular markers is required for understanding population genetics and species' life histories [START_REF] Selkoe | Microsatellites for ecologists: a practical guide to using and evaluating microsatellite markers[END_REF]. Here, we developed fifteen microsatellite loci for M. platyphylla and tested these new markers for cross-species amplification in five other Millepora species. Determining patterns of genetic diversity and differentiation within the Millepora genus is crucial to shed light on biological, ecological and evolutionary processes underlying their population persistence. Determining direct genetic estimates of dispersal and subsequent recruitment is crucial for understanding marine population dynamics and replenishment [START_REF] Jones | Larval retention and connectivity among populations of corals and reef fishes: history, advances and challenges[END_REF]. Using parentage analysis, we investigated dispersal patterns of sexual propagules of fire corals and estimated the contribution from self-recruitment in the population maintenance. Such information will provide important insights on their reproductive biology and early life ecology.

Chapter 7: How common is intracolonial genotypic variability in Millepora platyphylla due to mosaicism and chimerism processes?

Our understanding of life histories largely relies on the concept of the individual, where intraindividual genetic homogeneity is assumed [START_REF] Santelices | How many kinds of individual are there?[END_REF]. Nonetheless, an increasing number of studies have revealed intracolonial genetic variability in many modular organisms [START_REF] Pineda-Krch | Costs and benefits of genetic heterogeneity within organisms[END_REF]. Here, we investigated the occurrence of mosaicism and chimerism within populations of the hydrocoral M. platyphylla across various reef habitats; both of which are processes leading to intracolonial genetic variation.

Chapter 8: What can we learn from population genetic approaches on the adaptive potential of Millepora hydrocorals to future environmental changes? Are they 'winners' or 'losers'?

This chapter discusses the main findings of this PhD thesis in light of whether the life history of Millepora hydrocorals can benefit their survival and persistence to future environmental changes.

Futures scientific directions on ecological and evolutionary processes involved in species' responses to local stress are also discussed, such as local genomic adaptation and/or physiological plasticity of fire corals and their associated microbial organisms. Competitive interactions among reef-building organisms are among the major processes regulating coral reef communities [START_REF] Chadwick | Competition among sessile organisms on coral reefs[END_REF]. Hydrozoan corals of the genus Millepora are abundant in many Indo-Pacific reefs, and by a high cover can dominate shallow-water communities in some coral reef ecosystems [START_REF] Andréfouët | A monospecific Millepora reef in Marquesas Island, French Polynesia[END_REF]). Many studies have described these hydrocorals (also called fire corals) as opportunistic species that show rapid growth rates, with both high fecundity and the ability for clonal propagation through fragmentation (reviewed in [START_REF] Lewis | Biology and ecology of the hydrocoral Millepora on coral reefs[END_REF]. Stolonal expansion of encrusting bases and fast linear growth of branches in milleporids have been described as aggressive strategies to pre-occupy substratum space. Interactions involving fire corals can lead to the overgrowth of other sessile organisms. Previous studies have reported the overgrowth of branching Millepora on gorgonians [START_REF] Wahle | Detection, pursuit, and overgrowth of tropical gorgonians by milleporid hydrocorals: Perseus and Medusa revisited[END_REF] and scleractinian corals such as Porites murrayensis [START_REF] Müller | Histocompatability reactions in the hydrocoral Millepora dichotoma[END_REF]. This opportunistic spread of Millepora on living scleractinian corals confirm previous descriptions of overgrowth as a strategy employed by fire corals to quickly monopolize substratum space [START_REF] Brown | Long-term changes in the population dynamics of the Caribbean hydrocoral Millepora spp[END_REF]. This growth strategy may become an important component in the modeling of competition for space among benthic community assemblages in coral reefs. A total of 3651 colonies of fire corals were mapped and measured over 45,000 m 2 of surveyed reef. Due to the species' sensitivity to fragmentation in response to strong water movement, hydrodynamic conditions (e.g. waves, pass and lagoonal circulation) corresponded to marked differences in colony size distributions, morphology and recruitment dynamics among habitats. The size structure varied among reef habitats with higher proportions of larger colonies in calm nearshore reefs (fringing and patch reefs), while populations were dominated by smaller colonies in the exposed fore reefs. The highest densities of fire corals were recorded in fore reef habitats (0.12-0.20 n.m -2 ) where the proportion of recruits and juveniles was higher at mid slope populations (49.3%) than on the upper slope near where waves break (29.0%). In the latter habitat, most colonies grew as vertical sheets on encrusting bases making them more vulnerable to colony fragmentation, whereas fire corals were encrusting or massive in all other habitats. The lowest densities of M. platyphylla occurred in lagoonal habitats (0.02-0.04 n.m -2 ) characterized by a combination of low water movement and other physical and biological stressors. This study reports the first evidence of population structure of fire corals in two common reef environments and

Overgrowth of living scleractinian corals by the hydrocoral

Millepora platyphylla in

Coral reefs surrounding

Introduction

Coral reefs exhibit a remarkable diversity of organisms that reside within highly variable environments resulting in strong spatial variability in species' distribution patterns [START_REF] Wilkinson | Global Coral Reef Monitoring Network and Reef and Rainforest Research Center[END_REF]. For scleractinian corals, spatial differences in temperature, light, water flow and water quality conditions can influence their distribution and population dynamics [START_REF] Glynn | Coral reef bleaching: facts, hypotheses and implications[END_REF][START_REF] Vermeij | How are coral populations structured by light? Marine light regimes and the distribution of Madracis[END_REF][START_REF] Fabricius | Effects of terrestrial runoff on the ecology of corals and coral reefs: review and synthesis[END_REF][START_REF] Monismith | Hydrodynamics of coral reefs[END_REF]). Millepora hydrocorals, also called fire corals, are an important component of reefs communities worldwide where they, similar to scleractinian corals, contribute to reef accretion and community dynamics [START_REF] Nagelkerken | Loss of coral cover and biodiversity on shallow Acropora and Millepora reefs after 31 years on Curaçao, Netherlands Antilles[END_REF][START_REF] Lewis | Biology and ecology of the hydrocoral Millepora on coral reefs[END_REF]. Fire corals are gonochoric broadcast spawners that can colonize a wide range of reef environments through sexual reproduction [START_REF] Lewis | Biology and ecology of the hydrocoral Millepora on coral reefs[END_REF][START_REF] Bourmaud | Mass spawning events, seasonality and reproductive features in Milleporids (Cnidaria, Hydrozoa) from Reunion Island[END_REF]) and colony fragmentation [START_REF] Edmunds | The role of colony morphology and substratum inclination in the success of Millepora alcicornis on shallow coral reefs[END_REF][START_REF] Lewis | Biology and ecology of the hydrocoral Millepora on coral reefs[END_REF]. Fire corals often grow into large colonies that preempt space and compete with scleractinian corals [START_REF] Andréfouët | A monospecific Millepora reef in Marquesas Island, French Polynesia[END_REF][START_REF] Dubé | Overgrowth of living scleractinian corals by the hydrocoral Millepora platyphylla in Moorea, French Polynesia[END_REF]). On the other hand Millepora species also contribute to the survival of corals during Acanthaster outbreaks as this corallivorous predator tends to avoid Millepora species [START_REF] Lewis | Biology and ecology of the hydrocoral Millepora on coral reefs[END_REF][START_REF] Kayal | Colonies of the fire coral Millepora platyphylla constitute scleractinian survival oases during Acanthaster outbreaks in French Polynesia[END_REF].

Hydrodynamic forces in the form of water-displacement, velocity and acceleration have been recognized as a key factor in determining the shape and occurrence of many reef-building organisms (Madin et al. 2006;[START_REF] Williams | Benthic communities at two remote Pacific coral reefs: effect of reef habitat, depth, and wave energy gradients on spatial patterns[END_REF]. In coral reef ecosystems, the magnitude of water flow is mostly related to the wave energy dispersal [START_REF] Monismith | Hydrodynamics of coral reefs[END_REF]). On barrier reefs, the amount of wave energy is highest on the reef crest, where waves break, and subsequently attenuates towards fore reef and lagoonal environments [START_REF] Monismith | Hydrodynamics of coral reefs[END_REF][START_REF] Ferrario | The effectiveness of coral reefs for coastal hazard risk reduction and adaptation[END_REF]. Inside lagoons, internal waves and flows drive circulation and water exchange with the surrounding ocean [START_REF] Hench | Episodic circulation and exchange in a wave-driven coral reef and lagoon system[END_REF][START_REF] Leichter | Biological and physical interactions on a tropical island coral reef: Transport and retention processes on Moorea, French Polynesia[END_REF]. Such variation in hydrodynamic regimes, combined with other physical factors (e.g. light, nutrients and disturbances), differently affect the performance of individuals [START_REF] Hoogenboom | Defining fundamental niche dimensions of corals: synergistic effects of colony size, light, and flow[END_REF]Madin et al. 2012a;[START_REF] Darling | Evaluating life-history strategies of reef corals from species traits[END_REF] resulting in corresponding changes in population structure and community composition.

Water flow can drive the spatial distribution in adult populations through the distribution and dilution of larval settlement cues [START_REF] Koehl | Soluble settlement cue in slowly moving water within coral reefs induces larval adhesion to surfaces[END_REF] and dispersal of reproductive propagules [START_REF] Edmunds | Landscape-scale variation in coral recruitment in Moorea, French Polynesia[END_REF][START_REF] Gleason | Coral larvae: From gametes to recruits[END_REF]. Many studies have related the contribution of recruitment to colony size variation in scleractinian corals (e.g., [START_REF] Meesters | Colony sizefrequency distributions of scleractinian coral populations: spatial and interspecific variation[END_REF][START_REF] Harris | Scleractinian coral communities of the inner Seychelles 10 years after the 1998 mortality event[END_REF]) and the size structure of a population often reflects other species specific responses to environmental conditions and disturbances as well [START_REF] Hughes | Population dynamics based on size rather than age: a general model with a reef coral example[END_REF][START_REF] Albright | Ocean acidification impacts multiple early life history processes of the Caribbean coral Porites astreoides[END_REF]Madin et al. 2012b). The size-frequency distribution of fire coral populations could therefore provide insights on which biotic (e.g., recruitment of larvae and asexually produced fragments) and abiotic (e.g., wave energy) factors influence their population structure and dynamics.

Water flow also influences colony growth and morphology [START_REF] Storlazzi | A model for wave control on coral breakage and species distribution in the Hawaiian Islands[END_REF]Madin and Connolly 2006). Under the increasing influence of hydrodynamics, delicate branching corals transform into growth forms able to withstand strong water movement such as compact, robust plating or thick branching morphologies [START_REF] Kaandorp | Morphological models of radiate accretive growth and the influence of hydrodynamics[END_REF][START_REF] Chindapol | Modelling growth and form of the scleractinian coral Pocillopora verrucosa and the influence of hydrodynamics[END_REF]. Such inter-and intraspecific variation resulting in different coral morphologies affects not only their mechanical strength but also their ability to compete for space [START_REF] Jackson | Morphological strategies of sessile animals[END_REF][START_REF] Denny | Biology and the mechanics of the wave-swept environment[END_REF][START_REF] Swierts | Competitive interactions between corals and turf algae depend on coral colony form[END_REF] and capture light and food [START_REF] Darling | Evaluating life-history strategies of reef corals from species traits[END_REF][START_REF] Baird | Competitive dominance by tabular corals: an experimental analysis of recruitment and survival of understorey assemblages[END_REF].

Branching scleractinian corals, such as Acropora cervicornis, often grow into large and delicate arborescent colonies in areas of relatively high water flow [START_REF] Tunnicliffe | Breakage and propagation of the stony coral Acropora cervicornis[END_REF], but this growth strategy also renders them extremely vulnerable to breakage when large waves and storm events occur, often resulting in fragmentation or coral mortality [START_REF] Madin | Mechanical vulnerability explains sizedependent mortality of reef corals[END_REF]. Asexual reproduction through colony fragmentation can be a successful reproductive strategy to sustain local population growth in some species of scleractinian corals [START_REF] Tunnicliffe | Breakage and propagation of the stony coral Acropora cervicornis[END_REF][START_REF] Baums | Geographic variation in clonal structure in a reefbuilding Caribbean coral, Acropora palmata[END_REF][START_REF] Aranceta-Garza | Effect of tropical storms on sexual and asexual reproduction in coral Pocillopora verrucosa subpopulations in the Gulf of California[END_REF]. Fire corals are also known for their extensive intra-and interspecific morphological variability across hydrodynamic gradients with consequences due to their vulnerability to wave-induced breakage [START_REF] Jackson | Morphological strategies of sessile animals[END_REF][START_REF] Weerdt | Transplantation experiments with Caribbean Millepora species (Hydrozoa, Coelenterata), including some ecological observations on growth forms[END_REF][START_REF] Edmunds | The role of colony morphology and substratum inclination in the success of Millepora alcicornis on shallow coral reefs[END_REF][START_REF] Lewis | Biology and ecology of the hydrocoral Millepora on coral reefs[END_REF].

Determining to what degree the population structure of fire corals depends on water flow has so far not been determined.

In this study, we investigated whether and how different reef habitats with contrasting water regimes affect the population structure of Millepora platyphylla, the only species of fire coral identified in French Polynesia [START_REF] Bosserelle | Guide d'identification des coraux de Moorea[END_REF]. Surveys of M. platyphylla were conducted in five habitats on the north shore of Moorea with differing amounts of water flow: fore reef habitats with high water movement, especially on the upper slope and decreasing with depth to the mid slope. Lagoonal habitats (back reefs, fringing reefs and patch reefs) are sheltered from waves and oceanic swell, except during storms, and water movement in these habitats is less than on the fore reef [START_REF] Monismith | Hydrodynamics of coral reefs[END_REF][START_REF] Ferrario | The effectiveness of coral reefs for coastal hazard risk reduction and adaptation[END_REF]. We examined colony size distribution, morphological variability and recruitment dynamics to assess to what degree the variability in the population structure of M. platyphylla among reef habitats can be attributed to different flow regimes.

3

Population structure of Millepora hydrocorals

Materials and Methods

Study sites and field surveys

Between April and December 2013, a series of surveys were conducted on the north shore of Moorea,French Polynesia,in the South Pacific Ocean (17,5267 S,149,8348 W), at four different locations (Tiahura, Papetoai, Cook's Bay and Temae). Five habitats with contrasting water flow regimes were selected; two in a fore reef environment: the mid slope (13 m depth) and the upper slope (6 m depth), and three in the lagoon (< 1 m depth): the back reef, fringing reef and patch reef (Fig. 3.1 and Table S1). These habitats greatly differ in terms of water flow. The fore reef experiences strong wave action from incoming waves that break on the reef crest with gradual swell wave attenuation towards deeper waters [START_REF] Hearn | Wave-breaking hydrodynamics within coral reef systems and the effect of changing relative sea-level[END_REF][START_REF] Monismith | Hydrodynamics of coral reefs[END_REF]. Because of this strong linear relationship between wave forcing and water depth [START_REF] Hearn | Wave-breaking hydrodynamics within coral reef systems and the effect of changing relative sea-level[END_REF], we assumed that the colonies of M. platyphylla growing within fore reef habitats are exposed to lower wave energy on the mid slope compared to the those growing on the upper slope, near where the waves break. In the lagoon, the wave energy disperses from the reef crest towards nearshore reefs [START_REF] Monismith | Hydrodynamics of coral reefs[END_REF]. Using a meta-analysis approach, a recent study on wave energy across reef environments revealed that the reef crest dissipated 70% of the incident swell wave energy with gradual wave attenuation from the back reef to the shore [START_REF] Ferrario | The effectiveness of coral reefs for coastal hazard risk reduction and adaptation[END_REF]. Consequently, we assumed that wave energy is higher on the back reef, near the reef crest compared to the fringing reef, a nearshore reef. Although the patch reef is located in a nearshore narrow channel, the wave energy there is also higher than on the fringing reef due to its proximity to the reef crest and to the currents that run on either side of the channel (i.e. pass circulation). Variations in other physical constraints exist between the fore reef and lagoonal habitats in terms of e.g., temperature, water clarity, nutrient and disturbances [START_REF] Done | Patterns in the distribution of coral communities across the central Great Barrier Reef[END_REF][START_REF] Witman | Physical disturbance and community structure of exposed and protected reefs: A case study from St-John, U.S. Virgin Islands[END_REF]. Within each habitat, three 300 m long by 10 m wide belt transects were laid over the reef parallel to shore, at least 30 m apart, resulting in a total of 45,000 m 2 reef area being surveyed. All colonies of M. platyphylla that were at least 50% within the transect borders were measured, photographed and georeferenced using SCUBA.

Spatial distribution patterns

All M. platyphylla colonies were georeferenced by determining their position along the transect-line (0 to 300 m) and straight-line distance from both sides of the transect (0 to 10 m). From these measures, each colony was mapped with x and y coordinates, from which the distribution index (DI) and mean neighborhood distance (ND) were calculated using the spdep package [START_REF] Bivand | Hello World: Introducing spatial data[END_REF]) in R (R Development Core Team 2013). The DI is based on Ripley's method [START_REF] Ripley | The second-order analysis of stationary point processes[END_REF] and calculated for each transect to determine whether colonies were having a contagious (DI > 1), random (DI ≈ 1) or homogenous (DI < 1) pattern of distribution [START_REF] Urban | Spatial analysis in ecology[END_REF]. The mean distance to each colony's 10 nearest neighbors was estimated and the mean ND was calculated for each transect. The mean colony density (n.m -²) and cover (%) were also calculated for each transect (i.e. 3000 m 2 ). Using these variables, variability in the spatial distribution among habitats was quantified by one-way PERMANOVA tests in PRIMER 6 software [START_REF] Clarke | Testing of null hypotheses in exploratory community analyses: similarity profiles and biota-environment linkage[END_REF], since assumptions of parametric testing could not be met. Pair-wise tests followed the PERMANOVA to assess the degree of similarity among habitats. In order to determine how different habitats with contrasting water regimes affect the spatial distribution of M. platyphylla, we assumed that swell wave energy exposure decreases with habitat depth and its proximity to the coastline, as demonstrated in previous studies [START_REF] Hearn | Wave-breaking hydrodynamics within coral reef systems and the effect of changing relative sea-level[END_REF][START_REF] Ferrario | The effectiveness of coral reefs for coastal hazard risk reduction and adaptation[END_REF]. Consequently, the density, cover, DI and ND were regressed against the mean depth and mean distance from shore estimated from the three transects within each of the five surveyed habitats and Pearson's r coefficient was used to test for significant correlations.

3

Population structure of Millepora hydrocorals

Colony size distribution

The size-frequency distributions of M. platyphylla populations were generated from estimates of colony sizes computed from 2D photographs. Each colony size (projected surface) was then measured (in cm²) using ImageJ 1.4f software [START_REF] Abràmoff | Image processing with ImageJ[END_REF]). The size-frequency distribution for each transect was given as percentages of all colonies belonging to 10 size classes on a logarithmic scale. Data were then analyzed using basic statistical measures of size hierarchies [START_REF] Bendel | Comparison of skewness coefficient, coefficient of variation and Gini coefficient as inequality measures within populations[END_REF]): the coefficient of variation (CV) and skewness (g 1 ), indicative of the relative abundance of small and large colonies within a population. CV and g 1 were computed for each habitat per transect together with standard descriptive statistics, such as 95% percentile of the mean (describes the maximum colony size reached within a population, see [START_REF] Soong | Colony size as a species character in massive reef corals[END_REF] and the probability that the data are normally distributed (Kolmogorov-Smirnov test, Pnorm). Differences in size-frequency distributions among habitats were quantified using one-way PERMANOVA based on normalized abundances. Spearman's rank coefficient and pair-wise tests followed the PERMANOVA to assess the degree of similarity among habitats.

Recruitment dynamics

The mean abundance and proportion of recruits, juveniles and adults were estimated for each transect whereby the three life stages were defined based on colony size. Colonies with a size below 1 cm² were considered as recruits, colonies with a size between 1 and 20 cm² were juveniles and colonies with a size above 20 cm² were adults [START_REF] Penin | Early post-settlement mortality and the structure of coral assemblages[END_REF]. Differences in abundance and proportion (the fraction in the entire population) of early life stages (both recruits and juveniles) among habitats were quantified using one-way PERMANOVA, followed by a pair-wise test.

Pearson's correlation coefficient was used to determine whether the abundance of early life stages increased with the abundance and cover of adults, and whether differences in their proportions among habitats correlate with higher or lower water movement, i.e. depth and distance from shore.

Colony morphology

For each colony, the maximum height was recorded and the colony size was obtained from photographs. Colonies < 20 cm 2 were removed from our dataset to only estimate the mean height and size of adults for each transect. Adult colonies were assigned to one of these morphologies: 1) massive: solid colonies, roughly hemispherical in shape (Fig. 3.2A), 2) encrusting: thin colonies growing against the substratum (Fig. 3.2B) and 3) "sheet tree": encrusting bases with platelike outgrowths facing wave energy (see Jackson 1979) (Fig. 3.2C). Difference in morphology among habitats was quantified with one-way PERMANOVA and pair-wise tests.

Population structure assessment

Similarities in population structure based on the following parameters: density, cover, DI, ND, mean adult colony size and height, and proportion of recruits, juveniles and adults were calculated and visualized using a hierarchical complete-linkage agglomerative clustering (CLUSTER) method and a non-parametric multidimensional scaling (MDS) ordination on normalized data. Multivariate PERMANOVA on aforementioned characteristics was used to determine differences in population structure of M. platyphylla among the five surveyed habitats, i.e., those on the fore reef (mid and upper slopes) and those in lagoonal habitats (back, fringing and patch reefs).

Results

Spatial distribution of Millepora platyphylla

M. platyphylla was found in all habitats, but its population composition differed among habitats. A total of 3651 colonies of M. platyphylla were counted in the five surveyed habitats. Most colonies (77.7%) occurred on fore reef habitats, whereas M. platyphylla colonies on patch reefs accounted only for 5.2% of all colonies (Table S2). Colony density differed among habitats (PERMANOVA test, P < 0.01) and was higher on the upper slope (0.20 ± 0.03 n.m -2 , N = 1761) and mid slope (0.12 ± 0.05 n.m -2 , N = 1075), i.e. fore reef habitats, compared to lagoonal habitats (back reef: 0.03 ± 0.01 n.m -2 , N = 324, fringing reef: 0.04 ± 0.03 n.m -2 , N = 302 and patch reef: 0.02 ± 0.00 n.m -2 , N = 189) (Fig. 3.3A). M. platyphylla cover also differed among habitats (PERMANOVA test, P < 0.01) and was again highest on the upper slope (3.2 ± 0.4%, Fig.

Size structure of Millepora platyphylla

Across all habitats, 85% of the surveyed colonies were smaller than 1000 cm² and approximately one third (30%) of aforementioned colonies fell in recruit and juvenile size classes, i.e. were smaller than 20 cm². The size-frequency distributions of M. platyphylla populations differed among certain habitats, but were similar among the lagoonal fringing and patch reefs with populations dominated by both small and large colonies resulting in bimodal size-frequency distributions (Fig. 3.4, Spearman' rank coefficient 87.9%, P < 0.05).

Fig. 3.4

Size-frequency distributions of M. platyphylla across the five surveyed habitats. Colony size (cm 2 ) data were distributed among 10 size classes based on a logarithm scale (log 2 ). Frequencies (%) for each size class were averaged by habitats with total population size (N in Table S2) and error bars show the standard error for transect replicates.

3

Population structure of Millepora hydrocorals All fire coral populations were characterized by relatively symmetrical size distributions (g 1 : -0.01-0.71), but the degree of skewness was again lower on the fringing and patch reefs (Table 3.1). The maximum colony size differed among habitats and was smallest on the mid slope (95%: 1295 cm 2 ) and back reef (2512 cm 2 ) compared to other populations (upper slope: 8514 cm 2 , fringing reef: 7107 cm 2 and patch reef: 9890 cm 2 ) (Table 3.1). With 64% of all colonies falling in a few medium size classes (32-512 cm 2 , Fig. 3.4), colonies comprising back reef populations were very similar relative to each other as indicated by the lowest coefficient of variation (CV: 0.33, Table 3.1) of all habitats.

Overall, the composition of M. platyphylla populations in terms of colony density and size differed among the five habitats, except between the two lagoonal habitats, the fringing and patch reefs, located closest to shore.

Table 3.1 Index describing the population size structure and recruitment for M. platyphylla across the five habitats.

Recruitment of Millepora platyphylla

In total, 71 recruits (2%) and 1094 juveniles (30%) were observed within the five surveyed habitats (Table S2). The abundance of recruits and juveniles differed among habitats (PERMANOVA test, P < 0.05 and P < 0.01, respectively) with 96% of all recruits and juveniles occurring in fore reef habitats (48% for both the mid and upper slopes) and only small numbers were observed in lagoonal habitats (Table 3.1). The fraction of the entire population consisting of recruits and juveniles differed among habitats (PERMANOVA test, P < 0.01). Recruits (3.4 ± 0.4%) and juveniles (45.9 ± 5.1%) dominated populations occurring on the mid slope, i.e. deeper waters, compared to shallow waters in both fore reef and lagoon (Table 3.1;Fig. 3.5). Only in lagoonal habitats did the abundance of adults, not their total cover, and the abundance of both recruits and juveniles increase simultaneously suggesting the presence of a stock-recruitment relationship (Fig. 3.6A), that was not observed in fore reef habitats (Fig. 3

Morphology of Millepora platyphylla

M. platyphylla colonies ranged in size from 0.18 cm² to 189 062 cm² (projected surface) and 0.1 cm up to 130 cm in height. Mean colony size and height of adults (i.e., all colonies > 20cm 2 ) differed among habitats (PERMANOVA tests, P < 0.01). Fire corals were approximately 4 times larger on average in the upper reef slope (2308 ± 115 cm 2 ), fringing (1590 ± 329 cm 2 ) and patch reef (3090.48 ± 1294 cm 2 ), compared to colonies growing in the back reef and mid slope (510 ± 97 cm 2 and 819 ± 73 cm 2 , respectively, Table 3.1). The average height of fire coral colonies was highest in fringing (24 ± 5 cm) and patch reefs (25 ± 8 cm), i.e. nearshore habitats (Table S2). Morphologies of adult colonies differed among habitats (PERMANOVA test, P < 0.01). Massive morphologies dominated nearshore reefs (fringing reef: 79.7 ± 8.3% and patch reef: 59.0 ± 9.9%) whereas colonies were mostly encrusting on the mid slope (79.9 ± 1.1%) and back reef (74.5 ± 5.2%) (Fig. S3). On the upper slope, 69.5% (± 3.2) of the colonies displayed the sheet tree morphology, while the remaining colonies were encrusting.

and Table

3

Population structure of Millepora hydrocorals

Population structure assessment

Combining all variables into a single multivariate analysis, the population structure of M.

platyphylla varied significantly among reef habitats (PERMAVOVAs, P < 0.01). Based on MDS, two main clusters can be distinguished: one with populations from wave exposed fore reef habitats, i.e. mid and upper slopes, and a second cluster consisting of populations from lagoonal habitats, i.e.

back, fringing and patch reefs (Fig. 3.8) where calmer waters prevail. The main differences between these two clusters are that fore reef populations are characterized by a high relative abundance of recruits and juveniles (mid slope), or a high density and cover (upper slope). Populations from lagoonal habitats are characterized by large colony size and height (both fringing and patch reefs)

and widely spaced colonies. Back reef populations are characterized by the dominance of adult colonies. Using all variables of each transect surveyed within the fore reef habitat (i.e. six replicates), we found that adult colonies became smaller (i.e. colony size decreases) with increasing depth where wave energy was lower compared to shallow reefs (r = -1.00, P < 0.001; N = 6). Fractions of recruits and juveniles increased with increasing depth (r = 0.91, P < 0.05 and r = -0.92, P < 0.05; N = 6), while total cover decreased (r = -0.97, P < 0.01; N = 6). Colonies grew in an encrusting morphology at mid depth and in the sheet tree morphology in shallow waters (Fig. 3.7). Among shallow lagoonal habitats, we found that adult colonies became smaller towards the back reef, far from shore (r = -0.76, P < 0.01; N = 9), where wave energy was higher and colonies mostly occurred in the encrusting morphology (Fig. 3.7). Total cover increased with increasing distance from the coast (r = -0.69, P < 0.05; N = 9).

3

Population structure of Millepora hydrocorals ) and adults (> 20 cm 2 ). The second transect of the fringing reef is shown as a single group mostly related to a small population size (i.e. 27 colonies, Table S2).

Discussion

In Moorea, M. platyphylla colonized a wide range of habitats reflecting its ability to adapt and survive in a large variety of environmental settings and this study is, to our knowledge, the most extensive sampling ever conducted to assess local patterns in population structure of Milleporid corals. Reef habitats where M. platyphylla colonies were found were selected because of their difference in water regimes according to their depth and proximity to the coastline (see Materials and Methods for details). Due to M. platyphylla's sensitivity, especially of larger colonies to fragmentation induced by wave action or water movement (Fig. 3.2), we sought for possible relationships between hydrodynamic conditions and the population structure of fire corals on Moorea. Differences in population size structure, recruitment and morphology existed among habitats and confirmed expected relationships between such characteristics and the amount of water flow in several of the five surveyed habitats (i.e. mid slope, upper slope, back reef, fringing reef, and patch reef). The highest densities of fire corals, including that of recruits and juveniles, occurred on the exposed fore reef (i.e. mid and upper slopes) whereby colonies were often observed growing in contagious pattern of distribution. In calm lagoonal environments (i.e. back, fringing and patch reefs) fire coral colonies occurred in low densities, where the number of recruits and juvenile was low and colonies grew in a random pattern of distribution. Variability in density among fore reef and lagoonal habitats has been described for numerous other sessile organisms and related to a large number of environmental factors such as water flow, solar irradiance, sedimentation and/or species' life history traits (e.g., reproductive mode, competitive ability, morphological plasticity; [START_REF] Vermeij | Effects of reproductive mode on habitat-related differences in the population structure of eight Caribbean coral species[END_REF][START_REF] Roth | Distribution, abundance, and microhabitat characterization of small juvenile corals at Palmyra Atoll[END_REF][START_REF] Doropoulos | Linking demographic processes of juvenile corals to benthic recovery trajectories in two common reef habitats[END_REF][START_REF] Adjeroud | The size-structure of corals with contrasting life-histories: A multi-scale analysis across environmental conditions[END_REF].

Although differences in size-frequency distributions among habitats were found, e.g. few larger colonies in the calm fringing and patch reefs, smaller colonies in the mid slope and medium size colonies in the back reef, the degree of skweness was similar among all habitats with populations consisting of both small and large colonies. This result likely reflects low mortality in small size classes, as well as the persistence of the larger ones [START_REF] Adjeroud | Spatio-temporal heterogeneity in coral recruitment around Moorea, French Polynesia: Implications for population maintenance[END_REF]. Our results showed that the proportion of recruits and juveniles was highest on the mid slope, an exposed reef where wave energy is reduced due to increased depth [START_REF] Hearn | Wave-breaking hydrodynamics within coral reef systems and the effect of changing relative sea-level[END_REF]. Earlier reports have also shown the influence of depth and water flow on the recruitment dynamics in some scleractinian coral species in many reef locations [START_REF] Chiappone | Distribution, abundance and species composition of juvenile scleractinian corals in the Florida reef tract[END_REF][START_REF] Penin | Spatial distribution of juvenile and adult corals around Moorea (French Polynesia): Implications for population regulation[END_REF][START_REF] Penin | Relative importance of recruitment and post-settlement processes in the maintenance of coral assemblages in an insular, fragmented reef system[END_REF].

These studies revealed an increase in the occurrence of recruits and juveniles with increasing depth.

Another study compiling juvenile data of all coral species surveyed in Palmyra Atoll in the central Pacific has shown that most juveniles were growing at middle depth (i.e. 14 m) in a fore reef habitat [START_REF] Roth | Distribution, abundance, and microhabitat characterization of small juvenile corals at Palmyra Atoll[END_REF], as for M. platyphylla. Water flow is also considered as an important factor influencing a colony's morphology [START_REF] Veron | Corals of the world[END_REF][START_REF] Todd | Morphological plasticity in scleractinian corals[END_REF]), generally showing a transition from easily fragmented morphologies towards more robust morphologies with increasing water movement [START_REF] Kaandorp | Morphological models of radiate accretive growth and the influence of hydrodynamics[END_REF][START_REF] Chindapol | Modelling growth and form of the scleractinian coral Pocillopora verrucosa and the influence of hydrodynamics[END_REF]). This study shows a similar trend whereby large and high colonies were more common in protected nearshore habitats (i.e. fringing and patch reef) and small and encrusting in exposed mid slope and back reef habitats. On the upper slope, near where the waves break, fire corals are large, but largely encrusting, and of the unusual sheet tree morphology of Millepora that was only observed in low proportions in all other habitats (0-9%).

Fire corals, like many other reef-building organisms, reproduce through both asexual and sexual reproduction with a dimorphic life cycle, with a pelagic dispersive phase (i.e. medusoids and larvae), followed by a sessile adult phase [START_REF] Lewis | Biology and ecology of the hydrocoral Millepora on coral reefs[END_REF]. If dispersal distances are small due to low water movement or retention, the spatial distribution of adults could influence the distribution of

3

Population structure of Millepora hydrocorals young colonies as previously shown for scleractinian corals [START_REF] Edmunds | Patterns in the distribution of juvenile corals and coral reef community structure in St. John, US Virgin Islands[END_REF][START_REF] Penin | Spatial distribution of juvenile and adult corals around Moorea (French Polynesia): Implications for population regulation[END_REF][START_REF] Vermeij | Density-dependent settlement and mortality structure the earliest life phases of a coral population[END_REF][START_REF] Penin | Relative importance of recruitment and post-settlement processes in the maintenance of coral assemblages in an insular, fragmented reef system[END_REF]. On Moorea the abundance of M. platyphylla recruits and juveniles could not be related to adult population size in fore reef habitats. The proportions of recruits and juveniles were highest at mid-depths (13 m) on the fore reef where wave energy and solar irradiance are lower compared to the shallower depths (as described in [START_REF] Roth | Distribution, abundance, and microhabitat characterization of small juvenile corals at Palmyra Atoll[END_REF]. Low wave energy can indeed increase settlement success of both coral larvae and fragments [START_REF] Price | Habitat selection, facilitation, and biotic settlement cues affect distribution and performance of coral recruits in French Polynesia[END_REF]. At shallow depths (6 m) on the fore reef, high wave energy and irradiance can reduce the abundance of settlement cues [START_REF] Price | Habitat selection, facilitation, and biotic settlement cues affect distribution and performance of coral recruits in French Polynesia[END_REF]), but also indirectly affect settler survival through high grazing pressure by herbivorous fishes at this depth which constitutes a major source of mortality for juvenile corals on the upper slope in Moorea [START_REF] Penin | Early post-settlement mortality and the structure of coral assemblages[END_REF]. The abundance of coral fragments that re-attached to the reefs can also be reduced due to high wave energy and subsequent increased mortality [START_REF] Highsmith | Reproduction by fragmentation in corals[END_REF]. Such physical and biological constraints in a dynamic environment likely reduce local recruitment rates and prevent high coral cover [START_REF] Hughes | Multiple stressors on coral reefs: a long-term perspective[END_REF]. However, the highest cover of M. platyphylla (3.2%) occurred on the upper slope where wave breaking first occurs, i.e. wave energy is the highest. Many studies investigating spatial distributions in coral reef communities often find that high energy reef zones restrict species' distributions and cover [START_REF] Dollar | Wave stress and coral community structure in Hawaii[END_REF][START_REF] Storlazzi | Wave control on reef morphology and coral distribution: Molokai, Hawaii[END_REF]. M. platyphylla shows the opposite trend: we observed high density and cover in the upper slope, a high energy reef zone, where colonies are growing in a contagious pattern of distribution. Such differences in fire coral distribution patterns in habitats of high energy are mostly related to the wave-vulnerable sheet tree morphology of Millepora. This growth form occurred nearly exclusive on the upper slope, while colonies were massive or encrusting in other habitats. The unusual sheet tree morphology observed in the upper slope has been described as a successful strategy exploited by Millepora to preempt the space and to compete with other coral taxa [START_REF] Jackson | Morphological strategies of sessile animals[END_REF][START_REF] Dubé | Overgrowth of living scleractinian corals by the hydrocoral Millepora platyphylla in Moorea, French Polynesia[END_REF]. Waves can easily break the blades and enhance population size through clonal propagation [START_REF] Edmunds | The role of colony morphology and substratum inclination in the success of Millepora alcicornis on shallow coral reefs[END_REF], while the encrusting bases remain intact and grow through stolonal spreading [START_REF] Dubé | Overgrowth of living scleractinian corals by the hydrocoral Millepora platyphylla in Moorea, French Polynesia[END_REF]). The fact that M. platyphylla can rapidly overtake newly available space through clonal propagation and stolonal spreading may explain the increase of fire coral cover on Moorea's reefs following the massive decline in coral cover from the Acanthaster outbreaks and cyclone Oli [START_REF] Kayal | Predator crown-of-thorns starfish (Acanthaster planci) outbreak, mass mortality of corals, and cascading effects on reef fish and benthic communities[END_REF].

Between 2006 and 2010, M. platyphylla cover was stable at approximately 1% at 6 m on the fore reef, i.e. more than 3 times lower than in 2013 at the same location. On the other hand, fragmentation usually induces corals to regress in size and increases mortality, especially in small size classes [START_REF] Wallace | Reproduction, recruitment and fragmentation in nine sympatric species of the coral genus Acropora[END_REF]. Here, the sheet tree morphology is more easily fragmented, but the unilateral growth of Millepora allows them to reach larger sizes. This study shows that asexual reproduction through fragmentation and stolonal spreading likely play a key role in structuring M.

platyphylla populations where water flow is high and where fire corals suffer wave-induced breakage.

In the lagoonal environment, the wave energy is reduced by the reef crest [START_REF] Ferrario | The effectiveness of coral reefs for coastal hazard risk reduction and adaptation[END_REF] likely explaining the positive stock-recruitment relationship found in these habitats. There is evidence showing that the fecundity in populations of sessile marine broadcast spawners, such as Millepora species, is strongly determined by the local density of adults [START_REF] Coma | Effects of spatial distribution and reproductive biology on in situ fertilization rates of a broadcast-spawning invertebrate[END_REF]Hughes et al. 2000), and especially where water movement is reduced and local retention occurs.

The low abundance of early life stages observed in all lagoonal habitats may result from competition with macroalgae and sediment smothering affecting back, patch and fringing reefs inside the lagoon of Moorea [START_REF] Galzin | Moorea Island, Society Archipelago[END_REF]. The presence of macroalgae and high sedimentation can additionally reduce adults' fecundity [START_REF] Richmond | Coral reefs: present problems and future concerns resulting from anthropogenic disturbance[END_REF][START_REF] Hughes | Phase shifts, herbivory, and the resilience of coral reefs to climate change[END_REF][START_REF] Foster | Competitive effects of macroalgae on the fecundity of the reef-building coral Montastraea annularis[END_REF], larval settlement cues [START_REF] Kuffner | Inhibition of coral recruitment by macroalgae and cyanobacteria[END_REF], larval survival [START_REF] Gilmour | Experimental investigation into the effects of suspended sediment on fertilisation, larval survival and settlement in a scleractinian coral[END_REF]) and settlement space [START_REF] Box | Effect of macroalgal competition on growth and survival of juvenile Caribbean corals[END_REF]. Greater impacts of anchoring and poorer water quality compared to fore reef habitats also likely contribute to the low abundance of Milleporid corals inside the lagoon [START_REF] Fichez | A review of selected indicators of particle, nutrient and metal inputs in coral reef lagoon systems[END_REF][START_REF] Cooper | Gradients in water column nutrients, sediment parameters, irradiance and coral reef development in the Whitsunday Region, central Great Barrier Reef[END_REF]). The back and patch reefs are the nearest to the reef crest where waves break resulting in low residence times and high flushing rates from large incoming waves that break on the north shore of Moorea during the austral summer [START_REF] Hench | Episodic circulation and exchange in a wave-driven coral reef and lagoon system[END_REF]). These dynamics of water flow are known to negatively affect local recruitment rates of sexual propagules in scleractinian corals on the back reef of Moorea [START_REF] Edmunds | Landscape-scale variation in coral recruitment in Moorea, French Polynesia[END_REF]) and could also apply to M. platyphylla. In the lagoon, fire corals are characterized by wave-tolerant morphologies (i.e. encrusting and massive) suggesting that asexual reproduction through colony fragmentation is less likely of structuring importance compared to fore reef habitats. Colonies on the fringing reef, where wave energy is typically low, were distributed in patches. In Moorea, the fringing reef is exposed to large waves in the austral summer [START_REF] Hench | Episodic circulation and exchange in a wave-driven coral reef and lagoon system[END_REF]), which has the potential to enhance the breakage of the colonies during short periods. Subsequent calm periods can facilitate fragment survival and reattachment resulting in the patches of M. platyphylla observed.

It must be noted that abundance of recruits and juveniles was likely underestimated in this study as they are difficult to find due to their small size during field surveys. Still, we identified 32% of colonies < 20 cm 2 (recruit and juvenile), a higher fraction than observed for 14 different genera of scleractinians corals in Moorea (13-29%, see [START_REF] Penin | Spatial distribution of juvenile and adult corals around Moorea (French Polynesia): Implications for population regulation[END_REF]). The abundance of fire corals around Moorea is also higher compared to more diverse and healthy reefs, such as the Great Barrier

Reef [START_REF] Done | Patterns in the distribution of coral communities across the central Great Barrier Reef[END_REF]) and the shallow fringing reefs in the Virgin Islands [START_REF] Brown | Long-term changes in the population dynamics of the Caribbean hydrocoral Millepora spp[END_REF].

Our results thus suggest that fire coral populations are relatively resilient in the face of recent and major disturbances that have impacted Moorea's reefs. The maintenance and recovery of fire coral

Abstract

Quantifying the genetic diversity in natural populations is crucial to address ecological and evolutionary questions. Despite recent advances in whole-genome sequencing, microsatellite markers have remained one of the most powerful tools for a myriad of population genetic approaches. Here, we used the 454 sequencing technique to develop microsatellite loci in the fire coral Millepora platyphylla, an important reef-builder of Indo-Pacific reefs. We tested the crossspecies amplification of these loci in five other species of the genus Millepora and analyzed its success in correlation with the genetic distances between species using mitochondrial 16S sequences. We succeeded in discovering fifteen microsatellite loci in our target species M.

platyphylla, among which twelve were polymorphic with 2 to 13 alleles and a mean observed heterozygosity of 0.411. Cross-species amplification in the five other Millepora species revealed a high probability of amplification success (71%) and polymorphism (59%) of the loci. Our results

show no evidence of decreased heterozygosity with increasing genetic distance. However, only one locus enabled measures of genetic diversity in the Caribbean species M. complanata due to high proportions of null alleles for most of the microsatellites. This result indicates that our novel markers may only be useful for the Indo-Pacific species of Millepora. Measures of genetic diversity revealed significant linkage disequilibrium, moderate levels of observed heterozygosity (0.323-0.496) and heterozygote deficiencies for the Indo-Pacific species. The accessibility to new polymorphic microsatellite markers for hydrozoan Millepora species creates new opportunities for

Introduction

Coral reefs are increasingly threatened by chronic and acute stressors [START_REF] Bellwood | Confronting the coral reef crisis[END_REF]) and are expected to be highly vulnerable to future climate change due to rapidly increasing sea surface temperatures and ocean acidification [START_REF] Hoegh-Guldberg | Coral reefs under rapid climate change and ocean acidification[END_REF][START_REF] Pandolfi | Projecting coral reef futures under global warming and ocean acidification[END_REF][START_REF] Kuffner | A century of ocean warming on Florida Keys coral reefs: historic in situ observations[END_REF]. These anthropogenic disturbances can further change the biodiversity in coral reefs and may hamper their capacity to deliver important sources of ecosystem services to millions of people [START_REF] Wilkinson | Global Coral Reef Monitoring Network and Reef and Rainforest Research Center[END_REF][START_REF] Cardinale | Biodiversity loss and its impact on humanity[END_REF]. The capacity of reef organisms to survive and adapt to such environmental changes will partially depend on their levels of genetic diversity, which is key for a species' ability to persist in changing environments [START_REF] Frankham | Genetics and extinction[END_REF] Millepora hydrocorals are an important component of reef communities worldwide where they, similar to scleractinian corals, significantly contribute to reef accretion (Nagelkerken and Nalgelkerken 2004;[START_REF] Lewis | Biology and ecology of the hydrocoral Millepora on coral reefs[END_REF]. Although fire corals compete with other reef-building taxa [START_REF] Wahle | Detection, pursuit, and overgrowth of tropical gorgonians by milleporid hydrocorals: Perseus and Medusa revisited[END_REF][START_REF] Dubé | Overgrowth of living scleractinian corals by the hydrocoral Millepora platyphylla in Moorea, French Polynesia[END_REF], they also favor coral survival during Acanthaster outbreaks, highlighting their key ecological role in reef resilience [START_REF] Kayal | Colonies of the fire coral Millepora platyphylla constitute scleractinian survival oases during Acanthaster outbreaks in French Polynesia[END_REF]. Despite their major importance for reef conservation, fire corals have been relatively understudied and not much is known with respect to their genetic diversity, population structure or life history (e.g. reproductive strategies).

Few studies have shown that Millepora species can colonize a wide range of reef environments via both sexual propagules [START_REF] Lewis | Biology and ecology of the hydrocoral Millepora on coral reefs[END_REF][START_REF] Bourmaud | Mass spawning events, seasonality and reproductive features in Milleporids (Cnidaria, Hydrozoa) from Reunion Island[END_REF]) and asexual reproduction through fragmentation [START_REF] Edmunds | The role of colony morphology and substratum inclination in the success of Millepora alcicornis on shallow coral reefs[END_REF][START_REF] Lewis | Biology and ecology of the hydrocoral Millepora on coral reefs[END_REF]). While they are sessile and have limited tolerance to environmental changes [START_REF] Lewis | Biology and ecology of the hydrocoral Millepora on coral reefs[END_REF], species of Milleporidae have a wide distribution range, i.e.

circumtropical [START_REF] Boschma | Milleporina and Stylasterina[END_REF]). Fire corals are also known for their extensive morphological variability, which has caused problems in resolving their systematics [START_REF] Boschma | The species problem in Millepora[END_REF]

Materials and Methods

Preparation of genomic DNA for 454 sequencing for the target species

The calcification processes [START_REF] Stanley | Photosymbiosis and the evolution of modern coral reefs[END_REF]) and metabolic pathways [START_REF] Trench | The cell biology of plant-animal symbiosis[END_REF] . DNA was purified with phenol/chloroform (24:1) and precipitated with isopropanol as described by [START_REF] Mieog | Quantification of algal endosymbionts (Symbiodinium) in coral tissue using real-time PCR[END_REF]. Samples from the 14 colonies were pooled together to increase detection of polymorphism. A total of 1 µg of genomic DNA was sent to GenoScreen platform (Lille, France) for the development of the microsatellite library using 454 GS-FLX Titanium reagents as described in [START_REF] Malausa | High-throughput microsatellite isolation through 454 GS-FLX Titanium pyrosequencing of enriched DNA libraries[END_REF]. Briefly, total DNA was mechanically fragmented and enriched for TG, TC, AAC, AAG, AGG, ACG, ACAT and ACTC repeat motifs. Enriched fragments were subsequently amplified and PCR products were purified and quantified. GS-FLX libraries were then carried out following manufacturer's protocols and sequenced on a GS-FLX PTP. The Quality Detection Device (QDD) pipeline [START_REF] Martin | Representativeness of microsatellite distributions in genomes, as revealed by 454 GS-FLX titanium pyrosequencing[END_REF] was used to analyze the 454 sequences and to design primers for amplification of the detected microsatellite motifs. Primer pairs were then selected depending on the motif (di-, tri-, tetranucleotide), the number of repeats (≥ 5) and the product size (≥ 100 bp) and tested on agarose gels for amplification.

Microsatellite discovery and primer testing

A panel of 16 M. platyphylla colonies was used to optimize PCR amplification and identify polymorphic loci. Small fragments of tissue-covered skeleton (< 2 cm 3 ) were incubated at 55 ºC for 1 hr in 450 µL of digest buffer with proteinase K (QIAGEN, Hilden, Germany). Genomic DNA was extracted using a QIAxtractor automated genomic DNA extraction instrument, according to manufacturer's instructions. PCRs were performed in a final volume of 10 µL including 5 µL Typeit Multiplex PCR Master Mix (1x) (QIAGEN, Hilden, Germany), 3 µL RNase-free water, 1 µL primers (2 µM for both forward and reverse primers diluted in TE buffer) and 1 µL of template ( 10to 50 ng/µL). The PCR program included an initial denaturing step of 5 min at 95 ºC, followed by 40 cycles of 30 sec at 95 ºC, 90 sec at optimal temperature (57-60 ºC) depending on the microsatellite locus (see Table 4.1), and 30 sec at 72 ºC, followed by a final 30 min elongation step at 60 ºC. The PCR products were electrophoresed on 2% agarose gels. For loci with high-quality and consistent amplification, the PCR was repeated on DNA template isolated from Symbiodinium strains (clade A to F identified based on 23S chloroplast rDNA, Table S1) to identify coral specific loci and to exclude putative Symbiodinium specific loci. Symbiodinium strains were provided by the BURR laboratory at Buffalo, US (BURR; http://www.nsm.buffalo.edu/Bio/burr/). For the loci that are specific to Millepora, the forward primer was fluorescently labelled with the G5 dye set including 6-FAM, VIC, NED and PET (Applied Biosystems, Foster City, CA). Amplified fragments were visualized on an Applied Biosystems 3730 Sequencer using a GeneScan 500 LIZ ladder.

Sampling, genotyping and cross-species amplification

The optimized loci were genotyped in our target species in addition to five other Millepora species to test for their transferability. For the characterization of newly developed microsatellites, small fragments (< 2 cm 3 ) from 50 M. platyphylla colonies were collected on the reefs of Moorea in French Polynesia (CITES -FR1298700028-E). For cross-species amplification transferability tests, samples were collected from various locations in the Indo-Pacific and the Caribbean for five other species of fire corals: 11 M. intricata in Papua New Guinea, 30 M. dichotoma in Europa Island (Mozambique Canal), 30 M. tenera and 14 M. exaesa both in Reunion Island and 30 M. complanata in Curaçao (Table S2). DNA from the 165 Millepora colonies was extracted as described above and optimized loci were combined in four multiplex panels according to their allele size range and 4.1). PCRs (10 µL) were performed with 2 µM of labelled forward primer and reverse primer with the same amplification conditions described above.

PCR products were sent to GenoScreen (Lille, France) for fragment analysis and were visualized using an Applied Biosystems 3730 Sequencer. An internal size ladder (GeneScan 500 LIZ, Applied Biosystems) was used for accurate sizing and alleles were scored and checked manually using GENEMAPPER v.4.0 (Applied Biosystems, Foster City, CA). Samples that were ambiguous in scoring were re-amplified and re-scored. All peak profiles that were faint or ambiguous (i.e.

multiple peaks) were considered as missing data.

Phylogenetic analyses

Additionally, a 461 bp portion of the mitochondrial 16S gene was amplified for 30 specimens (five colonies per species) and used to estimate the genetic distances among the six Millepora species.

The PCR amplifications were performed using the primers 16S-SHA and 16S-SHB [START_REF] Cunningham | Molecular evidence for multiple episodes of paedomorphosis in the family Hydractiniidae[END_REF] in 20 µL reactions containing: 1.5 mM of MgCl 2 , 0.2 mM of each dNTP, 1X final concentration of buffer, 0.5 µM of each primer, 0.25 unit of Red Hot Taq polymerase, 2 µL of DNA template (80 to 100 ng/µL) and sterilized water up to 20 µL. The cycling parameters were as follows: an initial denaturation step of 5 min at 94 °C, followed by 35 cycles of 1 min at 94 °C, 1 min at 50 °C, 1.5 min at 72 °C and a final elongation step of 5 min at 72 °C. Sequencing of the PCR products was performed by GenoScreen (Lille, France).

Data analyses

Control for the presence of null alleles, scoring errors and large allele dropout were performed with MICROCHECKER v.3.7 (van Oosterhout et al. 2004). To assess the discriminative power of the microsatellite markers, the genotype probability (GP) was estimated for each locus and for a combination of all loci using GENALEX v.6.5 [START_REF] Peakall | GENALEX 6: genetic analysis in Excel. Population genetic software for teaching and research[END_REF]. Repeated multilocus genotypes (MLGs) were also identified in GENALEX and were considered as clone mates at GP < 0.001. The probability of identity, P (ID) , was computed to evaluate the power of our microsatellites to accurately distinguish closely related genotypes from those produced by asexual reproduction [START_REF] Waits | Estimating the probability of identity among genotypes in natural populations: cautions and guidelines[END_REF]. Population genetic analyses were then performed after the removal of all clonal replicates. Indices of genetic diversity were estimated for each species in all locations using GENALEX, including Na, the total number of alleles per locus, observed (H O ) and expected (He) heterozygosity [START_REF] Weir | Estimating F-statistics for the analysis of population structure[END_REF]. The inbreeding coefficient F IS and linkage disequilibrium were estimated using GENETIX v.4.02 [START_REF] Belkhir | GENETIX 4.05 Logiciel sous Windows pour la Génétique des Poplulations[END_REF], applying a permutation procedure (1000 permutations) to assess statistical significance. GENETIX was also used to estimate genetic distance among populations of M. platyphylla and the other Millepora species with the microsatellite dataset using the θ estimator of F ST [START_REF] Weir | Estimating F-statistics for the analysis of population structure[END_REF] based on a permutation procedure (1000 permutations). Genetic p-distances among species at the mtDNA 16S gene were calculated in Mega v.6 [START_REF] Tamura | MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0[END_REF]). In addition to the p-distance, we also computed other genetic distances (i.e. Kimura-2-Parameters, Tamura & Nei and Maximum composite Likelihood, all available in the software Mega v.6) and found similar species rank among all measures tested. We also examined the cross-species amplification success of the new microsatellite markers by plotting the genetic diversity (Ho) and the proportions of missing data (non amplified loci after 3x repeat PCR, and this at different annealing temperatures) in each species against genetic distance (16S) and relationships were tested using Pearson's correlation coefficient.

Results

Development of de novo microsatellites in Millepora platyphylla

Sequencing of the microsatellite-enriched library from 14 partially bleached fragments of M. platyphylla yielded 78,784 reads. The Quality Detection Device (QDD) for bioinformatic filtering resulted in a final set of 5976 sequences containing microsatellite motifs. For the characterization of new microsatellites, 127 primer pairs (out of the 186 resulting from the QDD filtering, 68.3%) were tested in 16 individuals of M. platyphylla collected on Moorea's reefs. Fifteen loci showed clear amplification profiles and no Symbiodinium specific locus was identified, proving the efficiency of the DNA extraction technique. For the 50 M. platyphylla colonies collected on Moorea's reefs, twelve loci were polymorphic (from 2 to 13 alleles) and three additional monomorphic loci were retained for further cross-species transferability tests (Table 4.1). Contig sequences containing the microsatellites identified in this study are available in GenBank (KX670763-KX670777, Table 4.1).

Significant linkage disequilibrium was identified and distributed among all microsatellite loci in M. platyphylla. 9.1% of the pairwise locus combinations showed a significant probability of linkage disequilibrium at P < 0.05 (Table 4.2). The presence of null alleles was detected at Mill47 and Mill67 with frequencies of null alleles at both loci estimated at 10.1% and 14.4%, respectively. These two loci were removed from our dataset for further genetic analyses, although there was no evidence of scoring error or large allele dropout for any locus. Given the low P (ID) value estimated (1.3E-6), our panel of microsatellites had a high power to distinguish colonies that were clonal replicates. For the ten polymorphic loci showing no evidence of null alleles, the mean number of alleles (Na) per locus was 3.462 and the observed heterozygosity (Ho) was 0.411 (Table 4.2). Only three loci out of fifteen showed significant deficiency in heterozygotes compared to HWE and only one of them showed no evidence of null alleles (Mill07, F IS : 0.121, Table 4.1). Clonal replicates were found in the three branching species: 1 clonal MLG in M. intricata, 4 in M.

Cross-species amplification in Milleporidae

dichotoma and 6 in M. tenera (Table 4.2). The mean observed heterozygosity per locus was highly variable in all species, although more limited in M. tenera and M. complanata due to high proportions of null alleles in both species (Fig. 4.1B and Table S3). No significant correlation was found between the genetic diversity and mtDNA genetic distance (r = -0.175, P = 0.101). The mean observed heterozygosity was slightly reduced for M. complanata (0.250) compared to other species (0.323 for M. dichotoma ≤ Ho ≤ 0.496 for M. exaesa) (Table 4.2). However, Ho estimate in M.

complanata was based on only one microsatellite locus (Mill 103,Fig. 4.1B). For the four other non-target species, 2 loci out of 15 showed significant deficiencies in heterozygotes compared to HWE in M. dichotoma (Mill07 and Mill67, F IS : 1.000) and another one in M. intricata (Mill101, F IS : 0.500) (Table S3).

The transferability of microsatellites in the Milleporidae also revealed strong genetic differentiation among some species (

Discussion

Development of microsatellites and their transferability in Milleporidae

To date, there is no study assessing the genetic diversity and population structure of fire coral species. This gap is mostly due to the lack of highly variable genetic markers in the genus until very recently, whereas microsatellite loci have been identified in the Caribbean species Millepora alcicornis (Ruiz-Ramos and Baums 2014). [START_REF] Heckenhauer | Isolation, characterization and cross amplification of eleven novel microsatellite loci for the hydrozoan coral Millepora[END_REF] have succeeded in developing eleven microsatellite markers for M. dichotoma from the Great Barrier Reef and showed that their transferability was successful between geographic regions (Red Sea) and the species M. platyphylla.

Their study has shown that eight of the eleven microsatellite markers (72.7%) were transferable to M. platyphylla which is less to what we had in the present study (i.e. 86.7% between M. dichotoma and M. platyphylla). Six of their loci had only 2 alleles for M. platyphylla, which is not informative enough depending on the analyses performed (e.g. parentage analyses). Furthermore, most of the microsatellite markers developed by [START_REF] Heckenhauer | Isolation, characterization and cross amplification of eleven novel microsatellite loci for the hydrozoan coral Millepora[END_REF] were characterized by significant deficiencies in heterozygotes, whereas only two of our loci showed such HWE disequilibrium in both of these species. Depending on the target species, a combination of markers from the two studies would thus seem a good strategy for population genetic approaches in Millepora hydrocorals.

Our cross-amplification tests show a higher cross-taxon transferability success (73.3-86.7%) for a genetic distance below 5% from our target species (i.e. M. intricata, M. dichotoma and M. tenera)

and a reduced transferability above this level (≤ 60% for M. complanata and M. exaesa). Overall, our results show a high probability to amplify a microsatellite locus within the genus Millepora, where 71% of the loci were successfully amplified in the five non-target species. This value is slightly lower to what was demonstrated for the Caribbean Montastraea species complex (scleractinian corals), i.e. ~80% of amplification success in two other species within the same location [START_REF] Davies | Novel polymorphic microsatellite markers for populations genetics of the endangered Caribbean star coral, Montastraea faveolata[END_REF]. Our lower value, while still very high, is not surprising as we tested cross-amplification between six species of the genus Millepora (i.e. no species complex as for Montastraea spp), which were also collected throughout their entire geographic range. The nonamplification of some microsatellite loci in the non-target species is most likely due to specific mutations in the primer binding sites in M. platyphylla, i.e. null alleles [START_REF] Paetkau | The molecular-basis and evolutionary history of a microsatellite null allele in bears[END_REF]. These loci, specific to Moorea's population, may result from local evolutionary processes at this location, such as bottlenecks, expansions, life history traits, inbreeding and outbreeding [START_REF] Keller | Inbreeding effects in wild populations[END_REF][START_REF] Leffler | Revisiting an old riddle: what determines genetic diversity levels within species?[END_REF][START_REF] Romiguier | Comparative population genomics in animals uncovers the determinants of genetic diversity[END_REF]. Our cross-amplified loci show a high probability to be polymorphic in non-target species (58.7%), which is much higher to what is generally found in other taxa, such as fishes (~25-30% in [START_REF] Barbará | Cross-species transfer of nuclear microsatellite markers: potential and limitations[END_REF][START_REF] Reid | High-throughput microsatellite marker development in two sparid species and verification of their transferability in the family Sparidae[END_REF]) and birds (~20-50% in [START_REF] Dawson | New methods to identify conserved microsatellite loci and develop primer sets of high cross-species utilityas demonstrated for birds[END_REF]. Many other studies using cross-amplification have shown a significant decrease in the transferability success and polymorphism with evolutionary distance from the target species [START_REF] Jan | Development of conserved microsatellite markers of high cross-species utility in bat species (Vespertilionidae, Chiroptera, Mammalia)[END_REF][START_REF] Maduna | Microsatellite crossspecies amplification and utility in southern African elasmobranchs: a valuable resource for fisheries management and conservation[END_REF][START_REF] Moodley | Evolutionary factors affecting the cross-species utility of newly developed microsatellite markers in seabirds[END_REF].

Usefulness of cross-species amplification in Milleporidae

The level of genetic diversity is key for the persistence of a species in changing environments and represents a fundamental aspect of biodiversity [START_REF] Romiguier | Comparative population genomics in animals uncovers the determinants of genetic diversity[END_REF]. Quantifying the genetic diversity in natural populations and species is critical to address ecological and evolutionary questions [START_REF] Nair | Conservation genomics[END_REF], which requires the development of suitable molecular resources. In this study, our cross-species amplification approach for the development of new microsatellites shows no significant evidence of lower genetic diversity nor greater proportion of null alleles with increasing genetic distance from our target species, which is in contradiction with previous studies [START_REF] Carreras-Carbonell | Utility of pairwise mtDNA genetic distances for predicting cross-species microsatellite amplification and polymorphism success in fishes[END_REF][START_REF] Hendrix | Strong correlation between crossamplification success and genetic distance across all members of 'True Salamanders' (Amphibia: Salamandridae) revealed by Salamandra salamandra-specific microsatellite loci[END_REF][START_REF] Moodley | Evolutionary factors affecting the cross-species utility of newly developed microsatellite markers in seabirds[END_REF]. Our results also show that most of our microsatellite markers are not useful to estimate the genetic diversity in the Caribbean species M. complanata due to the high proportion of null alleles. Hence, this study reveals that the transferability of our microsatellites ensures comparable estimations of the genetic diversity among closely related Millepora species, although restricted to the Indo-Pacific region.

Further investigations with other Caribbean species, such as M. alcicornis, are needed to test their transferability in this geographic region.

In this study, we also found that genetic distance from interspecific microsatellite data were not congruent with mtDNA distance among the studied species. It is not surprising as such highly variable markers would suffer from homoplasy as one look into higher taxon relationships, while microsatellites are well-known to be mostly useful for intra-specific studies [START_REF] Selkoe | Microsatellites for ecologists: a practical guide to using and evaluating microsatellite markers[END_REF]. Nonetheless, assessment of the population structure among closely related Indo-Pacific species revealed a clear genetic differentiation between the branching species and the plate-like M.

platyphylla. Our panel of new microsatellite loci is therefore useful for species delineation and can help resolve the century-old species problem in Milleporids [START_REF] Boschma | The species problem in Millepora[END_REF].

Patterns of genetic diversity and population structure in Milleporidae

The was described for many tropical scleractinian species [START_REF] Baums | A restoration genetics guide for coral reef conservation[END_REF][START_REF] Shearer | Restoration of coral populations in light of genetic diversity estimates[END_REF] and to what is expected in populations of partially clonal organisms. In this study, linkage disequilibrium, relatively high levels of allelic and genetic diversity, and heterozygote deficiencies were estimated for the six studied hydrocoral species, as previously described in some scleractinian corals [START_REF] Baums | A restoration genetics guide for coral reef conservation[END_REF]. Overall, these new microsatellites are suitable to infer genetic diversity and to evaluate reproductive strategies in the partially clonal fire corals.

Conclusions

This study highlights the utility of cross-species amplification of microsatellites in assessing population genetics of the Millepora genus in the Indo-Pacific region. Surprisingly, this approach does not result in lowering genetic diversity (Ho) in non-target species, thus ensuring an unbiased estimation of genetic diversity among fire coral species. The development of microsatellites can be complex and difficult in many taxa, such as birds [START_REF] Primmer | Low frequency of microsatellites in the avian genome[END_REF]) and plants [START_REF] Lagercrantz | The abundance of various polymorphic microsatellite motifs differ between plants and vertebrates[END_REF], due to biological constraints that can affect the abundance and motif repeats of

Supporting Information

M. complanata 30 0 0 --- --- 0 --- --- --- M. exaesa 14 0 0 --- --- 0 --- --- --- Mill30 57 M. intricata 11 0 0 --- --- 0 --- --- --- M. dichotoma 30 0 0 --- --- 0 --- --- --- M.
--- --- 1 0 0 --- Mill61 57 M. intricata 11 0 0 --- --- 0 --- --- --- M. dichotoma 30 0 0 --- --- 0 --- --- --- M. tenera 30 0 0 --- --- 0 --- --- --- M. complanata 30 0 0 --- --- 0 --- --- --- M. exaesa 14 0 0 --- --- 0 --- --- --- Mill67
0 --- --- 0 --- --- --- M. exaesa 14 0 0 --- --- 0 --- --- --- 4 Genetic diversity and differentiation in reef-building Millepora Mill86 55 M. intricata 11 0 0 --- --- 0 --- --- --- M. dichotoma 30 30 97 --- --- 1 0 0 --- M. tenera 30 0 0 --- --- 0 --- --- --- M. complanata 30 0 0 --- --- 0 --- --- --- M. exaesa 14 0 0 --- --- 0 --- --- --- Mill91 57 M. intricata 11 11 116 --- --- 1 0 0 --- M. dichotoma 30 30 116 --- --- 1 0 0 --- M. tenera 30 30 116 --- --- 1 0 0 --- M.

Fire coral clones demonstrate phenotypic plasticity among reef habitats

Caroline E. Dubé* †, Emilie Boissin* †, Jeffrey A. Maynard † ‡, Serge Planes* † Nearly all fire corals in the other habitats are encrusting or massive. M. platyphylla population is highly clonal (80% of the colonies are clones), while characterized by the highest genotype diversity ever documented for terrestrial or marine populations (1064 genotypes). The proportion of clones varies greatly among habitats (≥ 58-97%) and clones (328 clonal lineages) are distributed perpendicularly from the reef crest, perfectly aligned with wave energy. There are six clonal lineages with clones dispersed in at least two adjacent habitats that strongly demonstrate phenotypic plasticity. 80% of the colonies in these lineages are 'sheet tree' on the upper slope, while 80 to 100% are encrusting or massive on the mid slope and back reef. This is a unique example of phenotypic plasticity among reef-building coral clones as corals typically have wave-tolerant growth forms in high-energy reef areas.

Introduction

There are terrestrial and marine species that can reproduce both sexually and asexually, including: bacteria, fungi, plants and invertebrates. Each reproductive mode confers different advantages under variable environmental conditions [START_REF] Williams | Sex and evolution[END_REF][START_REF] Eckert | The loss of sex in clonal plants[END_REF]. Sexual reproduction produces genetically diverse propagules able to survive within a range of environmental conditions and generates the genotypic variation required for adaptation [START_REF] Rice | Sexual recombination and the power of natural selection[END_REF]. Asexual reproduction allows the propagation of locally adapted genotypes and their persistence in the absence of sexual partners [START_REF] Miller | The role of sexual and asexual reproduction in structuring high latitude populations of the reef coral Pocillopora damicornis[END_REF][START_REF] Gorospe | Genetic relatedness does not retain spatial pattern across multiple spatial scales: dispersal and colonization in the coral, Pocillopora damicornis[END_REF][START_REF] Baums | Marginal coral populations: the densest known aggregation of Pocillopora in the Galapagos Archipelago is of asexual origin[END_REF]).

However, the production of asexual offspring only preserves existing genotypic diversity, because it prevents recombination [START_REF] Honnay | Prolonged clonal growth: escape route or route to extinction[END_REF]. Determining the relative contributions of sexual and asexual reproduction to population persistence can reveal insights into species' response to local stress.

Our understanding of how the contribution of each reproductive mode affects the genetic makeup and connectivity of marine species has improved considerably over the last decade (Pinzόn et al. 2012;[START_REF] Adjeroud | Genetic diversity, clonality and connectivity in the scleractinian coral Pocillopora damicornis: a multi-scale analysis in an insular, fragmented reef system[END_REF][START_REF] Baums | Marginal coral populations: the densest known aggregation of Pocillopora in the Galapagos Archipelago is of asexual origin[END_REF]. This research has shown that clonal reproduction can be an efficient means to expand populations locally when unfavorable conditions impede sexual reproduction. Such conditions include: fragmented [START_REF] Adjeroud | Genetic diversity, clonality and connectivity in the scleractinian coral Pocillopora damicornis: a multi-scale analysis in an insular, fragmented reef system[END_REF]) and marginal habitats [START_REF] Baums | Marginal coral populations: the densest known aggregation of Pocillopora in the Galapagos Archipelago is of asexual origin[END_REF], high disturbance frequency [START_REF] Foster | Hurricane-driven patterns of clonality in an ecosystem engineer: the Caribbean coral Montastraea annularis[END_REF], or high stress related to human activities [START_REF] Oliva | Reproductive strategies and isolation-by-demography in a marine clonal plant along an eutrophication gradient[END_REF]. Many coral reef organisms can reproduce through both sexual and asexual reproduction, such as scleractinian corals [START_REF] Harrison | Sexual reproduction of scleractinian corals[END_REF], hydrocorals [START_REF] Lewis | Biology and ecology of the hydrocoral Millepora on coral reefs[END_REF], coralline algae [START_REF] Pearson | Patterns of reproduction, genetic diversity, and genetic differentiation in California populations of the geniculate coralline alga Lithothrix aspergillum (Rhodophyta)[END_REF] and sponges [START_REF] Whalan | Mode of reproduction, recruitment, and genetic subdivision in the brooding sponge Haliclona sp[END_REF]. Environmental conditions (e.g. temperature [START_REF] Glynn | Coral reef bleaching: facts, hypotheses and implications[END_REF], light [START_REF] Vermeij | How are coral populations structured by light? Marine light regimes and the distribution of Madracis[END_REF], water flow [START_REF] Monismith | Hydrodynamics of coral reefs[END_REF]) and water quality conditions [START_REF] Fabricius | Effects of terrestrial runoff on the ecology of corals and coral reefs: review and synthesis[END_REF])) vary greatly among coral reef habitats and these conditions can impose divergent selection pressures. Consequently, populations of reefbuilding organisms can evolve differences in morphology, reproductive modes and dispersal abilities [START_REF] Sanford | Local adaptation in marine invertebrates[END_REF][START_REF] Darling | Evaluating life-history strategies of reef corals from species traits[END_REF].

Most reef-building corals (e.g. scleractinian corals, gorgonian corals and hydrozoan corals) are vulnerable to wave-induced breakage and dislodgment, and rely on a pelagic dispersal phase for subsequent recruitment. For that reason, hydrodynamic forces, especially flow velocity [START_REF] Lenihan | Hydrodynamics influence coral performance through simultaneous direct and indirect effects[END_REF], are key factors in determining coral distribution patterns and life history traits (Brown 1997;Madin et al. 2006;[START_REF] Denny | Marine ecomechanics[END_REF]. In most reefs, water flow velocity is driven by wave energy dispersal [START_REF] Hearn | Wave-breaking hydrodynamics within coral reef systems and the effect of changing relative sea-level[END_REF][START_REF] Hench | Episodic circulation and exchange in a wave-driven coral reef and lagoon system[END_REF][START_REF] Lowe | Wave-driven circulation of a coastal reef-lagoon system[END_REF][START_REF] Monismith | Wave transformation and wavedriven flow across a steep coral reef[END_REF]).

On barrier reefs (as in Moorea), the amount of wave energy is highest on the upper slope and reef crest, where wave breaking first occurs, and subsequently attenuates towards lagoonal environments [START_REF] Monismith | Hydrodynamics of coral reefs[END_REF][START_REF] Ferrario | The effectiveness of coral reefs for coastal hazard risk reduction and adaptation[END_REF]. This gradient in wave energy (and flow velocity), combined with other specific habitat physical factors (e.g. light, nutrients) and disturbances (e.g. cyclones, Acanthaster outbreaks, sewages) can influence coral performance [START_REF] Lenihan | Hydrodynamics influence coral performance through simultaneous direct and indirect effects[END_REF]. Wave energy gradients can also mediate the distribution of corals within reefs due to its influence on colony growth and skeleton density [START_REF] Highsmith | Reproduction by fragmentation in corals[END_REF][START_REF] Heyward | Fragmentation in Montipora ramosa: the genet and ramet concept applied to a reef coral[END_REF][START_REF] Bruno | Clonal variation for phenotypic plasticity in the coral Madracis mirabilis[END_REF]. Further, wave energy gradients can affect the local dispersal of both sexual and asexual propagules [START_REF] Lirman | Lesion regeneration in the branching coral Acropora palmata: effects of colonization, colony size, lesion size, and lesion shape[END_REF][START_REF] Harrison | Sexual reproduction of scleractinian corals[END_REF]).Though all corals reproduce sexually and grow using asexual budding (i.e. modular organisms) [START_REF] Jackson | Competition on marine hard substrata: the adaptive significance of solitary and colonial strategies[END_REF], colony dispersal through fragmentation is generally restricted to corals with morphologies vulnerable to wave-induced breakage [START_REF] Storlazzi | A model for wave control on coral breakage and species distribution in the Hawaiian Islands[END_REF]Madin and Connolly 2006). Patterns of morphological plasticity driven by wave energy in corals have been modeled in a general form, with spherical and compact morphologies more prevalent in high energy reef habitats [START_REF] Kaandorp | Morphological models of radiate accretive growth and the influence of hydrodynamics[END_REF][START_REF] Chindapol | Modelling growth and form of the scleractinian coral Pocillopora verrucosa and the influence of hydrodynamics[END_REF]). However, the vast majority of studies on clonal reproduction and phenotypic plasticity in reef-building organisms have focused on scleractinian corals. The focus here is on Millepora hydrocorals ('fire corals'), which are component of reef communities worldwide and significantly contribute to reef accretion [START_REF] Nagelkerken | Loss of coral cover and biodiversity on shallow Acropora and Millepora reefs after 31 years on Curaçao, Netherlands Antilles[END_REF][START_REF] Lewis | Biology and ecology of the hydrocoral Millepora on coral reefs[END_REF].

Millepora species are conspicuous reef-builders that have successfully colonized a wide range of reef environments via both sexual propagules [START_REF] Lewis | Biology and ecology of the hydrocoral Millepora on coral reefs[END_REF][START_REF] Bourmaud | Mass spawning events, seasonality and reproductive features in Milleporids (Cnidaria, Hydrozoa) from Reunion Island[END_REF]) and clonal reproduction through fragmentation [START_REF] Edmunds | The role of colony morphology and substratum inclination in the success of Millepora alcicornis on shallow coral reefs[END_REF][START_REF] Lewis | Biology and ecology of the hydrocoral Millepora on coral reefs[END_REF]. Fire coral morphologies vary across the wave energy gradient in reef environments and vulnerability to fragmentation varies greatly among these morphologies [START_REF] Lewis | Biology and ecology of the hydrocoral Millepora on coral reefs[END_REF]. Millepora platyphylla is an important reef-builder in the Indo-Pacific, where it can dominate shallow reef communities [START_REF] Andréfouët | A monospecific Millepora reef in Marquesas Island, French Polynesia[END_REF]). This species can be encrusting or massive and can also grow as vertical sheet on encrusting bases (i.e. the 'sheet tree' morphology, [START_REF] Jackson | Morphological strategies of sessile animals[END_REF]). However, it is unknown whether/how phenotypic responses can govern clonal reproduction dynamics in natural populations. Assessing phenotypic plasticity within species exposed to contrasting environmental conditions requires clonal replicates of a single genotype.

We conducted an extensive field survey in five reef habitats in Moorea to examine the distribution of fire coral clones among reef habitats and assess whether/how morphologies vary among habitats.

We genotyped all georeferenced colonies of M. platyphylla (N = 3651) observed in five habitats using microsatellite markers and classified them into distinct morphologies to address these questions: (i) How does sexual and asexual reproduction and coral morphologies vary among

Materials and methods

Model species

Millepora platyphylla is a gonochoric broadcast spawner that reproduces sexually by producing medusoids and planula larvae [START_REF] Lewis | Biology and ecology of the hydrocoral Millepora on coral reefs[END_REF]. The medusoids release the gametes in the water column in one hour post-spawning and then external fertilization occurs. The larvae sink and move epibenthically (i.e. crawling not swimming) on the reef substratum and metamorphose in a new calcifying polyp in one day post-spawning [START_REF] Bourmaud | Mass spawning events, seasonality and reproductive features in Milleporids (Cnidaria, Hydrozoa) from Reunion Island[END_REF]. M. platyphylla also relies on clonal propagation through fragmentation [START_REF] Edmunds | The role of colony morphology and substratum inclination in the success of Millepora alcicornis on shallow coral reefs[END_REF][START_REF] Lewis | Biology and ecology of the hydrocoral Millepora on coral reefs[END_REF]) and stolonal spreading of their encrusting bases [START_REF] Dubé | Overgrowth of living scleractinian corals by the hydrocoral Millepora platyphylla in Moorea, French Polynesia[END_REF]). The production of asexual larvae has never been documented within the Millepora genus.

Field surveys

Between April and December 2013 a series of surveys were conducted on the north shore of Moorea, French Polynesia, at four different locations (Tiahura, Papetoai, Cook's Bay and Temae) across five distinct habitats; two on the fore reef: the mid slope (13 m depth) and upper slope (6 m depth), and three in the lagoon (< 1 m depth): the back reef, fringing reef and patch reef (Fig. S1 and Table S1). Wave energy generates an across-reef horizontal pressure from offshore reef towards the reef flat and lagoon [START_REF] Monismith | Hydrodynamics of coral reefs[END_REF]. The fore reef experiences strong wave action from incoming waves that break on the reef crest with a significant decrease in swell exposure towards deeper waters [START_REF] Hearn | Wave-breaking hydrodynamics within coral reef systems and the effect of changing relative sea-level[END_REF][START_REF] Monismith | Hydrodynamics of coral reefs[END_REF]. Fire coral colonies growing in the mid slope, at mid depth, are thus exposed to lower wave energy compared to those growing in the upper slope, near where waves break. A recent study demonstrated that the reef crest dissipates 70% of the incident swell wave energy with gradual wave attenuation from the back reef to nearshore fringing reefs [START_REF] Ferrario | The effectiveness of coral reefs for coastal hazard risk reduction and adaptation[END_REF]. Although the patch reef is located in a nearshore narrow channel, the wave energy there is similar to the back reef due to its proximity to the reef crest and is also influenced by the currents that run on either side of the channel (i.e. pass circulation). In summary, wave energy is low on the mid slope, high on the upper slope near where waves break, medium on the back reef and within patch reef and low on the fringing reef, a typical linear barrier reef environment. Within each habitat, three 300 m long by 10 m wide belt transects were set along the reef parallel to shore, representing 45,000 m 2 of reef. All colonies observed in our surveys were measured, photographed and georeferenced. Maps of the locations of each colony were produced using R (R Development Core Team 2013).

Morphology assessment

All colonies were classified as one of these morphologies: 1) encrusting: thin colonies growing against the substratum, 2) sheet tree: encrusting bases with vertical blade-like outgrowths and 3) massive: solid colonies, roughly hemispherical in shape (see photo series in Fig. 5.1). Colonies below 50 cm 2 were removed from our dataset to avoid misidentifying small colonies of M. platyphylla whose morphology is less distinct. Morphological variation among transects and habitats were quantified with a permutational multivariate analysis of variance using Bray-Curtis similarity coefficient (permanova test; PRIMER 6 software) [START_REF] Clarke | Testing of null hypotheses in exploratory community analyses: similarity profiles and biota-environment linkage[END_REF].

DNA extraction and microsatellite genotyping

Samples were preserved in 80% ethanol until DNA extraction. Small fragments of tissue-covered skeleton (< 2 cm 3 ) were incubated at 55 ºC for 1 hr in 450 µL of digest buffer with proteinase K (QIAGEN, Hilden, Germany). Genomic DNA was extracted using a QIAxtractor automated genomic DNA extraction instrument, according to manufacturer's instructions. Samples were amplified and genotyped at 12 microsatellite loci shown to be coral-specific and polymorphic in M. platyphylla. The primers used are listed in (Table S2). PCRs were performed in a final volume of 10 µL including 5 µL Type-it Multiplex PCR Master Mix (1x) (QIAGEN, Hilden, Germany), 3 µL RNase-free water, 1 µL primers (2 µM of fluorescently labelled forward primer -G5 dye set including 6-FAM, VIC, NED and PETand reverse primer diluted in TE buffer) and 1 µL of template (10 to 50 ng.µL -1 ). The PCR program included an initial denaturing step of 5 min at 95 ºC, followed by 40 cycles of 30 sec at 95 ºC, 90 sec at optimal temperature (53-63 ºC) depending on the microsatellite locus (see Table S2), and 30 sec at 72 ºC, followed by a final 30 min elongation step at 60 ºC. PCR products were sent to GenoScreen platform (Lille, France) for fragment analysis and were visualized using an Applied Biosystems 3730 Sequencer. An internal size standard (GeneScan 500 LIZ, Applied Biosystems) was used for accurate sizing and alleles were scored and checked manually using GENEMAPPER v.4.0 (Applied Biosystems, Foster City, CA). Samples that were ambiguous in scoring were re-amplified and re-scored. All peak profiles that were faint or ambiguous (i.e. multiple peaks) were considered as missing data. Control for the presence of null alleles and large allele dropout were performed with MICRO-CHECKER v.3.7 (van Oosterhout et al. 2004). Mille_04, Mille_06, Mille_08 and Mille_09 (Heckenhauer et al. 2014). Multilocus lineages (MLLs) were defined as clustering ramets with the occurrence of somatic mutations belonging to the same clonal lineage.

Once MLLs were assigned, the proportion of clones was estimated for each transect in all habitats.

A standard genotypic diversity index was estimated, the clonal richness: R = (G -1)/(N -1), where G is the number of MLLs and N the number of genotyped samples [START_REF] Arnaud-Haond | GENCLONE: a computer program to analyze genotypic data, test for clonality and describe spatial clonal organization[END_REF]. This index ranges from zero (all samples belong to the same lineage) to one (each sample belongs to a unique lineage). The Simpson index D* [START_REF] Simpson | Measurements of diversity[END_REF], corrected for sample size, was estimated for each transect. The clonal equitability was also investigated using the Simpson's evenness index: ED* = (D -D min )/(D max -D min ), with D min and D max being the approximate minimum and maximum values of D*. This index also ranges from zero (population dominated by one lineage) to one (population composed of lineages reaching an equal number of ramets). The maximum number of ramets per lineage (MAX) was estimated. Colony size data (projected surface) were estimated from 2D photos using ImageJ 1.4f [START_REF] Abràmoff | Image processing with ImageJ[END_REF]). Size frequency distributions of both single and clonal ramets within each of the five surveyed habitats were generated. Multivariate permanova tests were used to quantify the variation in sexual and asexual reproduction among transects and habitats.

Distribution and morphology of clonal lineages

The maximum geographic distance between two ramets belonging to the same clonal lineage is the clonal subrange (CR). CR was estimated within and among habitats using GENCLONE. Pairwise geographic distances between clones were computed in GENALEX v.6.4 [START_REF] Peakall | GENALEX 6: genetic analysis in Excel. Population genetic software for teaching and research[END_REF]). Variation among transects and habitats were quantified with multivariate permanova tests.

Maps showing the distribution of all ramets within each clonal lineage across habitats were produced using R. Clonal lineages that were shared in at least two habitats were identified; these were used to assess whether morphologies varied among clones between habitats with contrasting levels of wave energy (i.e. phenotypic plasticity). Only clonal lineages with at least five clones in at least two habitats were retained to assess phenotypic plasticity.

Results

Sexual versus asexual reproduction

A total of 3651 colonies of Millepora platyphylla were counted over the five surveyed habitats. 77.7% of the colonies were observed on the fore reef habitats (i.e. 1761 colonies on the upper slope and 1075 on the mid slope), while only 5.2% on the patch reef (Table S3). Out of the 3651 samples analyzed, 1157 multilocus genotypes (MLGs) were detected with our 12 microsatellite loci. The probability of repeated MLG to arise from distinct sexual reproductive events (P SEX ) was negligible (≤ 0.001). Based on this analysis, 93 MLGs showed evidence of somatic mutations and reduced the probability of distinguishing clone mates. By sequentially replacing the mismatched allele at one locus between MLGs, a total of 1064 multilocus lineages (MLLs) were retained for further analyses. Overall, 69% of the 1064 lineages were assigned to a single ramet belonging to a unique lineage (G SR ), while the remaining 31% were identified as clonal lineages with multiple ramets (G MR ). The proportion of single ramets was higher on the mid slope (42.7%) and back reef (29.3%), while lower for other habitats (≤ 18.9%) (Fig. S2, left side). On the mid slope, the proportion of single ramets was highest in small size classes with 32.3% represented in sizes below 32 cm 2 , i.e. mostly juveniles (> 1-20 cm 2 , 27.2 ± 5.5%). Single ramets were distributed at 19.3% in medium size classes on the back reef, i.e. mostly young adults (> 20-128 cm 2 , 10.7 ± 3.8%). Sexual propagules were less abundant in other habitats. On the upper slope, single ramets (11.7%) were equally distributed among size classes (0.2 ± 0.0% ≤ frequency ≤ 2.7 ± 0.2%), while mostly distributed among large size classes (> 512 cm 2 ) in the fringing (5.1%) and patch reefs (11.7%). The size frequency distribution of single ramets was significantly different among habitats (permanova; 999 permutations, P < 0.001), while similar for the clonal ramets (Fig. S2, right side).

Morphology of sexual and clonal ramets

In addition to assigning each georeferenced colony to a genetic lineage, the morphology of each single and clonal ramet was classified (Fig. 5.1). On the upper slope, 76.7% (± 5.1, SE) of the colonies (i.e. single and clonal ramets) displayed the sheet tree morphology, while the remaining colonies were encrusting (Fig. S4 and Table S4). Colonies on the mid slope and back reef were mostly encrusting (64.4 ± 3.1% and 71.9 ± 9.9%, respectively), while the massive morphology was dominant in the fringing and patch reefs (84.5 ± 8.4% and 74.4 ± 9.1%, respectively). There was no significant difference in morphology between the two reproductive strategies on the mid slope, upper slope and back reef (Table S5). Lastly, all single ramets were massive on the fringing and patch reefs, while significant lower proportions of massive colonies (≤ 83.3%) were observed for clonal ramets in both fringing (permanova; 999 permutations, P < 0.05) and patch reefs (P < 0.01).

Distribution and morphology of clonal lineages

The 328 distinct clonal lineages identified were distributed in lines perpendicular to the reef crest, aligned with wave energy (Fig. 5.2 and Fig. S5). Clone mates of each clonal lineage were close to one another with a mean distance of 17.98 m (± 35.40,SE) between clones. The back and patch reefs are the habitats where the wave energy disperses. These habitats had higher values of clonal subrange, with respectively 87.6 m (± 18.3, SE) and 142.7 m (± 64.5, SE) (Table S3). One clonal lineage was found in two different transects within the patch reef with a clonal subrange of 448.9 m (Fig. S6). Clonal dispersal is more limited within the mid slope (29.6 ± 3.2 m), upper slope (39.6 ± 13.1 m) and fringing reef (56.3 ± 47.7 m) where wave energy is lower (mid slope and fringing) and where waves break (upper slope) (Table S3). 57 lineages had clones shared in at least two of the mid slope, upper slope and back reef habitats (Fig. 5.2 and Fig. S7). Clone mates of each of these lineages were at a mean distance of 58.90 m (± 44.61, SE) with a maximum clonal subrange of 239.9 m. Six of these clonal lineages had clones (5-33) shared in at least two habitats. 80% of these clones displayed the sheet tree morphology on the upper slope but five of these six lineages are 100% encrusting or massive on the mid slope and back reef (the other is 80% massive or encrusting) (Table 5.1). Fire corals within these lineages demonstrate phenotypic plasticity (see photo series in

Discussion

This study reports evidence of phenotypic plasticity among fire coral clones with clones expressing different morphologies (i.e. phenotypes) among reef habitats. Phenotypic plasticity among genetically identical individuals has been suggested in natural coral populations based on early genetic work (i.e. electrophoresis analyses, see [START_REF] Ayre | Population structure in the coral Pavona cactus: clonal genotypes show little phenotypic plasticity[END_REF]. Using contemporary genetic tools, we find that M. platyphylla clones have a vulnerable morphology that increases colony fragmentation. Corals typically have wave-tolerant growth forms in high-energy reef areas. This is almost certainly due to the costs of being injured outweighing the benefits of fragmenting [START_REF] Highsmith | Reproduction by fragmentation in corals[END_REF]. The results presented here suggest that fire corals being susceptible to fragmentation on the upper slope has greater benefits than costs in the marginal reef habitat of Moorea Island.

Genetic diversity

The genotype diversity (> 1000 genotypes) observed in this study is the highest ever documented for terrestrial or marine populations. Most studies assessing genetic variation in clonal organisms are not spatially explicit [START_REF] Arnaud-Haond | Genetic structure at different spatial scales in the pearl oyster (Pinctada margaritifera cumingii) in French Polynesian lagoons: beware of sampling strategy and genetic patchiness[END_REF][START_REF] Schwartz | Why sampling scheme matters: the effect of sampling scheme on landscape genetic results[END_REF][START_REF] Gorospe | The importance of sampling design: spatial patterns and clonality in estimating the genetic diversity of coral reefs[END_REF], are based on sampling few individuals (~50) [START_REF] Becheler | Scaling of processes shaping the clonal dynamics and genetic mosaic of seagrasses through temporal genetic monitoring[END_REF][START_REF] Adjeroud | Genetic diversity, clonality and connectivity in the scleractinian coral Pocillopora damicornis: a multi-scale analysis in an insular, fragmented reef system[END_REF][START_REF] Ardehed | Complex spatial clonal structure in the macroalgae Fucus radicans with both sexual and asexual recruitment[END_REF], or involve sampling of a single habitat [START_REF] Gorospe | Genetic relatedness does not retain spatial pattern across multiple spatial scales: dispersal and colonization in the coral, Pocillopora damicornis[END_REF]. Such studies may therefore underestimate genotype diversity in clonal populations. [START_REF] Gorospe | Genetic relatedness does not retain spatial pattern across multiple spatial scales: dispersal and colonization in the coral, Pocillopora damicornis[END_REF] identified ~80 genotypes from more than 2700 colonies of Pocillopora corals. These authors exhaustively sampled colonies in a single patch reef in Kaneohe Bay, where coral reef cover has declined greatly over recent decades due to human activities (e.g. [START_REF] Smith | Kaneohe Bay sewage diversion experiment: perspectives on ecosystem responses to nutritional perturbation[END_REF]Jokiel et al. 1993). Despite recent disturbances on Moorea's reefs (Acanthaster outbreaks and cyclone), the M. platyphylla population is still characterized by a high genotype diversity. This suggests that some aspects of its life history (e.g. reproduction and growth) successfully increase its resilience under such environmental stress. Fire corals on the exposed fore reefs had the highest genotype diversity. In fore reefs (mid and upper slopes), the survival of both sexual and clonal colonies can be greater. These areas have lower disturbance frequencies than the habitats closer to the coast where anchoring impacts are greater and water quality is poorer due to human interactions [START_REF] Fichez | A review of selected indicators of particle, nutrient and metal inputs in coral reef lagoon systems[END_REF][START_REF] Fabricius | Effects of terrestrial runoff on the ecology of corals and coral reefs: review and synthesis[END_REF][START_REF] Cooper | Gradients in water column nutrients, sediment parameters, irradiance and coral reef development in the Whitsunday Region, central Great Barrier Reef[END_REF]). On the mid slope, the high investment in sexual reproduction maintains fire coral populations where wave energy is low and settlement success is high [START_REF] Roth | Distribution, abundance, and microhabitat characterization of small juvenile corals at Palmyra Atoll[END_REF].

Consequently, genotype diversity is greater on the mid slope (see Appendix S1 for more details). On the upper slope, the high number of genotypes is mostly due to the low but continuous supply of sexual larvae and the high level of clonal propagation of these well established recruits (i.e. the 'memory-effect' in [START_REF] Bengtsson | Genetic variation in organisms with sexual and asexual reproduction[END_REF], see Appendix S1 for more details). In near coast habitats (fringing and patch reefs), genotype diversity is relatively low and, correspondingly, abundance and sexual reproduction are lowest. This confirms and extends earlier findings demonstrating that recruitment and disturbance histories can play an important role in maintaining genetic diversity in local populations [START_REF] Bengtsson | Genetic variation in organisms with sexual and asexual reproduction[END_REF][START_REF] Schwartz | Genetic monitoring as a promising tool for conservation and management[END_REF].

In highly clonal populations, local adaptation (i.e. via genetic changes) in response to selection pressures is expected to be much slower due to these populations having lower genetic diversity [START_REF] Halkett | Tackling the population genetics of clonal and partially clonal organisms[END_REF]. We find high genotype diversity and a lack of population structure (Table S6) likely driven by larval and fragment dispersal among habitats, which creates a genetically homogenous population. This result emphasizes that genetic adaptation through the selection of a particular adapted genotype may not have taken place in M. platyphylla population at Moorea. With the exception of the fringing reef, the system is characterized by a mix of reproductive processes leading to high genotype diversity.

Clone distribution

M. platyphylla populations in Moorea are highly clonal with 80% of all individuals produced through fragmentation. Here, the probability that sexually produced genotypes belong to a clonal lineage outside the study area is low due to our exhaustive sampling design, extensive field surveys (45,000 m 2 of reef) and the proximity between clone mates (average separation ~17 m). Variance in the proportion of clones among habitats strongly suggests wave energy and flow velocity as environmental drivers of clonal dynamics in the study population. The great majority of colonies are clones where wave energy is high (upper slope) and where waves and resultant coral fragments disperse (back and patch reefs). The proportion of clones is lower in deeper waters where wave energy is lower (mid slope). The fringing reef is characterized by the highest contribution from asexual reproduction through fragmentation. Very few sexual or clonal lineages are spread within the fringing reef, which reduces the effective population size and potential for mating (i.e. reproductive success is lowered). Wave energy is typically lower in the fringing reef, which is sheltered. However, this habitat is exposed to large waves during the austral summer [START_REF] Hench | Episodic circulation and exchange in a wave-driven coral reef and lagoon system[END_REF], which likely drives asexual reproduction through fragmentation of the colonies there. This result highlights the importance of asexual reproduction at the margins (see also [START_REF] Baums | A restoration genetics guide for coral reef conservation[END_REF][START_REF] Silvertown | The evolutionary maintenance of sexual reproduction: evidence from the ecological distribution of asexual reproduction in clonal plants[END_REF], even highly locally, of M. platyphylla range [START_REF] Randall | Shallow water hydrozoan corals[END_REF].

Maps of colony locations reveal that clones are dispersed in line perpendicular to the reef crest. This distribution is in perfect alignment with wave energy attenuation after waves break on the upper slope and crest. Although there is previous evidence of water flow driving coral clone dispersal, to our knowledge, this is the first example of distribution patterns of clones being perfectly aligned with wave energy dispersal [START_REF] Japaud | High clonality in Acropora palmata and Acropora cervicornis populations of Guadeloupe, French Lesser Antilles[END_REF]. Clonal dispersal (i.e. maximum distance between two clones) is higher on the back and patch reefs, which may be due to the hydrodynamic regime there. These habitats are located at the limits of the lagoon where the waves break on the reef crest creating a turbulent kinetic energy [START_REF] Hench | Episodic circulation and exchange in a wave-driven coral reef and lagoon system[END_REF]. The distribution patterns also suggest water flow disperses clones of the same genetic lineage across adjacent habitats (i.e. mid slope, upper slope and back reef). Numerous studies have demonstrated that wave breaking drives water flow across the reef into the lagoon [START_REF] Hearn | Wave-breaking hydrodynamics within coral reef systems and the effect of changing relative sea-level[END_REF][START_REF] Gourlay | Wave-generated flow on coral reefs -an analysis for twodimensional horizontal reef-tops with steep faces[END_REF][START_REF] Hench | Episodic circulation and exchange in a wave-driven coral reef and lagoon system[END_REF]. Clone locations in Moorea indicate that water can disperse clones up to several hundred meters from the fore reef to the lagoon through multiple generations. This could occur via a 'stepping stone' process via different fragmentation events of the same clonal lineage and potentially within a single generation depending on flow velocities during fragmentation.

Phenotypic plasticity and future research

The three morphologies displayed by M. platyphylla (i.e. encrusting, sheet tree and massive) are unevenly distributed among the five reef habitats studied. The sheet tree morphology of M. platyphylla, the most vulnerable to wave-induced breakage, is nearly exclusive to colonies encountered in the upper slope. Waves can break the blades there, while the encrusting bases remain intact [START_REF] Edmunds | The role of colony morphology and substratum inclination in the success of Millepora alcicornis on shallow coral reefs[END_REF]. During the study, M. platyphylla colony fragments were observed that had clearly broken and were re-attaching to the reef framework. Among the genotypes represented, six clonal lineages with clones dispersed among habitats show distinct morphologies, demonstrating phenotypic plasticity in M. platyphylla. This is a unique example of highly local-scale developmental plasticity through morphological changes.

For long-lived sessile modular organisms, such as fire corals, morphological responses to local environmental conditions among clones can occur in the early development of the colony. For a fragmented colony, this is when many interconnected polyps are produced after the breakage of the colony (i.e. regeneration) [START_REF] Todd | Morphological plasticity in scleractinian corals[END_REF]). These plastic responses may be due to stem-cell regulation, known to play an important role in asexual cloning in marine invertebrates [START_REF] Rinkevich | Stem cells in marine organisms[END_REF], and/or skeleton structures in corals (e.g. corallite shapes, skeletal mass, branch diameter and length) [START_REF] Bruno | Clonal variation for phenotypic plasticity in the coral Madracis mirabilis[END_REF][START_REF] Tambutté | Morphological plasticity of the coral skeleton under CO2-driven seawater acidification[END_REF]. Information on both structural modifications and signaling pathways in coral is scarce. More research is needed to identify the mechanisms behind their developmental plasticity. Responses of sessile organisms to environmental stress are often discussed in terms of physiological plasticity since changes in physiological traits constitute the basis of homeostasis at the individual level [START_REF] Piersma | Rapid reversible changes in organ size as a component of adaptive behaviour[END_REF][START_REF] Hoogenboom | Interactions between morphological and physiological plasticity optimize energy acquisition in corals[END_REF][START_REF] Padilla-Gamiño | Phenotypic plasticity of the coral Porites rus: Acclimatization responses to a turbid environment[END_REF]). More information on physiological plasticity in fire coral clones is also needed to understand the relative importance of morphological and physiological traits in determining population maintenance in various environments.

Conclusions

M platyphylla is the only species of fire corals identified in French Polynesia to date. However, corals of the Millepora genus can be found in all tropical coral reef regions [START_REF] Lewis | Biology and ecology of the hydrocoral Millepora on coral reefs[END_REF]. Some previous studies on Millepora species have demonstrated intraspecific morphological variation, where compact and robust morphologies are found in high energy reef zones [START_REF] Weerdt | Transplantation experiments with Caribbean Millepora species (Hydrozoa, Coelenterata), including some ecological observations on growth forms[END_REF][START_REF] Kaandorp | Morphological analysis of growth forms of branching marine sessile organisms along environmental gradients[END_REF]. We find the opposite pattern in Moorea. The extensive sampling performed for this study showed that nearly all genets invest in the vulnerable sheet tree morphology in the upper reef slope and very rarely do so in the habitats with less energy. Reef environments are so dynamic that the percentage of fragmented colonies able to re-attach must be very low. Even so, enough are re-attaching to make asexual reproduction through fragmentation the primary means by which M. platyphylla is colonizing reefs in Moorea. M. platyphylla morphologies clearly vary among the reef habitats in Moorea and many of these reef-building coral clones demonstrate phenotypic plasticity. S3) and error bars show the standard error for transect replicates. Appendix S1 Further details on size distribution of single and clonal ramets.

Our results indicate that wave energy forcing highly impacts the dynamics of sexual colonies in local populations (Fig. S2). In the mid slope, most sexual colonies are small recruits and juveniles (< 20 cm 2 , 63.7%, i.e. 27.2% out of the 42.7%) suggesting that low level of wave energy facilitates settlement success of recently produced propagules. The survival of these new settlers can increase the genotype diversity in the mid slope and their longevity will further influence the genetic variability within M. platyphylla population in Moorea. Contrastingly, the high level in wave energy on the upper slope seems to reduce recruitment success, although settlement of sexual larvae appears constant through times (frequencies among size classes, 0.2 to 2.7%). The survival of early established sexual propagules (i.e. recruitment history) can enhance the genotype diversity in the upper slope. This phenomenon is known as the 'memory-effect'; even low investment in sexual recruitment is enough to retain high genotype diversity through time in highly clonal populations [START_REF] Bengtsson | Genetic variation in organisms with sexual and asexual reproduction[END_REF]. Further, the hydrodynamic regime in the back reef has promoted the recruitment of sexual larvae in the past (> 20-512 cm 2 , 65.9%, i.e. 19.3% out of the 29.3%). Recent natural and/or anthropogenic disturbances may have recently impacted the back reef habitat, reducing settlement success and/or increasing post settlement mortality of newly established recruits.

Contrastingly, there is no such evidence of disturbance effect on clonal dynamics. Clones may have higher survivorship compared to sexual recruits in all habitats regardless of the habitat specific conditions, likely due to low survivorship of larval propagules during the settlement stage microsatellite markers revealed a high contribution of self-recruitment with 58% of the juveniles identified as self-recruits. Most of the offspring settled at less than 10 meters from their parents with a decrease in dispersal success over a distance of 300 meters. Limited connectivity among adjacent habitats via cross-reef transport was also detected. Sibship analyses showed that both full and half siblings recruit together on the reef resulting in sibling aggregations. Additionally, local families revealed that offspring are dispersed with currents that run along the reef and settled in alignment with the location of their parents. Even though most of the adults were clones, we found that parents with clonal replicates (asexual fragments) do not increase the number of self-recruits nor the dispersal potential of their offspring. Overall, this study is the first to provide direct estimates for local dispersal and self-seeding in Millepora hydrocorals and provides important information on their reproductive biology and early life ecology. Our work presents new evidence on the importance of self-recruitment in stabilizing population dynamics, as it enhances local sustainability and resilience to disturbance.

Introduction

Understanding patterns of larval dispersal is a major goal in ecology and conservation biology [START_REF] Warner | Local retention of production in marine populations: evidence, mechanisms and consequences[END_REF][START_REF] Cowen | Population connectivity in marine systems: an overview[END_REF][START_REF] Botsford | Connectivity and resilience of coral reef metapopulations in marine protected areas: matching empirical efforts to predictive needs[END_REF]). These patterns shape species' distribution and abundance [START_REF] Strathmann | Evolution of local recruitment and its consequences for marine populations[END_REF] and have major consequences for the persistence and adaptation of their populations [START_REF] Garant | The multifarious effects of dispersal and gene flow on contemporary adaptation[END_REF][START_REF] Underwood | Ecologically relevant dispersal of corals on isolated reefs: Implications for managing resilience[END_REF][START_REF] Gilmour | Recovery of an isolated coral reef system following severe disturbance[END_REF]. For most marine species whose adults are sessile or relatively sedentary, the early life history includes a propagule stage and represents the first step for successful recruitment. Propagule dispersal depends on many biological and physical processes, including the survival and development rates of propagules [START_REF] Figueiredo | Synthesizing larval competence dynamics and reefscale retention reveals a high potential for self-recruitment in corals[END_REF][START_REF] Johnson | Phenotypic variation and selective mortality as major drivers of recruitment variability in fishes[END_REF][START_REF] Doropoulos | Characterizing the ecological trade-offs throughout the early ontogeny of coral recruitment[END_REF], larval behavior [START_REF] Paris | Surfing,spinning, or diving from reef to reef: effects on population connectivity[END_REF][START_REF] Gerlach | Smelling home can prevent dispersal of reef fish larvae[END_REF], and hydrodynamic regimes and seascapes [START_REF] Cowen | Scaling connectivity in marine populations[END_REF][START_REF] Cowen | Larval dispersal and marine population connectivity[END_REF][START_REF] White | Ocean currents help explain population genetic structure[END_REF]. In coral reefs, many organisms, (e.g. fishes and scleractinian corals), rely on the dispersal of a larval stage for population replenishment and colonization of fragmented habitats.

Determining whether the maintenance of reef populations is more heavily influenced by local recruitment (i.e. most propagules settle close to their parents) or longer-distance dispersal is an issue of much debate [START_REF] Cowen | Connectivity of marine populations: open or closed?[END_REF][START_REF] Strathmann | Evolution of local recruitment and its consequences for marine populations[END_REF]. As larvae are relatively small and difficult to track in the pelagic environment, many studies investigating marine dispersal have relied on virtual simulations of hydrodynamics rather than empirical estimates [START_REF] Treml | Modeling population connectivity by ocean currents, a graph-theoretic approach for marine conservation[END_REF][START_REF] Andutta | Sticky water'enables the retention of larvae in a reef mosaic[END_REF][START_REF] Wood | Modelling dispersal and connectivity of broadcast spawning corals at the global scale[END_REF]). Parentage analysis is an efficient tool for determining selfrecruitment and connectivity. Such a genetic approach in reef fishes uncovered high levels of recruitment back to the parental source at some reefs (e.g. 30-60%, see [START_REF] Jones | Coral reef fish larvae settle close to home[END_REF][START_REF] Almany | Local replenishment of coral reef fish populations in a marine reserve[END_REF]). This research reinforces the idea that reef populations are less open than previously thought.

In scleractinian corals, the extent of dispersal is largely governed by their reproductive biology and early life history ecology. Our ability to make inferences on what specific biological processes are driving dispersal and subsequent recruitment patterns in corals is limited due to their diverse dispersal strategies; gamete broadcasting, larval brooding, clonal propagation through fragmentation and polyp bailout [START_REF] Harrison | Sexual reproduction of scleractinian corals[END_REF]). Nevertheless, field surveys and classical population genetic studies have suggested high levels of self-recruitment and limited dispersal in corals [START_REF] Baums | Regionally isolated populations of an imperiled Caribbean coral, Acropora palmata[END_REF][START_REF] Gilmour | Biannual spawning, rapid larval development and evidence of self-seeding for scleractinian corals at an isolated system of reefs[END_REF][START_REF] Torda | Genetic assignment of recruits reveals short-and long-distance larval dispersal in Pocillopora damicornis on the Great Barrier Reef[END_REF]. Recently, the application of genetic parentage analysis in reef corals provided the first direct estimates of restricted larval dispersal in brooding species [START_REF] Ledoux | Fine-scale genetic structure and inferences on population biology in the threatened Mediterranean red coral, Corallium rubrum[END_REF][START_REF] Warner | Sperm dispersal distances estimated by parentage analysis in a brooding scleractinian coral[END_REF]. Although broadcast spawning of gametes with planktonic development of larvae is the most common reproductive strategy in coral reefs [START_REF] Baird | Systematic and biogeographical patterns in the reproductive biology of scleractinian coral[END_REF], dispersal patterns of their sexual propagules using parentage analyses have yet to be determined. Such information will provide us with the ability to disentangle whether or not this reproductive strategy optimizes larval dispersal, as commonly thought.

Millepora hydrocorals, also called fire corals, are an important component of reef communities where they, similar to scleractinian corals, contribute to the accretion of reefs [START_REF] Nagelkerken | Loss of coral cover and biodiversity on shallow Acropora and Millepora reefs after 31 years on Curaçao, Netherlands Antilles[END_REF][START_REF] Lewis | Biology and ecology of the hydrocoral Millepora on coral reefs[END_REF]. Despite their importance in reef community dynamics, fire corals have been relatively understudied and not much is known with respect to their reproduction and dispersal patterns (reviewed in [START_REF] Lewis | Biology and ecology of the hydrocoral Millepora on coral reefs[END_REF]. Millepora platyphylla has successfully colonized a wide range of reef environments in the Indo-Pacific region via both asexual and sexual reproduction [START_REF] Lewis | Biology and ecology of the hydrocoral Millepora on coral reefs[END_REF][START_REF] Dubé | Overgrowth of living scleractinian corals by the hydrocoral Millepora platyphylla in Moorea, French Polynesia[END_REF] unpublished data1 ). M. platyphylla is a gonochoric broadcast spawner that reproduces sexually by producing medusoids (modified medusa) and planula larvae. Medusoids are developed at the surface of the polyp coenosteum in cavities called ampullae and undergo sexual reproduction [START_REF] Lewis | The ampullae and medusae of the calcareous hydrozoan Millepora complanata[END_REF]. The medusoids are shed freely in the water and release their gametes at the surface in one hour post-spawning (i.e. short-lived). After fertilization, the zooxanthellate planula larvae sink and move epibenthically (i.e. crawling not swimming) on the reef substratum and metamorphose into a new calcifying polyp in one day to several weeks after spawning [START_REF] Bourmaud | Mass spawning events, seasonality and reproductive features in Milleporids (Cnidaria, Hydrozoa) from Reunion Island[END_REF]. Fire corals also rely on clonal propagation through fragmentation for local replenishment (Dubé et al. unpublished data 1 ). The production of asexual larvae has never been documented within the Millepora genus. To date, there is no genetic study that has identified patterns of dispersal and recruitment in these reef-building species, although such information is crucial for understanding their population replenishment and recovery.

Here, we conducted an extensive field survey of 3160 georeferenced colonies of M. platyphylla over 9000 m² of reef based on replicated transects across three adjacent habitats (mid slope, upper slope and back reef) in Moorea, French Polynesia. Using parentage analysis, we attempted to resolve local patterns for the dispersal of sexual propagules and to establish the degree of selfreplenishment and local sustainability of a population of fire corals. This study is the first to provide accurate estimations of local dispersal and self-seeding in Millepora hydrocorals from empirical data collected in situ. 2. Materials and Methods

Population sampling and microsatellite genotyping

Between April and December 2013, a series of surveys were conducted on the north shore of Moorea, French Polynesia, across three adjacent reef habitats at Papetoai: the mid slope (13 m depth) and upper slope (6 m depth), both fore reef habitats, and the back reef (Fig. 6.1). Within each habitat, three 300 m long by 10 m wide belt transects were laid over the reef parallel to shore, at least 30 m apart, for a total of 9000 m 2 of reef area. All colonies of M. platyphylla that were at least 50% within the transect borders were georeferenced by determining their position along the transect-line (0 to 300 m) and straight-line distance from both sides of the transect (0 to 10 m).

From these measures, each colony was mapped with x and y coordinates. Map of the locations of each colony was produced using R (R Development Core Team 2013). The colony size (projected surface) of each colony was estimated (in cm 2 ) from 2D photographs using ImageJ 1.4f [START_REF] Abràmoff | Image processing with ImageJ[END_REF]). To determine the gender in Millepora it requires the presence of medusoids at the surface of the colony as well as their release in the water column to observe the reproductive gametes, i.e. oocytes and sperm sacs. Such observations are difficult in the field and were thus made only from specimens in aquariums [START_REF] Weerdt | Taxonomic characters in Caribbean Millepora species (Hydrozoa, Coelenterata)[END_REF][START_REF] Lewis | The ampullae and medusae of the calcareous hydrozoan Millepora complanata[END_REF][START_REF] Soong | Synchronised release of medusae from three species of hydrozoan fire corals[END_REF][START_REF] Bourmaud | Mass spawning events, seasonality and reproductive features in Milleporids (Cnidaria, Hydrozoa) from Reunion Island[END_REF]. Consequently, the sex of the colonies was not determined for this study. Small fragments of tissue-covered skeleton (< 2 cm 3 ) were sampled during field surveys and preserved in 80%

ethanol and stored at -20°C until DNA extraction. All samples were incubated at 55 ºC for 1 hr in 450 µL of digest buffer with proteinase K (QIAGEN, Hilden, Germany) and genomic DNA was extracted using a QIAxtractor automated genomic DNA extraction instrument, according to manufacturer's instructions. Each colony was amplified at twelve polymorphic microsatellite loci in four multiplex polymerase chain reactions (PCRs) using the Quiagen Multiplex PCR Kit (Table S1). Further details on these loci and the genotyping procedure are described in Dubé et al. (in revision). Samples were sent to GenoScreen platform (Lille, France) for fragment analysis on an Applied Biosystems 3730 Sequencer with the GeneScan 500 LIZ size standard. All alleles were scored and checked manually using GENEMAPPER v4.0 (Applied Biosystems, Foster City, CA).

Multilocus genotypes and population genetic analyses

To assess the discriminative power of the microsatellite markers, we estimated the genotype probability (GP) for each locus and a combination of all loci in GENALEX v.6.5 [START_REF] Peakall | GENALEX 6: genetic analysis in Excel. Population genetic software for teaching and research[END_REF]. Repeated multilocus genotypes (MLGs) were identified in GENCLONE v2.0 (Arnaud-Haond and Belkir 2007) and were considered as clone mates at GP < 0.001. The probability of identity, P (ID) , was also computed to evaluate the probability that two identical MLGs arise from distinct random reproductive events [START_REF] Waits | Estimating the probability of identity among genotypes in natural populations: cautions and guidelines[END_REF]. Population genetic analyses were performed after the removal of all clonal replicates. Indices of genetic diversity, including the total number of alleles per locus (Na), observed (H O ) and expected (He) heterozygosity [START_REF] Weir | Estimating F-statistics for the analysis of population structure[END_REF] were computed in GENALEX. Null allele frequencies were estimated with MICROCHECKER 3.7 [START_REF] Van Oosterhout | MICRO-CHECKER: software for identifying and correcting genotyping errors in microsatellite data[END_REF]). Deviations from HWE (F IS ) were assessed with a permutation procedure (N = 1000) implemented in GENETIX v4.02 [START_REF] Belkhir | GENETIX 4.05 Logiciel sous Windows pour la Génétique des Poplulations[END_REF].

The probability of exclusion (P ex ) indicates the efficiency of a panel of microsatellite markers to exclude unrelated individuals when both parents are unknown [START_REF] Jamieson | Comparisons of three probability formulae for parentage exclusion[END_REF]. Pairwise relatedness (2x [START_REF] Lynch | Estimation of pairwise relatedness with molecular markers[END_REF], with relatedness varying from -1 to 1) and pairwise geographic distances between colonies were computed in GENALEX.

Parentage analysis

Kinship analyses were performed in COLONY v.2.0 (Jones and Wang 2010) to infer sibship and parentage relationships using individual MGLs. For the following analyses, only mature colonies (> 20 cm 2 ) were considered as potential parents. Colonies smaller than 20 cm 2 were considered as juveniles (used currently for scleractinian species, see [START_REF] Penin | Early post-settlement mortality and the structure of coral assemblages[END_REF] and were assumed to be the pool of potential offspring. Parent-offspring relationships were assessed with all parental genotypes entered into the analysis as candidate fathers because the sex of colonies was unknown. COLONY was also used to identify siblings (i.e. full-and half-sibs) in the juvenile samples only. Parentage analyses were run with the assumption that 80% of potential parents were sampled due to the high number of adults and the large surveyed area. COLONY was launched with the following parameters for each of the three medium length runs: both sexes are polygamous and the organism is dioecious, with inbreeding, full-likelihood method and a medium likelihood precision. Each run included explicit marker error rates, allele frequencies for the studied population computed with GENALEX and 80% sampled candidate fathers and unknown maternal sibs. Only inferred assignments with a probability of 0.95 or greater were considered for the results. Pairwise geographic distances were computed in GENALEX for all parentage relationships, i.e. parentoffspring, parent-parent, full and half siblings, and differences in dispersal patterns were assessed with a non-parametric statistical test (Kruskal-Wallis). Pearson's correlation coefficient was used to determine whether the number of offspring produced by each of the identified parents increased with the number of ramets and colony size of parents.

Results

Population sampling and clones

A total of 3160 colonies of M. platyphylla were surveyed over the 9000 m 2 of reef area (Fig. 6.2).

The population density was approximately one colony per 10 m 2 and the mean pairwise geographic distance between all colonies within the entire study area was 347 m (± 228 SE; range: 0.01-979 m; median = 310 m). The size-frequency distribution of the population was skewed towards small colonies (g 1 = 0.395; Pnorm < 0.001) with 64% of all colonies below 125 cm 2 (Fig. S1). Of all surveyed colonies, 1059 were considered as juveniles (< 20 cm 2 ) and 2101 as adults (Table 6.1).

Table 6.1 Details of Millepora platyphylla population sampling based on colony size (ramet level) and parentage assignments across the three surveyed habitats at Moorea. Number of colonies surveyed (# col), number of adults (# adu, > 20 cm 2 ) and number of juveniles (# juv, < 20 cm 2 ) are given. Percentages give the proportions of juveniles within that habitat that were i) offspring of parents sampled at the same habitat (SR = self-recruitment), ii) offspring of parents sampled at other habitats (HC = habitat connectivity), or iii) were not assigned to parents sampled within the entire area surveyed (UA = unassigned). pairwise comparisons revealed that a mean distance of 314 m (± 281, SE) separated the 2 potential parents for the 13 parent-offspring pairs. On the contrary, some of these parent pairs were very far from each other (up to 892 m; median = 178 m) (Table S2). Furthermore, the mean pairwise genetic relatedness (2x [START_REF] Lynch | Estimation of pairwise relatedness with molecular markers[END_REF]) between parents contributing to self-recruitment (mean r = -0.011 ± 0.002 SE) was less than the average among all the potential parents surveyed in the study area (mean r = -0.002 ± 0.151 SE), indicating that biparental inbreeding was limited.

Habitats

While most local parents produced less than 2 offspring each, 32% of them produced three or more offspring within the study area. We identified 4 parents with more than 5 assigned offspring. One parent produced 7 offspring and 3 other parents produced 5 offspring each within the study area (Fig. 6.3). Of these 4 families (i.e. one parent and several offspring), 2 were from clonal parents (Fig. 6.3C and D). Despite our expectations, clonal replicates and colony size of parents do not increase the number of offspring produced in the population (r = 0.067, P = 0.514 and r = 0.053, P = 0.605, respectively). Furthermore, the mapping of these families revealed that offspring seemed to settle parallel to the reef crest in alignment with the location of their parents (Fig. 6.3 and see Table S3 for details on each family). This result supports the assumption that limited connectivity exists among adjacent reef habitats due to dispersal along the reef and not from crossing the reef crest.

Dispersal distances and sibling distribution patterns

Observed dispersal distances between offspring and parents ranged from 0.05 to 921 m (Table 6.2).

50% of assigned offspring settled within 300 m of their parental sources with a gradual decrease in the proportions of offspring that settled at larger distances (Fig. 6.4A). At a smaller spatial scale (i.e. 100 m), 34% of offspring settled within the first 10 m, a distance very close to their parents (Fig.

6.4B

). Parent-offspring distances revealed no difference in the dispersal abilities of unique genotype parents and clonal parents (Kruskal-Wallis test, P = 0.480, Table 6.2). This result could be related to the fact that clonal replicates for each of the 54 clonal parents were closely related in space with a mean distance of 15 m (± 28 SE; max = 226 m; median = 4 m).

Over the 375 offspring surveyed, 78 (21%) were involved in a full sibling relationship; 13 were assigned to local parent pairs, 40 to local single parents and 25 to unsampled parents. 132 offspring (35%) were also involved in a half sibling relationship from one local parent. Although dispersal distance distributions among full-and half-sibs were significantly different (Kruskal-Wallis test, P < 0.001), all siblings occurred within an aggregated pattern of distribution (Fig. 6.5). S3. One full sib relationship was found for P1 and an unknown parent with a distance of 723.41 m between the two full siblings. Observed dispersal distribution, determined using parentage analyses, is given by the percentages of dispersal events (N = 216) distributed among ten distance classes, assigned at 100 m each over the entire dispersal range (A) and assigned at 10 m each over the first hundred meters of the dispersal range (B).

Discussion

In this study, the parentage analysis revealed a high contribution from self-recruitment (58%) in the population of M. platyphylla in Moorea. Offspring were dispersed with currents that run along the reef. While most of the new recruits settled within a few meters, adjacent habitats were also connected via cross-reef transport (7% of inter-habitat connectivity). Dispersal events were ranging up to approximately 1 km with half of the recruits settling within 300 m from the location of their parents. Still, 42% of the juveniles surveyed had parents located outside the study population and only 3% had both of their parents located within the surveys, which suggest a potential for longerdistance dispersal. Sibship analyses showed that siblings recruit together on the reef, a process that results in the aggregation of siblings. Although most of the adults were clones, we found no difference between the contributions of parents with clonal replicates (i.e. asexual fragments) to local replenishment than those produced sexually (i.e. unique genotype). Clones do not increase the number of self-recruits nor do they increase the dispersal potential of their offspring.

High self-recruitment rates and limited connectivity among habitats

Parentage analyses revealed a self-recruitment rate of 58% in M. platyphylla population, which is much higher than previous studies that focused on brooding species of gorgonians and scleractinians (~25%, see [START_REF] Lasker | Male reproductive success during spawning events of the octocoral Pseudopterogorgia elisabethae[END_REF][START_REF] Warner | Sperm dispersal distances estimated by parentage analysis in a brooding scleractinian coral[END_REF]). For M. platyphylla, we were expecting a lower contribution from self-recruitment to local population replenishment because of its larval development mode, i.e. broadcast spawning. This reproductive strategy was often associated with high dispersal ability in natural populations of countless reef-building organisms (reviewed in [START_REF] Harrison | Sexual reproduction of scleractinian corals[END_REF]). To our knowledge, our study is the first to provide direct estimations of self-recruitment in a population of a broadcast spawner. A high investment in self-seeding might well be an efficient process to sustain populations in an isolated and fragmented reef system such as Moorea (as described in [START_REF] Gilmour | Biannual spawning, rapid larval development and evidence of self-seeding for scleractinian corals at an isolated system of reefs[END_REF]. This high proportion of self-recruits in M. platyphylla can result from the interplay of its early life history ecology (e.g. pelagic larval duration and behavior) and/or local environmental conditions (e.g. water circulation and reef seascapes). Our results reveal that M. platyphylla exhibits low dispersal ability, where most of the new recruits settle within only a few meters from their parents (less than 10 m). In addition, we found a limited connectivity among adjacent reef habitats. While very few studies have investigated the reproductive biology and early life stages of Millepora hydrocorals (reviewed in [START_REF] Lewis | Biology and ecology of the hydrocoral Millepora on coral reefs[END_REF], this where wave energy is reduced [START_REF] Hearn | Wave-breaking hydrodynamics within coral reef systems and the effect of changing relative sea-level[END_REF]. Overall, our results indicate that the distribution of fire corals in Moorea is strongly influenced by the dispersal of sexual propagules with along-reef currents, a process accentuated in deeper waters, but also by the dispersal of asexual fragments with cross-reef currents.

Gamete dispersal and fertilization lead to sibling aggregations

In this study, sibship analyses suggested that siblings may complete their pelagic larval phase together. It is commonly assumed that the medusoid, the early life stage during which a fire coral releases its gametes, facilitates fertilization rates through synchronous spawning. This reproductive strategy enables gametes to aggregate at the water surface once they are released [START_REF] Soong | Synchronised release of medusae from three species of hydrozoan fire corals[END_REF][START_REF] Bourmaud | Mass spawning events, seasonality and reproductive features in Milleporids (Cnidaria, Hydrozoa) from Reunion Island[END_REF]) and most likely contributes to the sibling aggregation observed in the study population. This suggests strong selection on early life history traits that minimizes the dilution of gametes. In many broadcast spawning species, the success of fertilization is proximity dependent [START_REF] Carlon | The evolution of mating systems in tropical reef corals[END_REF]. For fire corals, we observed important variations in the geographical distances between identified parent pairs (i.e. 4 to 900 m) indicating that fertilization can be successful for both nearby and distant parents. Many studies have focused on comparisons between sperm and egg dispersal in reef invertebrates to assess dispersal potential [START_REF] Pennington | The ecology of fertilization of echinoid eggs: the consequences of sperm dilution, adult aggregation and synchronous spawning[END_REF][START_REF] Coma | Effects of spatial distribution and reproductive biology on in situ fertilization rates of a broadcast-spawning invertebrate[END_REF][START_REF] Lasker | Male reproductive success during spawning events of the octocoral Pseudopterogorgia elisabethae[END_REF][START_REF] Warner | Sperm dispersal distances estimated by parentage analysis in a brooding scleractinian coral[END_REF]). This research demonstrated that sperm dispersal often limits fertilization success, even at the scale of few meters. A previous study on M.

platyphylla in southern Japan revealed that males released medusoids a few minutes earlier than females [START_REF] Soong | Synchronised release of medusae from three species of hydrozoan fire corals[END_REF]. Such asynchrony within a species increases both the probability that sperm will encounter an unfertilized egg and that the eggs will be fertilized immediately after spawning, at which point they will sink to the bottom near the female. This reproductive strategy also contributes to sibling aggregations. Furthermore, successful mating and recruitment was found for parent pairs that were 900 m apart from one another suggesting that sperm dispersal may enhance fertilization success over large distances. Our results indicate that the eggs are most likely dispersed over small distances via reef currents parallel to the reef and are fertilized by sperm, which can disperse over great distances once they are released. Our estimates of offspring dispersal in M. platyphylla highlight their potential for long distance dispersal within a single reef (> 1 km), while we reported that several aspects of their early life history promote local dispersal and sibling aggregations. Based on a growing body of work on marine dispersal patterns, there is evidence that sexual propagules rarely reach their full dispersal potential [START_REF] Jones | Self-recruitment in a coral reef population[END_REF][START_REF] Swearer | Larval retention and recruitment in an island population of a coral-reef fish[END_REF][START_REF] Buston | Probability of successful larval dispersal declines fivefold over 1 km in a coral reef fish[END_REF][START_REF] Iacchei | Combined analyses of kinship and F ST suggest potential drivers of chaotic genetic patchiness in high gene-flow populations[END_REF][START_REF] Pusack | Spatial and temporal patterns of larval dispersal in a coral-reef fish metapopulation: evidence of variable reproductive success[END_REF]. Sexual propagules of Millepora hydrocorals seem to be no exception. Overall, our study supports the current view that self- recruitment may be more common than previously thought [START_REF] Ayre | Genotypic diversity and gene flow in brooding and spawning corals along the Great BarrierReef, Australia[END_REF][START_REF] Gilmour | Biannual spawning, rapid larval development and evidence of self-seeding for scleractinian corals at an isolated system of reefs[END_REF][START_REF] Saavedra-Sotelo | Limited genetic connectivity of Pavona gigantea in the Mexican Pacific[END_REF].

Impact of clonal reproduction on self-recruitment and dispersal

Even though most of the adults were clones, we found that adults with a unique genotype (i.e. only one ramet) contributed equally to self-recruitment than those of clonal genotypes. Previous studies have shown that colonies that have suffered from stress due to fragmentation may further invest in growth rather than reproduction [START_REF] Okubo | Successful methods for transplanting fragments of Acropora formosa and Acropora hyacinthus[END_REF][START_REF] Okubo | When fragmented coral spawn? Effect of size and timing on survivorship and fecundity of fragmentation in Acropora formosa[END_REF]. Since half of the clonal parents were smaller than 130 cm², it is reasonable to assume that these fragments may preserve their energy to reach a larger size and to increase their survival. Despite the fact that clonal reproduction only increases local replenishment via the production of new colonies through fragmentation, one could wonder if their propagation is increasing the area over which sexual propagules are dispersed. In plants, the dispersal of seeds increases through clonal propagation and further reduces competition among siblings in the next generation [START_REF] Van Drunen | Consequences of clonality for sexual fitness: Clonal expansion enhances fitness under spatially restricted dispersal[END_REF]. Our estimates for the dispersal distances were not higher for clonal parents suggesting that Millepora fragments have no better ability for the dispersal of their offspring, as clones of each clonal lineage were in close proximity to one another.

Most of the juveniles sampled were genetically identical to parents. This result confirms that clonal aggregation of large colonies (i.e. where clones are distributed in patches) can increase local replenishment by supplying new recruits through their fragmentation [START_REF] Highsmith | Reproduction by fragmentation in corals[END_REF]. Despite the fact that large fragments are assumed to have a higher chance of survival [START_REF] Lirman | Lesion regeneration in the branching coral Acropora palmata: effects of colonization, colony size, lesion size, and lesion shape[END_REF][START_REF] Okubo | When fragmented coral spawn? Effect of size and timing on survivorship and fecundity of fragmentation in Acropora formosa[END_REF], the large proportion of small fragments (< 20 cm 2 ) observed in this study suggests that they can survive and effectively contribute to local sustainability. Still, these aggregations of clones combined with sibling aggregations and limited dispersal can increase inbreeding in the population due to cross fertilization of genetically related neighbors. Despite all of these reproductive features, the mating between closely related adults is less likely to contribute to the observed population inbreeding, as revealed when the genetic relatedness of all parents sampled and those contributing to self-recruitment were compared. This result suggests that the dispersal of sexual propagules, although limited, is enough to restrict biparental inbreeding. Furthermore, half of local parents relied on multiple breeding, i.e. reproduce with more than two other adult colonies within or without the study area. As in numerous broadcast spawning marine invertebrates (Jonhson and Yund 2007;[START_REF] Lasker | Male reproductive success during spawning events of the octocoral Pseudopterogorgia elisabethae[END_REF]Mokhtar-Jamai et al. 2013;[START_REF] Warner | Sperm dispersal distances estimated by parentage analysis in a brooding scleractinian coral[END_REF], multiple mating may limit inbreeding in populations [START_REF] Foerster | Females increase offspring heterozygosity and fitness through extra-pair matings[END_REF] and increase the performance and survival of offspring by increasing the genetic diversity in the brood [START_REF] Mcleod | Do genetic diversity effects drive the benefits associated with multiple mating? A test in a marine invertebrate[END_REF].

Conclusions

Clonal propagation, self-recruitment and local dispersal of sexual propagules are all features known to reduce levels of genetic diversity. Nonetheless, high self-recruitment involving genetically unrelated parents and high clonal diversity seem to be enough to maintain relatively high levels of genetic diversity in M. platyphylla population. This study confirmed theoretical considerations claiming that self-recruitment is a key factor in stabilizing population dynamics of reef organisms, such as fishes and reef-building corals [START_REF] Hastings | Persistence of spatial populations depends on returning home[END_REF]. Despite major differences in reproductive strategies, e.g. clonal reproduction and planula larvae, reef fishes and fire corals have similar self-recruitment rates in Moorea with sibling aggregations [START_REF] Beldade | Larger female fish contribute disproportionately more to self-replenishment[END_REF]Bernardi et al. 2012). This recruitment dynamics enables local sustainability and great opportunities to recover from major disturbances, which can occur frequently in coral reef ecosystems such as Moorea Island. variation, evaluating the occurrence of these processes in threatened species such as reef-building corals carries important implications for conservation biology.

Coral reefs are increasingly threatened by chronic and acute anthropogenic stressors [START_REF] Bellwood | Confronting the coral reef crisis[END_REF][START_REF] Hoegh-Guldberg | Coral reefs under rapid climate change and ocean acidification[END_REF][START_REF] Pandolfi | Projecting coral reef futures under global warming and ocean acidification[END_REF][START_REF] Kuffner | A century of ocean warming on Florida Keys coral reefs: historic in situ observations[END_REF]. Reef-building corals (e.g. scleractinian. gorgonian and hydrozoan corals) provide much of the habitat framework in reefs. Therefore, their adaptive capacity to increasing sea temperature and ocean acidification in the context of climate change is an issue of much debate. As a consequence of their small populations, poor dispersal abilities, clonality and/or high levels of inbreeding, many coral species are predicted to have low genetic diversity [START_REF] Kimura | The neutral theory of molecular evolution[END_REF][START_REF] Willi | Limits to the adaptive potential of small populations[END_REF][START_REF] Frankham | Introduction to conservation genetics[END_REF].

Low genetic variability correlates with limited adaptive potential in the face of environmental change and increases the risk of extinction (Frankman 2005). However, many studies have shown the occurrence of intracolonial genetic variability in scleractinian corals, which provides an additional source of genotypic diversity in their populations [START_REF] Amar | Coral kin aggregations exhibit mixed allogeneic reactions and enhanced fitness during early ontogeny[END_REF][START_REF] Puill-Stephan | Chimerism in wild adult populations of the broadcast spawning coral Acropora millepora on the Great Barrier Reef[END_REF], 2012a;[START_REF] Maier | Intracolonial genetic variation in the scleractinian coral Seriatopora hystrix[END_REF][START_REF] Schweinsberg | Transfer of intracolonial genetic variability through gametes in Acropora hyacinthus corals[END_REF][START_REF] Schweinsberg | More than one genotype: How common is intracolonial genetic variability in scleractinian corals?[END_REF]. Due to the lack of germ line segregation in corals, the propagation of somatic mutations within a colony is highly likely [START_REF] Van Oppen | Novel genetic diversity through somatic mutations: fuel for adaptation of reef corals?[END_REF], and these mutations are almost certainly passed on to the next generation of gametes [START_REF] Schweinsberg | Transfer of intracolonial genetic variability through gametes in Acropora hyacinthus corals[END_REF]. Evaluating intracolonial genetic variation (i.e. mosaicism and chimerism) in reef-building species can therefore reveal valuable insights on their adaptive potential under rapid and unpredictable climate change.

Our understanding of intracolonial genetic variability in colonial reef species (e.g. soft corals [START_REF] Barki | Soft-coral natural chimerism: a window in ontogeny allows the creation of entities comprised of incongruous parts[END_REF], sponges [START_REF] Blanquer | Living together apart'': the hidden genetic diversity of sponge populations[END_REF] and scleractinian corals [START_REF] Amar | Coral kin aggregations exhibit mixed allogeneic reactions and enhanced fitness during early ontogeny[END_REF][START_REF] Schweinsberg | More than one genotype: How common is intracolonial genetic variability in scleractinian corals?[END_REF][START_REF] Rinkevich | Venturing in coral larval chimerism: a compact functional domain with fostered genotypic diversity[END_REF])) has improved over the last decade. However, such information remains unavailable for Millepora hydrocorals (also called fire corals) despite their major contribution to the reef framework in some reef ecosystems [START_REF] Andréfouët | A monospecific Millepora reef in Marquesas Island, French Polynesia[END_REF].

Millepora species can colonize a wide range of reef habitats through sexual reproduction and colony fragmentation [START_REF] Lewis | Biology and ecology of the hydrocoral Millepora on coral reefs[END_REF]. In Moorea, French Polynesia, populations of M. platyphylla displayed differences in sexual / asexual reproduction investment and morphology in response to habitat variability (Dubé et al. unpublished

Results

Colony reproduction and morphology

All fifteen tested microsatellites had between 2 and 18 alleles (Na in Table S1). Out of the 255 samples collected from 51 colonies of the hydrocoral M. platyphylla, 65 multilocus genotypes were identified (Table 7.1). Clone mates were detected in almost all reef habitats: two individuals shared the same genotype in the patch reef, fringing reef and back reef and three individuals in the upper slope (Table 7.1). In the mid slope, all sampled colonies are genetically distinct. However, the larger survey of M. platyphylla colonies (N = 3651) revealed that only one of the 10 colonies sampled in the mid slope was produced through sexual reproduction, while all others belonged to clonal lineages (Table 7.1). Sexually produced colonies were also detected in the patch reef (N = 2) and fringing reef (N = 3), but were absent in the back reef and upper slope (Table 7.1). The sheet tree morphology was dominant in the upper slope (85%) and back reef (75%), while all colonies were massive in nearshore habitats (fringing and patch reef). The growth form of fire coral colonies was highly variable in the mid slope, where the three morphologies were found in equal proportions.

Colonies were smaller in the back reef compared to other habitats (Table 7.1).

Identification of intracolonial genetic variability

Among the 51 tested colonies of fire corals, 16 (31.4%) harboured more than one single genotype (Fig. 7.2). The percentage of genetically heterogeneous colonies was highest in the patch reef (60.0%) and upper slope (46.2%), followed by the fringing reef and mid slope (20.0% each), and finally the back reef, where all colonies were homogeneous (Fig. 7.2 and Table 7.1). In the patch reef and upper slope, where heterogeneous colonies are more common, nearly 70% of the deviating genotypes were caused by a one-step and four-to twelve-step mutations. Two-step and four-to twelve-step mutations contributed equally in creating divergent genotypes in the fringing reef (Fig. 7.3). In the mid slope, deviating genotypes were mostly caused by one-step mutations.

Clustering analyses

In total, 14 mosaic colonies and 2 chimeras were identified among the 51 tested colonies (Fig. 7.4).

In the patch reef, M. platyphylla showed the highest proportion of heterogeneous colonies with 4 mosaics and 2 chimeras, all of which were detected in colonies belonging to clonal lineages. Mosaic colonies differed from the main genotype with a maximum of two loci and one of the mosaics harboured multiple genotypes, i.e. more than two genotypes (colony # 7). Chimeras were detected for two colonies with only one deviant genotype found within each colony. These chimeras had height (colony # 3) or nine (colony # 9) divergent alleles due to one-to twelve-step mutations. In the fringing reef, 2 mosaic colonies were identified; one belonged to a clonal lineage and displayed multiple genotypes (colony # 4), and the other was produced sexually and had only one divergent allele (colony # 9). In the upper slope, 3 of the 6 deviating genotypes were detected within the three colonies sharing the same genotype (clones) and one clone (colony # 13) displayed multiple genotypes. In this latter heterogeneous colony, one genotype was the most common within clones platyphylla and a second differed by only one allele from the main genotype (as for the three other mosaic colonies). A third genotype had four divergent loci (mostly from one-and two-step mutations) and was shared with one of its clone mates (colonies # 12). A one-step mutation in the highly divergent genotype (M 5 in the upper slope bar plot, Fig. 7.4) resulted in another deviating genotype in the third clone (colonies # 11). In the mid slope, 2 mosaic colonies were identified and differed by four to five loci from the main genotype mostly due to one-step mutations. Overall, our results showed that intracolonial genetic variability occurred in all growth forms (Table 7.1). Among the twenty five massive colonies sampled, 9 were genetically heterogeneous (7 mosaics and 2 chimeras). Among the twenty sheet tree colonies and the six encrusting colonies, 6

and 1 mosaic colonies were identified, respectively.

Discussion

This study demonstrates the occurrence of intracolonial genetic variability in M. platyphylla with important variations in its frequency among reef habitats. Genotypes that differed at only one single allele were observed in half of the heterogeneous colonies and most of the deviating genotypes were due to one-step and four-to twelve-step mutations (38.6% and 29.5%, respectively). Most of the deviating genotypes were caused by somatic mutations (87.5% mosaicism). Chimerism also contributed to increase genetic variability within individuals, although restricted to the patch reef habitat. Nearly all mosaic colonies were detected in individuals belonging to clonal lineages indicating that clonal propagation favors the accumulation of somatic mutations. Only one mosaic was identified within a sexually produced colony. Mosaicism was also identified in all of the three morphologies indicating that differences in growth forms do not affect the accumulation of mutations within a colony.

Pattern of intracolonial genetic variability among reef habitats

The occurrence of intra-individual genotypic diversity was traditionally assumed to be a phenomenon of rare exception [START_REF] Santelices | Mosaicism and chimerism as components of intraorganismal genetic heterogeneity[END_REF][START_REF] Folse | Direct benefits of genetic mosaicism and intraorganismal selection: modeling coevolution between a long-lived tree and a short-lived herbivore[END_REF]. However, recent

In this study, our results show that intracolonial genotypic diversity is also common in the fire coral M. platyphylla. Our genotypic data from 51 colonies, all subjected to multiple sampling (five replicates), revealed a high mean proportion of heterogeneous colonies (31.4%). Such occurrence of intracolonial genetic variability was similar to previous studies that focused on branching Acropora corals (38.7%, in [START_REF] Schweinsberg | More than one genotype: How common is intracolonial genetic variability in scleractinian corals?[END_REF], but much higher when compared to another branching species, Seriatopora hystrix (17.4%, in [START_REF] Maier | Intracolonial genetic variation in the scleractinian coral Seriatopora hystrix[END_REF]). In the shallow patch reef, 60.0% of the sampled colonies displayed intracolonial genetic variability, which is much higher than expected based on previous studies [START_REF] Maier | Intracolonial genetic variation in the scleractinian coral Seriatopora hystrix[END_REF][START_REF] Schweinsberg | More than one genotype: How common is intracolonial genetic variability in scleractinian corals?[END_REF].

Fire corals were sampled in five different reef habitats, where colonies were exposed to different environmental conditions, which can potentially influence the rate of somatic mutational divergence within a species [START_REF] Witte | Longevity of clonal plants: why it matters and how to measure it[END_REF]. Furthermore, colonies were collected at different depths with varying exposure to UV-induced DNA damage, which often derives in somatic mutation [START_REF] Zvuloni | de services écosystémiques à des millions de personnes. Dans ce contexte actuel de changement climatique, évaluer les stratégies d'histoire de vie des espèces récifales est essentiel afin de comprendre le fonctionnement de leurs populations et prédire les conséquences à long terme sur la dynamique des communautés face aux changements environnementaux[END_REF]. In coral reefs, this process occurs more frequently in shallow and clear waters, because UV radiation decreases with increasing depth [START_REF] Lesser | Depth-dependent photoacclimatization to solar ultraviolet radiation in the Caribbean coral Montastraea faveolata[END_REF]. Variations in the proportions of heterogeneous colonies among the five surveyed habitats (0-60%) seemed unrelated to differences in their exposure to solar radiation. In Moorea, fire corals are exposed to high solar irradiance in the back reef and fringing reefs [START_REF] Lesser | Exposure to solar radiation increases damage to both host tissues and algal symbionts of corals during thermal stress[END_REF]. However, both of these shallow habitats (< 1 m depth) were characterized by low proportions of heterogeneous colonies (0% and 20%, respectively), similar to those of the mid slope at 13 m depth where irradiance is much lower (20%). Environmental heterogeneity was recognized as a key factor in determining important life history traits of M. platyphylla including the levels of clonality and morphological plasticity (Dubé et al. unpublished data 1 ). These traits can influence the opportunity for mosaicism and chimerism to occur in natural populations of colonial reef organisms [START_REF] Van Oppen | Novel genetic diversity through somatic mutations: fuel for adaptation of reef corals?[END_REF][START_REF] Schweinsberg | Transfer of intracolonial genetic variability through gametes in Acropora hyacinthus corals[END_REF][START_REF] Rinkevich | Venturing in coral larval chimerism: a compact functional domain with fostered genotypic diversity[END_REF]. Therefore, determining how sexual / asexual reproduction and intraspecific morphological variation affect the prevalence of intracolonial genetic variability can reveal insights into species' response to environmental changes.

Mosaicism

In this study, 14 adult colonies exhibited genotypic variability most likely caused by mosaicism indicating that the accumulation of somatic mutations is a common phenomenon in M. platyphylla in nearly all reef habitats, except in the back reef. The incidence of genetic mosaicism is expected to increase with longevity and size due to a higher number of dividing cells available for mutation [START_REF] Orive | Somatic mutations in organisms with complex life histories[END_REF]. Therefore, the absence of heterogeneous colonies in the back reef could be related to the higher mortality of ger colonies (Dubé et M. platyphylla is also morphologically variable and can either have a massive, encrusting or sheet tree morphotype. In this study, mosaicism was identified in all M. platyphylla growth forms, where most of the mosaics were found in massive and sheet tree morphology. In the upper slope, most of the colonies grew as isolated vertical blades on encrusting bases (i.e. sheet tree). All six mosaics identified in this habitat were exclusively detected in sheet tree colonies suggesting that this growth form can increase somatic mutations within a colony. In many colonial organisms, such as longlived trees and corals, branching growth forms exhibit more deviating genotypes throughout the entire colony due to mutations that only occur within isolated branches [START_REF] Whitham | Evolution by individuals, plant-herbivore interactions, and mosaics of genetic variability: the adaptive significance of somatic mutations in plants[END_REF][START_REF] Van Oppen | Novel genetic diversity through somatic mutations: fuel for adaptation of reef corals?[END_REF]. When displaying the unusual sheet tree morphology, Millepora are potentially similar to branching growth forms due to their isolated vertical blades.

However, an additional five sheet tree colonies were identified as genetically homogeneous in the upper slope and raise questions on whether colony morphology influence mosaicism processes.

This uncertainty is strengthened by the high number of mosaics in massive colonies (6 out of 14).

Somatic mutations are less likely to occur in such growth forms because polyps are in close contact with one another and favor intracolonial competition. Competition within a colony is a driving force in lowering genetic variability due to the elimination of alternative mutant cells. [START_REF] Schweinsberg | More than one genotype: How common is intracolonial genetic variability in scleractinian corals?[END_REF] also demonstrated a conflicting pattern of mosaicism among coral growth forms, whereby highest and lowest proportions of mosaic individuals were both detected in branching species.

Whether more extensive studies could verify an increased accumulation of somatic mutations in branching corals (or tubular or sheet) compared to massive or encrusting growth forms remains to be determined. What is certain, however, is that further investigations on intracolonial competition during colony development in fire corals are needed to fully understand the complex interaction between morphological plasticity and intracolonial genetic variability.

In addition, we investigated whether genetic variation caused by mosaicism is associated with one specific reproductive mode, i.e. sexual or asexual reproduction. Thirteen of the 14 mosaic individuals were detected in colonies belonging to a clonal lineage indicating that colony fragmentation can increase genotypic variation, although evolutionary theories predict otherwise. In this study, our sampling design targeted the larger colonies, from which fragmentation was most likely to occur over time. Further investigations on whether asexual reproduction can increase genetic diversity in populations due to mosaicism are needed. Such research requires an explicit experimental design with equal numbers of sexually and asexually produced colonies. Still, in M platyphylla population, all colonies with more than two genotypes (3 of 14 mosaic colonies) were detected in asexually produced colonies and despite our random sampling scheme, three clone mates were collected in the upper slope. These colonies represented five different genotypes, some shared between clones and others found only in one of the three clones. This result indicates that when fire corals spread via colony fragmentation, the fragments inherit somatic mutations from their mother colony, in addition to acquiring their own over time [START_REF] Schweinsberg | Transfer of intracolonial genetic variability through gametes in Acropora hyacinthus corals[END_REF]. Hence, clonal reproduction can often result in colonies with deviating genotypes of more than four divergent loci, although mosaicism is commonly thought to induce divergent genotypes at one or two loci [START_REF] Orive | Somatic mutations in organisms with complex life histories[END_REF]. Overall, this study reveals that mosaicism is a very promising strategy to increase genetic variability in M. platyphylla, a species that mostly relies on colony fragmentation for colonization and population persistence (Dubé et al. unpublished data 1 ).

Chimerism

In this study, a low proportion of chimeras was identified in fire coral colonies (2 out of 51 colonies sampled, i.e. 3.9%), which is similar to earlier reports for scleractinian corals (from 1.3 to 4.5% depending on the coral species, e.g. [START_REF] Maier | Intracolonial genetic variation in the scleractinian coral Seriatopora hystrix[END_REF][START_REF] Schweinsberg | More than one genotype: How common is intracolonial genetic variability in scleractinian corals?[END_REF]. This result further confirms that chimeric fusion between conspecific are rare events in dynamic environments such as coral reefs. Here, two chimeras were detected in adults that belong to two distinct clonal lineages in the patch reef, where M. platyphylla colonies primarily reproduce through fragmentation (Dubé et al. unpublished data 1 ). Despite low investment in sexual reproduction, fire corals have limited dispersal abilities and are often aggregated due to the co-settlement of their larvae (Dubé et al. unpublished data3 ). In Moorea, fusion between siblings is likely to occur as recruits settle together and grow in proximity on the reef (Dubé et al. unpublished data 3 ). The fusion of siblings could be related to a low conspecific acceptance threshold and/or a delay in allorecognition maturation for Millepora hydrocorals, as described in some hermatypic corals [START_REF] Amar | Coral kin aggregations exhibit mixed allogeneic reactions and enhanced fitness during early ontogeny[END_REF]Puill-Stephan et al. 2012a). Puill-Stephan et al. (2012b) demonstrated that high levels of relatedness between juvenile corals correlate with late maturation of allorecognition. Such delay in the recognition system can increase opportunities for chimeric fusion between adjacent recruits, which allows a rapid growth during early development (Pineda-Krch and Lehtila 2004;[START_REF] Santelices | Size increments due to interindividual fusions: how much and for how long[END_REF].

sampled using ImageJ 1.4f software [START_REF] Abràmoff | Image processing with ImageJ[END_REF]. A total of 255 small fragments of tissue-covered skeleton (< 2 cm 3 ) were sampled and preserved in 80% ethanol and stored at -20 °C until DNA extraction.

Microsatellite genotyping

Samples were incubated at 55 ºC for 1 hr in 450 µL of digest buffer with proteinase K (QIAGEN, Hilden, Germany). Genomic DNA was extracted using a QIAxtractor automated genomic DNA extraction instrument, according to manufacturer's instructions. Samples were amplified and genotyped at 15 microsatellite loci shown to be coral-specific and polymorphic in M. platyphylla [START_REF] Heckenhauer | Isolation, characterization and cross amplification of eleven novel microsatellite loci for the hydrozoan coral Millepora[END_REF][START_REF] Dubé | Overgrowth of living scleractinian corals by the hydrocoral Millepora platyphylla in Moorea, French Polynesia[END_REF] in revision) (Table S1). All loci were combined in three multiplex panels according to their size range and primer annealing temperature. PCRs were performed in a final volume of 10 µL including 5 µL Type-it Multiplex PCR Master Mix (1x) (QIAGEN, Hilden, Germany), 3 µL RNase-free water, 1 µL primers (2 µM of fluorescently labelled forward primer -G5 dye set including 6-FAM, VIC, NED and PETand reverse primer diluted in TE buffer) and 1 µL of template (10 to 50 ng.µL -1 ). The PCR protocol included an initial denaturing step of 5 min at 95 ºC, followed by 40 cycles of 30 sec at 95 ºC, 90 sec at 57-63 ºC, and 30 sec at 72 ºC, and by a final 30 min elongation step at 60 ºC. Samples were analyzed on a 3730 sequencer and scored manually using GENEMAPPER (Applied Biosystems, Foster City, CA). Samples that were ambiguous in their scoring were re-amplified and re-scored, as for missing alleles. Alleles were individually re-scored by a second and third person to ensure accurate genotyping. All peak profiles that were faint or ambiguous (i.e. multiple peaks) were considered as missing data and only samples with no more than two missing loci were retained for further genetic analyses. Control for the presence of null alleles and large allele dropout were performed with MICRO-CHECKER (van Oosterhout et al. 2004).

Molecular analyses

Multilocus genotypes were produced for each sample and compared within each colony to detect the occurrence of intracolonial genetic diversity. Multilocus genotypes were also compared between colonies using GENALEX [START_REF] Peakall | GENALEX 6: genetic analysis in Excel. Population genetic software for teaching and research[END_REF] to identify clone mates among the sampled fire coral colonies (Table 7.1). Based on genotypic data acquired from 3651 colonies of M. platyphylla that were collected using an exhaustive sampling at the same locations within the five surveyed habitats, colonies that belonged to a clonal lineage (genet with multiple ramets) and those produced sexually (genet with single ramet) were identified (

General discussion

Deepening our understanding of genetic diversity patterns in species is crucial for ecological and evolutionary studies, and carries important implications for conservation biology. The capacity of reef organisms to survive is partially related to their degree of genetic variation, where low levels of diversity may limit adaptation to novel selective pressures [START_REF] Frankham | Genetics and extinction[END_REF][START_REF] Barrett | Adaptation from standing genetic variation[END_REF][START_REF] Hoffmann | Climate change and evolutionary adaptation[END_REF]. The degree of genetic variation in populations is highly influenced by a number of factors that are associated with life history traits, e.g. gene flow, genetic drift and mutation [START_REF] Gaggiotti | Disentangling the effects of evolutionary, demographic, and environmental factors influencing genetic structure of natural populations: Atlantic herring as a case study[END_REF]). The worldwide degradation of coral reefs has prompted a surge in understanding species' life history and population genetic structure in response to local and global changes. As coral reefs are heterogeneous ecosystems, different environmental and habitat conditions may impose divergent selection pressures, such that populations evolve differences in morphology, reproductive modes and dispersal abilities [START_REF] Sanford | Local adaptation in marine invertebrates[END_REF][START_REF] Darling | Evaluating life-history strategies of reef corals from species traits[END_REF]). Evaluating such differences in life history traits under contrasting local environmental conditions offer a glimpse into how such populations may survive and adapt to expected environmental changes. In conservation management, there is a particular concern regarding the vulnerability of marginal reefs, where sexual reproduction might be impeded due to their isolation, often resulting in lowered genetic diversity and adaptation potential [START_REF] Hennige | Acclimation and adaptation of scleractinian coral communities along environmental gradients within an Indonesian reef system[END_REF][START_REF] Goodkin | Coral communities of Hong Kong: long-lived corals in a marginal reef environment[END_REF]. Studying life history of keystone species in environments subjected to natural (cyclones, Acanthaster outbreaks) and anthropogenic disturbances (run off, sewages), such as Moorea, provide an example from which to comprehend population persistence in response to environmental changes.

In this thesis, we have provided an improved understanding of the life history of Millepora hydrocorals, a conspicuous component of coral reef ecosystems worldwide [START_REF] Lewis | The ecology of Millepora[END_REF][START_REF] Lewis | Biology and ecology of the hydrocoral Millepora on coral reefs[END_REF].

Based on an exhaustive sampling of more than 3600 colonies collected across various reef habitats at Moorea, we investigated reproductive modes (both sexual and clonal) and growth strategies (allogenic fusion, stolonal spreading and morphological plasticity) in M. platyphylla populations, as well as the occurrence of somatic mutations within a single colony. Using different population genetic approaches, new ecological and evolutionary perspectives have enabled insights into how the complex interaction between high clonal propagation, self-seeding and morphological plasticity, is making milleporids efficient competitors on coral reefs, but also into how these life history strategies maintain a relatively high level of genotypic diversity required for adaptation. In this thesis, we sought for possible differences in colony size distributions, morphologies and recruitment dynamics among various reef habitats to improve the knowledge and understanding of ecological and biological processes governing the population structure of M. platyphylla. We have demonstrated that fire corals colonized a wide range of habitats in Moorea reflecting its ability to adapt and survive in a large variety of environmental settings. Marked differences in population structure of fire corals in two common reef environments, the lagoon and fore reef, have illustrated the importance of environmental conditions in driving population dynamic processes. Such results underpin the urge of developing new molecular markers to evaluate several aspects of the M. platyphylla life history. Different population genetic approaches based on newly developed microsatellite markers were performed to determine how such populations can persist under rapid and unpredictable environmental changes.

High clonal propagation of locally adapted offspring

In the course of this thesis, we have demonstrated that M. platyphylla displays a wide range of strategies to ensure its survival by maximizing the acquisition of local resources. Our genetic data indicated that fragmentation is the dominant reproductive process generating the high abundance of fire corals on Moorea's reefs (80% of colonies were clones). Even small recruits were having multilocus genotypes identical to adults and were often positioned below the reef substratum, i.e.

frequently on branches of dead coral colonies or side of crevices. These observations suggest that the successful recruitment of clones may be the result of other clonal reproduction processes, e.g.

asexual planula larvae, because asexual fragments are less likely to re-attach on such inclined substrate. The release of ameiotic planula larvae was reported in a great number of coral species [START_REF] Harrison | Sexual reproduction of scleractinian corals[END_REF], where larval behavior allows the settlement of a new individual characterized by its mother genotype (clone mates). However, such clonal reproductive strategy has never been described for the Millepora genus and requires further investigations. While we cannot be certain that M. platyphylla reproduces asexually only through fragmentation, determining the environmental setting under which clonal reproduction is favored and maintained remains a difficult task.

A review of empirical studies in plants showed that clonality is often associated with rare taxa and prevails in populations of marginal environments, such as those located at the margin of species' geographical distribution [START_REF] Silvertown | The evolutionary maintenance of sexual reproduction: evidence from the ecological distribution of asexual reproduction in clonal plants[END_REF]. Clonal reproduction is also thought to hamper evolutionary potential because it prevents genetic recombination and leads to the selection of particularly well locally adapted clones, thus reducing genotypic diversity [START_REF] Halkett | Tackling the population genetics of clonal and partially clonal organisms[END_REF].

Furthermore, the overall population fitness is also predicted to be lowered in highly clonal populations due to the accumulation and spread of deleterious somatic mutations [START_REF] Lynch | Mutation load and the survival of small populations[END_REF]. Hence, clonal reproduction is often seen as an evolutionary dead-end and is regarded as a prolonged route to extinction for some marginal populations [START_REF] Honnay | Prolonged clonal growth: escape route or route to extinction[END_REF][START_REF] Silvertown | The evolutionary maintenance of sexual reproduction: evidence from the ecological distribution of asexual reproduction in clonal plants[END_REF]). Therefore, there was evidence that M. platyphylla in Moorea, at the edge of its distribution range [START_REF] Randall | Shallow water hydrozoan corals[END_REF], should undergo reduced levels of genetic diversity due to high clonal reproduction and reduced gene flow, both imperiling its ability for adaptation to environmental changes. Nonetheless, we have demonstrated that even a low investment in sexual reproduction is sufficient to maintain a relatively high level of genotypic diversity in M. platyphylla population in Moorea (He = 0.54, see Table S1), where a similar pattern was reported for the partially clonal scleractinian coral Pocillopora damicornis (0.50-0.53, see [START_REF] Adjeroud | Genetic diversity, clonality and connectivity in the scleractinian coral Pocillopora damicornis: a multi-scale analysis in an insular, fragmented reef system[END_REF].

In Moorea, fire corals are sustained by a high degree of self-seeding suggesting that despite low gene flow, genetically diverse and locally adapted recruits can successfully establish high local population abundance via their subsequent growth, survival and fragmentation (as described in [START_REF] Bengtsson | Genetic variation in organisms with sexual and asexual reproduction[END_REF]. However, such populations are predicted to be vulnerable to severe disturbances owing to their isolation from potential source reefs and are often associated with increased extinction risks [START_REF] Harrison | Reproduction, dispersal and recruitment of scleractinian corals[END_REF][START_REF] Harrison | Coral reefs: naturally dynamic and increasingly disturbed ecosystems[END_REF]. A high potential for gene flow and connectivity has been revealed among islands of the Society Archipelago in French Polynesia for some scleractinian species (i.e. Moorea, Raiatea, Taha'a and Tahiti) [START_REF] Adjeroud | Genetic diversity, clonality and connectivity in the scleractinian coral Pocillopora damicornis: a multi-scale analysis in an insular, fragmented reef system[END_REF]. Our local sampling design cannot confirm such dispersal patterns of sexual propagules in milleporids on a regional scale. Nevertheless, preliminary results from samples of M. platyphylla collected in several islands in French Polynesia revealed significant genetic differentiation among some Archipelagos (Marquesas, Austral, Society and Tuamotu), highlighting the importance of selfrecruitment processes in the population sustainability. Despite all of that, there is evidence that high clonal reproduction is an efficient means to expand populations locally in marginal reefs, but it remains unknown whether such populations retain sufficient functional genetic diversity (i.e. the degree to which clonal diversity translates into functional phenotypes) to adapt to changing environments. In the light of our results, it seems that the combination of high clonal propagation and early life history traits, which promote high self-recruitment, can generate sufficient clonal genotype diversity, such that populations can evolve through divergent selection pressures induced by environmental changes. Even though investment in clonal reproduction varied in response to habitat specific conditions, similar levels of genetic diversity were maintained between habitats (Table S1). Larval and asexual fragments dispersal among reef habitats lead to a genetically homogenous population.

Fusion and mutation: Additional source of genetic diversity

There is evidence that populations reproducing primarily via asexual reproduction possess highly dynamic and adaptive genomes [START_REF] Lashai | The dynamic clonal genome and its adaptive potential[END_REF] and maintain high levels of allelic diversity within individual [START_REF] Balloux | The population genetics of clonal and partially clonal diploids[END_REF]. In this study, we have demonstrated that M. platyphylla can accumulate somatic mutations while growing with a high potential of spreading these mutations in the population via colony fragmentation. Many cnidarians have no clear separation of somatic and germ cells, which ensure the passage of somatic mutations throughout the entire colony to the next generation via their gametes [START_REF] Extavour | Mechanisms of germ cell specification across the metazoans: epigenesis and preformation[END_REF][START_REF] Seipel | The germ line and somatic stem cell gene Cniwi in the jellyfish Podocoryne carnea[END_REF][START_REF] Watanabe | Immortality and the base of multicellular life: lessons from cnidarian stem cells[END_REF].

Such life history strategies enhance the genetic variability within colonies and their consecutive generations, but also have important implications for their adaptability [START_REF] Van Oppen | Novel genetic diversity through somatic mutations: fuel for adaptation of reef corals?[END_REF].

However, a recent study has shown conclusive evidence of germline segregation in the coral Orbicella faveolata [START_REF] Barfield | Evolutionary origins of germline segregation in Metazoa: evidence for a germ stem cell lineage in the coral Orbicella faveolata (Cnidaria, Anthozoa)[END_REF]. The lack of segregated germline has been reported in hydrozoans [START_REF] Seipel | The germ line and somatic stem cell gene Cniwi in the jellyfish Podocoryne carnea[END_REF], while there is no evidence for this phenomenon in fire corals. In Millepora hydrocorals, sexual reproduction occurs via the development of medusoids (i.e. modified medusa) via asexual budding from the lateral wall of polyps in cavities called ampullae [START_REF] Lewis | The ampullae and medusae of the calcareous hydrozoan Millepora complanata[END_REF]). More information is needed to better understand how the ampullae develop to confirm whether these cnidarians have the potential to transfer somatic mutations in their gametes, located in the medusoids. Nonetheless, such mutations result in genetically heterogeneous colonies and may have important ecological and evolutionary implications as they generate additional genotypic variation required for adaptation. Based on the common occurrence of intracolonial genetic variability in M. platyphylla population in Moorea, it is reasonable to suspect that clonal genotypes may accumulate allelic mutations that become functionally variable under strong selection pressures [START_REF] Lashai | The dynamic clonal genome and its adaptive potential[END_REF][START_REF] Pouchkina-Stantcheve | Functional divergence of former alleles in an ancient asexual invertebrate[END_REF]). Such mutation dynamics can result into more versatile phenotypic traits in populations and potentially compensate the reduced genotypic diversity usually associated with clonal reproduction [START_REF] Sniegowski | Beneficial mutations and the dynamics of adaptation in asexual populations[END_REF]. Although chimerism was less common in fire corals, sibling aggregations of early life stages facilitate fusion of two or more settling recruits and also contribute in generating novel genetic diversity. Because

Morphological plasticity: A means to promote clonal reproduction

Although genetic diversity is often linked to ecological functioning and adaptive capacity, population can also evolve within a single generation due to plasticity or natural selection altering phenotypic traits, such as changes in behavior, physiology and morphology [START_REF] Reed | Interacting effects of phenotypic plasticity and evolution on population persistence in a changing climate[END_REF].

Phenotypic plasticity provides another means for population persistence and understanding such phenotypic response to different selection pressures is a major challenge in evolutionary biology.

Here, we have demonstrated the occurrence of phenotypic plasticity in M. platyphylla, where a single genotype can produce multiple morphologies in response to habitat specific conditions. Such phenotypic changes occurring during the development of the colony enable a rapid response to local environmental conditions compared to genetic changes [START_REF] Auld | Re-evaluating the costs and limits of adaptive phenotypic plasticity[END_REF]). We found that M. and coral fragments. This phenotype potentially reduces colony fitness and should be unsuited for highly dynamic environments. Even so, our results have shown that enough fragments are reattaching to the reef substratum indicating that this high risk / reward morphological strategy promotes self-replenishment of a marginal population through clonal reproduction. In addition, colonies that have suffered from stress related to fragmentation can further invest their energy to reach larger size and increase their survival [START_REF] Okubo | Successful methods for transplanting fragments of Acropora formosa and Acropora hyacinthus[END_REF][START_REF] Okubo | When fragmented coral spawn? Effect of size and timing on survivorship and fecundity of fragmentation in Acropora formosa[END_REF], and further contribute to population growth via their own fragmentation and release of sexual propagules. This complex interaction between morphological changes and local replenishment highlights the importance of determining limits and trade-off to phenotypic plasticity and evolutionary potential in traits affecting survival, reproduction and dispersal. Nonetheless, more information on physiological plasticity associated to different morphologies and genotypes is needed to fully understand the limits of phenotypic plasticity in the adaptive response of fire corals to environmental changes. For instance, reciprocal transplant experiments of clonal genets can provide important information to determine whether these morphological changes are reversible in response to contrasting environments.

Millepora platyphylla: A competitive and resilient species

Overall, this work has demonstrated the importance of gathering genotypic and phenotypic data to produce a complete picture of ecological and evolutionary strategies involved in the population persistence of Millepora hydrocorals. Self-seeding and intracolonial genetic variability successfully establish diverse genotypes within M. platyphylla population, while colony fragmentation contributes effectively to population growth, where a high number of clonal genotypes have the potential for phenotypic plasticity in response to environmental changes (Fig. 8.2). Our evaluation of the life history of M. platyphylla suggests a competitive strategy, based on the production of few locally produced sexual recruits and their ability of reaching large sizes (fusion and stolonal spreading), which allows them to preempt space on coral reefs, but also brought evidence of high susceptibility to fragmentation. This life strategy is well suited for population persistence in the absence of sexual recruitment, but can be risky in unstable environments [START_REF] Courchamp | Inverse density dependence and the Allee effect[END_REF]).

Yet, M. platyphylla populations in Moorea have withstood severe disturbances, e.g. Acanthaster outbreaks and cyclones. Their recovery is foremost sustained by the rapid growth of remnant colonies, mostly those encrusting, and the subsequent local recruitment via both sexual and asexual reproduction. There is evidence that fire corals may 'win' under pressure from environmental changes, although more information on how they respond to bleaching events is needed, as Millepora species have been reported to be highly vulnerable to thermal stress in other reefs [START_REF] Marshall | Bleaching of corals on the Great Barrier Reef: differential susceptibilities among taxa[END_REF]. Nevertheless, the life history of M. platyphylla is most likely contributing to its colonization success in various reef environments in French Polynesia, where only this species of Millepora was reported in this geographic region. M. platyphylla is also characterized by one of the widest range of distribution in the entire Indo-Pacific region within the Millepora genus [START_REF] Randall | Shallow water hydrozoan corals[END_REF], although similar to the branching M. intricata.

Evaluating the life history of other Millepora species with different growth forms will enable to determine whether these strategies are unique to M. platyphylla or spread within the Millepora genus.

Is Millepora a good model to predict adaptation of reef corals?

Using M. platyphylla as a model species, we have made great progress in understanding the life history of Millepora hydrocorals, an understudied genus of calcifying species. It has been argued at many occasions when discussing the results of this PhD thesis that Millepora is not a good model to evaluate ecological and evolutionary strategies that influence the ability of reef-building corals to adapt to expected climate change, as for predicting long-term consequences on reef community dynamics. Predicting how coral reef ecosystems will respond to the inevitable increase of human activities and environmental changes remains a difficult task. In recent decades, declines in scleractinian coral cover have challenged their role as key ecosystem engineers of coral reefs [START_REF] Bellwood | Confronting the coral reef crisis[END_REF][START_REF] Bruno | Regional decline of coral cover in the Indo-Pacific: timing, extent, and subregional comparisons[END_REF][START_REF] De'ath | The 27-year decline of coral cover on the Great Barrier Reef and its causes[END_REF]. Assuming rising sea temperatures and increased ocean acidification, climate change can interfere with a range of key processes in the life history of corals, including growth, calcification, development, reproduction and behavior [START_REF] Orr | Anthropogenic ocean acidification over the twenty-first century and its impact on calcifying organisms[END_REF][START_REF] Kroeker | Meta-analysis reveals negative yet variable effects of ocean acidification on marine organisms[END_REF]. Despite the acclimatization and genetic adaptation of reef corals [START_REF] Hoegh-Guldberg | Coral reefs under rapid climate change and ocean acidification[END_REF], such persistent physical and chemical conditions can lead to shifts in reef community composition. This phenomenon has already been reported in many reefs, where alternative organisms are dominating reef assemblages (reviewed in [START_REF] Norström | Alternative states on coral reefs: beyond coral-macroalgal phase shifts[END_REF]. Only few studies have considered hydrocorals in ecological monitoring of coral reefs [START_REF] Marshall | Bleaching of corals on the Great Barrier Reef: differential susceptibilities among taxa[END_REF][START_REF] Glynn | Coral bleaching and mortality in Panama and Ecuador during the 1997-1998 El Niño-southern oscillation event: Spatial/temporal patterns and comparisons with the 1982-1983 event[END_REF][START_REF] Brown | Long-term changes in the population dynamics of the Caribbean hydrocoral Millepora spp[END_REF]. For instance, M. platyphylla can dominate some reefs in the Indo-Pacific region (Andréfoüet et al. 2014) and also contribute to the survival of corals during Acanthaster outbreaks as this corallivorous predator tends to avoid Millepora species [START_REF] Lewis | Biology and ecology of the hydrocoral Millepora on coral reefs[END_REF][START_REF] Kayal | Colonies of the fire coral Millepora platyphylla constitute scleractinian survival oases during Acanthaster outbreaks in French Polynesia[END_REF]. Therefore, it is crucial to gain insights into how populations of this keystone species can adapt and survive in the face of climate change and other natural and anthropogenic disturbances. In this thesis, we have demonstrated that M. platyphylla possesses a great variety of life history strategies that favor a high degree of genetic diversity and plasticity enabling this species to persist throughout environmental variations. Consequently, this species may become one of the major components in some modern reefs and requires more considering in ecological monitoring.

Because M. platyphylla is a long-lived species relaying heavily on fragmentation for local persistence, estimating the age of a clonal lineage (i.e. time since a clone's sexual origin) rather than its size could provide important information to predict the resilience of this species. Although many genetic approaches were used for determining age of multicellular organisms, such as the incorporation of environmental signals into tissues [START_REF] Prouty | Growth rate and age distribution of deep-sea black corals in the Gulf of Mexico[END_REF], telomere length [START_REF] Barrett | Telomere length and dynamics predict mortality in a wild longitudinal study[END_REF]) and phenotypic changes [START_REF] Caspari | Older age becomes common late in human evolution[END_REF]

New directions

In order to make further progress in evaluating adaptive potential to environmental changes it is necessary to study how local environmental conditions may shape the microbial community (e.g. bacteria and Symbiodinium algae) associated to fire corals as they ensure essential functions in maintaining host' homeostasis. Additionally, further investigations on epigenetic regulation of phenotypic variation are crucial to predict adaptation to environmental changes as this process plays a key role in gene regulation and expression. Such pending questions require extending our work based on neutral microsatellite markers to functional genes underlying fire coral physiology in order to unravel adaptive advantages of both symbiotic microbial organisms and epigenetic regulation processes.

Predicting how populations of Millepora hydrocorals can survive and adapt under ongoing environmental changes requires to determine the scope of genetic, epigenetic and physiological adaptation processes [START_REF] Brown | The potential for temperature acclimatisation of reef corals in the face of climate change[END_REF][START_REF] Collins | Long-term climate change: projections, commitments and irreversibility[END_REF]. A major source of variation in coral physiology and tolerance to environmental changes result from their association with symbiotic photosynthetic algae (Symbiodinium spp., e.g. [START_REF] Berkelmans | Time-integrated thermal bleaching thresholds of reefs and their variation on the Great Barrier Reef[END_REF][START_REF] Howells | Host adaptation and unexpected symbiont partners enable reef-building corals to tolerate extreme temperatures[END_REF] and other microbial organisms, such as bacteria [START_REF] Rosenberg | The role of microorganisms in coral health, disease and evolution[END_REF][START_REF] Kelly | Local genomic adaptation of coral reef-associated microbiomes to gradients of natural variability and anthropogenic stressors[END_REF][START_REF] Roder | Microbiome structure of the fungid coral Ctenactis echinata aligns with environmental differences[END_REF]. Symbiodinium algae derive inorganic compounds from the host for photosynthesis and provide phototrophic energy required for the metabolic requirements of the coral host [START_REF] Muscatine | The role of symbiotic algae in carbon and energy flux in reef corals[END_REF]). In corals, there are hundreds of Symbiodinium species comprised in nine evolutionary lineages ('clades') with differences in their function and performance [START_REF] Blackall | Coral-the world's most diverse symbiotic ecosystem[END_REF]. The assemblage of Symbiodinium clades can affect growth [START_REF] Little | Flexibility in algal endosymbioses shapes growth in reef corals[END_REF]), disease susceptibility whether host genotype limits phenotypic plasticity through the selection of particular Symbiodinium types and other microorganisms such as microbes. Such a study will improve our understanding of co-evolution processes among the host and its symbiotic microbial community by testing the following hypotheses: 1) the microbiome composition varies among clones of a clonal lineage exposed to various environmental conditions (adaptive plasticity); 2) all clones of the same clonal lineage exposed to various environmental conditions are characterized by a unique microbiome composition (genetic adaptation) and 3) all clonal lineages exposed to the same environmental conditions are characterized by a unique microbiome composition (co-speciation, ecotype) (Fig.

8.2).

Furthermore, phenotypic changes often involve modifications in gene expression and require further investigations. Using transplant experiment, Barshis and colleagues (2010)

Conclusions

Much of our understanding about the response of coral reef organisms to environmental changes has focused on acclimatization via phenotypic plasticity and the scope for genetic adaptation. In highly clonal populations, genetic adaptation through selective pressures is expected to be much slower due to low genetic recombination rates. Using both genetic and phenotypic data, we have demonstrated variability in genotypic diversity and phenotypic traits within populations of M.

platyphylla. As variability within populations is the source of adaptive changes, genetic and phenotypic adaptation in clonal organisms, such as fire corals, is likely to be greater than some have anticipated. We might also expect to see high variability in gene expression, even within hydrocoral genets in different habitats, and considerable phenotypic plasticity at the physiological level due to epigenetic regulation and associated microbial communities. Using knowledge of the life history of M. platyphylla, we can state that this species is heavily fit to 'win' under pressure from multiple

  Fig. 1.2 Spread of somatic mutations in corals from van Oppen et al. 2011. A: Mutant cells arisen in the upper part of the coral polyp migrate into the budding polyp; B: Massive coral colony in which a mutation has arisen and spreads as the colony grow. Partial mortality can divide the colony into two physically separated units that are of different genotypes (i.e. wild and mutant) and C: Branching coral in which a mutated branch has broken and re-attached to the substratum. The wild genotype colony produces wild gametes only, while the mutant genotype colony produces both wild and mutant gametes as corals are diploid and only half of their gametes in a heterozygous individual will carry the mutation following meiosis. .................... 30

  Fig. 3.6 Stock-recruitment relationship between the abundance of adults and coral new recruits and juveniles. (A) Significant positive relationship in the lagoon (i.e. back, fringing and patch reefs) and (B) no stock-recruitment relationship in the fore reef (i.e. mid and upper slopes).

  Fig. 4.1 Proportion of missing data (A) and observed heterozygosity (B) per microsatellite locus (circles) in five Millepora species plotted against phylogenetic distances (16S gene) from the target species Millepora platyphylla (p, red) to other species; Millepora intricata (i, green), Millepora dichotoma (d, pink), Millepora tenera (t, purple), Millepora complanata (c, blue) and Millepora exaesa (e, yellow). .............................................................................................. 80

  Fig. 5.2 Spatial distributions of clonal lineages identified on the mid slope, upper slope and back reef (left) and clones shared between at least two of these habitats (right). Clonal lineages are represented by a unique color. Data are for the transect with the greatest sample size (See Figs. S5 and S7 for all transects). ..................................................................................................... 101

  Fig. 6.4 Dispersal distance distribution of assigned offspring within the entire surveyed area (9000 m²). Observed dispersal distribution, determined using parentage analyses, is given by the percentages of dispersal events (N = 216) distributed among ten distance classes, assigned at 100 m each over the entire dispersal range (A) and assigned at 10 m each over the first hundred meters of the dispersal range (B). ............................................................................................ 132

  .................................................................................................................................................. 133 Table 7.1 Sampling pattern among the five surveyed habitats. Number of colonies (# Col), number of replicates within a single colony (# Repl), total number of samples (# Sam), number of

Fig. 1 . 1

 11 Fig. 1.1 Grime's triangle of life history strategies applied to reef corals from Darling et al. 2012. Principal Coordinates ordination of 143 coral species with four life history strategies (red: competitive, green: weedy, blue: stress-tolerant, grey: generalist). Arrows indicate trait loadings and traits are numbered from most important to least important in differentiating the life history strategies: (1) domed morphology (2) growth rate (3) brooding reproduction (4) fecundity (5) broadcast spawning reproduction (6) branching morphology (7) colony size (8) skeletal density (9) plating morphology (10) corallite diameter (11) depth (12) symbiont diversity (13) generation length and (14) solitary colonies.

Fig. 1 . 2

 12 Fig. 1.2 Spread of somatic mutations in corals from van Oppen et al. 2011. A: Mutant cells arisen in the upper part of the coral polyp migrate into the budding polyp; B: Massive coral colony in which a mutation has arisen and spreads as the colony grow. Partial mortality can divide the colony into two physically separated units that are of different genotypes (i.e. wild and mutant) and C: Branching coral in which a mutated branch has broken and re-attached to the substratum. The wild genotype colony produces wild gametes only, while the mutant genotype colony produces both wild and mutant gametes as corals are diploid and only half of their gametes in a heterozygous individual will carry the mutation following meiosis.

Fig. 1 . 3

 13 Fig. 1.3 Relation between coral growth forms and their vulnerability to wave-induced breakage. Branching morphologies are more vulnerable to fragmentation and occur in low wave energy reef zones. Silhouettes of characterized morphologies are from Madin 2005; branching, tabular, corymbose, convoluted hemispherical, massive and encrusting coral growth forms are shown from the left to the right.

Fig. 1 . 4

 14 Fig. 1.4 The position of hydrozoans, such as Millepora, in the animal tree of life from Houliston et al. 2010. Hydrozoans, cubozoans and scyphozoans are medusozoans and hermatypic corals are anthozoans.

Fig. 1 . 5

 15 Fig. 1.5 Millepora life cycle. Millepora platyphylla is a gonochoric broadcast spawner that reproduces sexually by producing medusoids and planula larvae. The medusoids release the gametes in the water column for external fertilization. The ciliate larvae sink and crawl on the reef substratum and metamorphose in a new calcifying polyp. M. platyphylla also relies on clonal propagation through fragmentation.

  Fig. 1.6 Wave energy dispersal on a barrier reef modified from Monismith 2007 and Ferrario et al. 2014. The fore reef experiences strong wave action from incoming waves that break on the reef crest, near the upper slope, with a significant decrease in swell exposure towards deeper waters. The reef crest dissipates ~70% of the incident swell wave energy with gradual wave attenuation from the back reef to nearshore fringing reefs.

Chapter 5 :

 5 How does sexual and asexual reproduction and fire coral morphologies vary among habitats? Clonal populations are often characterized by reduced levels of genotypic diversity, which can translate into lower numbers of functional phenotypes, both of which impede adaptation. Study of partially clonal animals enables examination of the environmental settings under which clonal reproduction and morphological plasticity are favored. Here, we investigated the relationship between levels of clonality in Millepora and reef habitats using a contemporary genetic and georeferencing characterization of clones, and examine the effect of habitats on the morphology of fire coral clones. Chapter 6: What is the relative contribution from self-recruitment and gene flow in the local replenishment of Millepora platyphylla population?

  Published as: Dubé CE, Boissin E, Planes S (2016) Overgrowth of living scleractinian corals by the hydrocoral Millepora platyphylla in Moorea, French Polynesia. Marine Biodiversity, 46, 329-330.

  Moorea Island in French Polynesia have undergone a massive decline in coral cover from a recent outbreak of Acanthaster planci and cyclone Oli, which provides a unique perspective from which to comprehend competitive interactions among reef species under environmental stress. Here, we provide the first report of the overgrowth of living scleractinian corals by the encrusting hydrocoral Millepora platyphylla, Hemprich & Ehrenberg, 1834. During field surveys undertaken at Moorea in 2013, M. platyphylla was found to overgrow several coral taxa, including Porites spp. (Fig. 2.1a, b, d), Pocillopora meandrina (Fig. 2.1c, d) and Phymastrea curta (Fig. 2.1e). The original morphologies (skeleton and corallites) of overgrown taxa remained visible (Fig.2.1), suggesting a thin layer of superficial overgrowth smothering these corals. A white band discerned at the edge of living corals delimits the growth area of the hydrocoral spreading from its encrusting base towards an adjacent coral colony. Our observations also revealed that such overgrowth triggers the damage and partial death of underlying coral colonies.

  Fig. 2.1 Millepora platyphylla corals (*) at Moorea overgrowing living corals of various scleractinian species: a and b at back reef Porites sp. (°); c Pocillopora meandrina (+) and d Porites sp. (°) and Pocillopora meandrina (+) on fore reef, 6 m depth; e Phymastrea curta ( §) on fore reef, 12 m depth.

  In revision:Dubé CE, Merciere A, Vermeij MJA, Planes S. Population Structure of the Hydrocoral Millepora platyphylla in Habitats Experiencing Different Flow Regimes in Moorea, French Polynesia. PLoS ONE patch reefs.

Fig. 3 . 1

 31 Fig. 3.1 Aerial views of the locations of each transect in the five surveyed habitats in Moorea, French Polynesia. The names of these surveyed locations are: (A) Tiahura, (B) Papetoai, (C) Cook's Bay and (D) Temae. Map data © 2015 Google.

Fig. 3 . 2

 32 Fig. 3.2 Morphologies of M. platyphylla colonies in habitats experiencing contrasting hydrodynamic regimes. (A) Massive wave-tolerant morphology in the patch reef, a lagoonal habitat (photo credit Gilles Siu); (B) encrusting wave-tolerant morphology in the mid slope, a fore reef habitat at 13 m and (C) sheet tree morphology vulnerable to wave-induced breakage in the upper slope, a fore reef habitat at 6 m.

  Fig. 3.3 Index describing the spatial distribution of M. platyphylla colonies across the five surveyed habitats. (A) density (B) cover (C) distribution index and (D) mean neighborhood distance. Values were average per habitat and error bars show the standard error for transect replicates. Similar letters indicate no statistical difference in post-hoc comparisons among habitats (P > 0.5).

Fig. 3 . 5

 35 Fig. 3.5 Recruitment dynamics across the five surveyed habitats. Proportions of recruits (< 1 cm 2 ), juveniles (1-20 cm 2 ) and adults (> 20 cm 2 ) were averaged by habitats with total population size (N in Table S2) and error bars show the standard error for transect replicates. Similar letters over each set of bars indicate no statistical difference in post-hoc comparisons for a given life history stage among habitats (P > 0.05).

Fig. 3 . 6

 36 Fig. 3.6 Stock-recruitment relationship between the abundance of adults and coral new recruits and juveniles. (A) Significant positive relationship in the lagoon (i.e. back, fringing and patch reefs) and (B) no stockrecruitment relationship in the fore reef (i.e. mid and upper slopes). Each circle represent the mean abundance for each transect surveyed. Note the different scales on x and y axes.

Fig. 3 . 7

 37 Fig. 3.7 Morphology of M. platyphylla adult colonies across the five surveyed habitats. Proportions of colonies with encrusting, sheet tree and massive morphology were averaged by habitats and error bars show the standard error for transect replicates. Similar letters over each set of bars indicate no statistical difference in post-hoc comparisons for a given life history stage among habitats (P > 0.05). See Fig. 3.2 for photos of each of the morphologies.

Fig. 3 . 8

 38 Fig. 3.8 Non-metric multidimensional scaling (MDS) plot of M. platyphylla population structure across the five surveyed habitats. Different shapes indicate the three transects for each habitat and grey lines show clusters given by dendogram based on Eucledian distance of 4 at a stress level of 0.09. The surimposed red lines define the Eucledian distance coefficient on normalized data based on Spearman ranking, with eachvector having lengths ≥ 0.4: density, cover, distribution index, mean neighborhood distance, mean height and size of adults, and proportion of recruits (< 1 cm 2 ), juveniles (1-20 cm 2 ) and adults (> 20 cm 2 ). The second transect of the fringing reef is shown as a single group mostly related to a small population size (i.e. 27 colonies, TableS2).

  Milleporaprimer annealing temperature (see MP in Table

Fig. 4 . 1

 41 Fig. 4.1 Proportion of missing data (A) and observed heterozygosity (B) per microsatellite locus (circles) in five Millepora species plotted against genetic distances (16S gene) from the target species Millepora platyphylla (p, red) to other species; Millepora intricata (i, green), Millepora dichotoma (d, pink), Millepora tenera (t, purple), Millepora complanata (c, blue) and Millepora exaesa (e, yellow).

  first evaluation of genetic diversity among species of Millepora across its geographic range in tropical reefs reveals moderate levels of heterozygosity and allelic richness. The lowest genetic diversity was found for the Caribbean species, M. complanata, likely resulting from the low proportion of polymorphic loci (46.7%) and the high proportion of loci showing evidence of null Millepora alleles (75.0%). Nonetheless, levels of genetic diversity estimated in this study are similar to what

  microsatellites in the genome(Tόth et al. 2000). A recent study has demonstrated high microsatellite coverage in several species of cnidarians, including Millepora alcicornis (Ruiz-Ramos and Baums 2014), indicating that there is no biological constraint for the development of microsatellite markers in this phylum. The availability of numerous microsatellite markers for reefbuilding Millepora species creates new opportunities for future research into the processes driving the complexity of their colonization success on many Indo-Pacific reefs.

  ii) What are the patterns of distribution and dispersal of asexual fragments? (iii) Are there clonal lineages with clones shared among habitats that display phenotypic plasticity?

  between sexual and asexual reproduction across habitatsAssessment of the relative contribution of sexual and asexual reproduction required assignment of identical multilocus genotype (MLG) among colonies. This analysis was performed with GENCLONE v.2.0[START_REF] Arnaud-Haond | GENCLONE: a computer program to analyze genotypic data, test for clonality and describe spatial clonal organization[END_REF]. The term clonal lineage is used for each MLG encompassing multiple ramets (G MR ). Each 'multi-ramet genotype' represents a lineage (originated from the same reproductive event) with all clones produced by fragmentation. MLGs with one single ramet (G SR ) were considered to be produced sexually with no clone. The probability that identical MLGs arise from distinct random reproductive events was estimated as P SEX[START_REF] Arnaud-Haond | GENCLONE: a computer program to analyze genotypic data, test for clonality and describe spatial clonal organization[END_REF]. The genotypic dataset was screened for somatic mutations. Samples showing evidence of slight allelic differences among ramets of MLGs were re-amplified and screened at five additional microsatellite loci to eliminate errors in clone assignment: Mille_01,

  Fig. 5.1 Spatial distribution of sexual versus asexual M. platyphylla colonies (left) and morphologies (right) across all five surveyed habitats. Photo series shown is of clones of the same clonal lineage found on the mid slope, upper slope, and back reef, respectively (see Fig. S7 for location of these colonies). The inset photo for sheet tree shows the horizontal view of this morphology; the vertical blades make the morphology vulnerable to fragmentation in the high energy upper slope habitat. Data shown are for the transect with the greatest sample size (See Figs. S3 and S4 for all transect replicates).

Fig

  Fig. 5.1).

  estimated for clonal lineages with less than 5 clones.

  Fig. S2The size frequency distributions of single ramets (left) and clonal ramets (right) across the five surveyed habitats (both sides add to 100%). Colony size (cm 2 ) data distributed among 10 size classes. Frequencies (%) of single and clonal ramets for each size class were averaged by habitats with total population size (N in TableS3) and error bars show the standard error for transect replicates.

Fig. S3

 S3 Fig. S3 Spatial distribution of single and clonal ramets across the five surveyed habitats within three belt transects (300 x 10 m).

Fig. S4

 S4 Fig. S4 Spatial distribution of colony morphologies across the five surveyed habitats within three belt transects (300 x10 m).

Fig. S5

 S5 Fig. S5 Spatial distribution of clonal lineages across the five surveyed habitats along three 300 x 10 m belt transects. Each clonal lineage is represented by a unique color (N = 328).

Fig. S6

 S6 Fig. S6 Spatial distribution of a single clonal lineage shared among two of the three transects within the patch reef.

Fig. S7

 S7 Fig. S7 Spatial distribution of clonal lineages with clones shared in at least two habitats across the mid slope, upper slope and back reef. Each clonal lineage is represented by a unique colour (N = 57). Arrows in T3 depict the location of clones used in the photo series shown in Fig. 5.1.

Fig. 6 . 1

 61 Fig. 6.1 Aerial views showing the study area in Moorea, French Polynesia and the locations of the three belt transects (300 x 10 m) within the three surveyed habitats. Map data © 2015 Google.

Fig. 6 . 2

 62 Fig. 6.2 Spatial distribution and size of the 3160 colonies sampled across the three surveyed habitats within three belt transects (300 x 10 m). Adult colonies (potential parents, N = 2101) are represented in grey and juvenile colonies (< 20 cm 2 , N = 1059) in white. Assigned offspring to parents sampled within the study area, as revealed by parentage analysis, are shown in red (N = 216).

Fig. 6 . 3

 63 Fig. 6.3 Dispersal patterns of four local families. Two are of parents with unique genotype (A) P1 with seven assigned offspring and (B) P2 with five assigned offspring, and two are of parents with clonal genotype (C) P3 and P4 (D) with five assigned offspring each. Dispersal estimates for parent-offspring relationship and mean dispersal distance among siblings are given in TableS3. One full sib relationship was found for P1 and an unknown parent with a distance of 723.41 m between the two full siblings.

Fig. 6 . 4

 64 Fig. 6.4 Dispersal distance distribution of assigned offspring within the entire surveyed area (9000 m²).Observed dispersal distribution, determined using parentage analyses, is given by the percentages of dispersal events (N = 216) distributed among ten distance classes, assigned at 100 m each over the entire dispersal range (A) and assigned at 10 m each over the first hundred meters of the dispersal range (B).

Fig. 6 . 5

 65 Fig. 6.5 Dispersal distance distribution of siblings (full-and half-sibs) within the entire surveyed area (9000 m²). Observed dispersal distribution of full-sibs (A) and half-sibs (B), determined using parentage analyses, is given by the percentages of dispersal events (N = 78 of full siblings; N = 132 of half siblings) distributed among nine distance classes, assigned at 100 m each over the entire dispersal range.

2

  Dubé CE et al. Population structure of the hydrocoral M. platyphylla in habitats experiencing different flow regimes.

  Fig. S1 Size frequency distribution of the 3160 colonies sampled in the entire study area. The colony size (cm²) of each colony was estimated from 2D photographs and data were distributed among the size classes based on a logarithm scale.

Fig. S2

 S2 Fig. S2 Spatial distribution and size of parents contributing to self-recruitment within the three belt transects (300 x 10 m) in each of the three surveyed habitats. Each clonal parent is represented by a unique color (N=54) and only the biggest clone was retained for parentage assignments. Each single genotype parent is represented in white (N = 42).

  Fig. 7.1 Aerial views of the locations of the five surveyed habitats in Moorea, French Polynesia. The names of these surveyed locations are: (A) Papetoai and (B) Temae. Map data © 2015 Google.

Fig. 7 . 2

 72 Fig. 7.2 Intracolonial genetic variability detected in M. platyphylla colonies in the five surveyed habitats. Frequency (%) of deviating genotypes caused by chimerism are shown in black; by mosaicism, i.e. somatic mutations, in grey and single genotypes, i.e. most common genotypes, are shown in light grey.

Fig. 7 . 3

 73 Fig. 7.3Frequency (%) of deviating genotypes caused by one-step to four-to twelve-step mutations over all loci in all surveyed habitats. Notice that the back reef is not shown since no deviating genotype was found within this habitat.

  history of Millepora hydrocorals: Are they 'winners'?

M

  . platyphylla is a long-lived organism mostly relying on fragmentation for local replenishment with high self-seeding and sibling aggregations on Moorea's reefs, intracolonial genetic variability is most likely a key process in population persistence by supplying additional genotypic diversity (Fig.8.1).

Fig. 8 . 1

 81 Fig. 8.1 Summary of life history strategies in M. platyphylla in Moorea, French Polynesia. M. platyphylla heavily relies on asexual reproduction through fragmentation for local replenishment (80% of the colonies are clones), allowing population growth and the persistence of a genotype over time when sexual reproduction is impeded. Although only 20% of the colonies of M. platyphylla are produced through sexual reproduction, its population is sustained via a high contribution of self-recruitment (58% of juveniles are self-recruits). Mosaicism and chimerism also contribute in creating novel genotypic diversity in the population.

  platyphylla clones have a vulnerable morphology that increases colony fragmentation in the upper slope. Such phenotypic response can increase mortality of both the colony subjected to breakage

Fig. 8 . 2

 82 Fig. 8.2Evolutionary perspectives for M. platyphylla. Self-seeding and intracolonial genetic variability (mosaicism and chimerism) create novel genetic diversity within M. platyphylla population, while colony fragmentation allows the persistence of these genotypes (shown as genotypes a-e). The interaction of these processes generates a high level of genetic variability required for adaptation via genetic changes. Also, each of these genotypes can express different phenotypes in response to environmental changes and even clones have demonstrated phenotypic plasticity. Further investigations on how fire coral-associated microbial communities (A-E) are impacted by variation in environmental conditions are needed to detangle adaptive plasticity, genetic adaptation and co-speciation of the holobionte.

  have demonstrated that host genotype limits protein expression in the coral Porites lobata, thus limiting phenotypic response to environmental changes. Investigating gene regulation and expression in clonal genotypes in different reef habitats provides a unique opportunity to assess these questions in natural populations. At last, epigenetic mechanisms are largely recognized as one of the principal mediators of gene expression and adaptive plasticity (Duncan et al. 2014). Dimond and Roberts (2016) have demonstrated that genes are differentially expressed in coral species in response to thermal stress and ocean acidification due to lower levels of DNA methylation. Because this epigenetic process can be influenced by the environment, further investigations of DNA methylation are needed to get the whole picture on the ability of M. platyphylla to acclimatize and adapt to environmental change.

  a good model to predict resilience of reef species due to its wide range of effective strategies involved in local population maintenance.

Moorea, French Polynesia Overgrowth of living scleractinian corals by the hydrocoral Millepora platyphylla in Moorea, French Polynesia

	Caroline E. Dubé 1 , Emilie Boissin 1 , Serge Planes 1
	Received: 30 May 2015 / Revised: 24 August 2015 / Accepted: 26 August 2015
	© Senckenberg Gesellschaft für Naturforschung and Springer-Verlag Berlin Heidelberg 2015
	1 USR 3278 CRIOBE EPHE-CNRS-UPVD, Laboratoire d'Excellence "CORAIL", BP 1013, 98 729
	Papetoai, Moorea, French Polynesia

  .6B).

	Habitat		Colony size (cm²)				Recruitment
		Non-transformed	ln-transformed		Abundance (n)	Proportion (%)
		Mean (SE)	95%	Pnorm	CV	g 1	Recruit	Juvenile	Recruit	Juvenile
	Patch	3090.48 (1293.52)	9889.89 <0.01	0.51	-0.01 1.00 (1.73) 11.30 (3.06)	1.47 (2.55) 17.93 (4.52)
	Fringing 1590.07 (328.94)	7107.16 <0.01	0.49	0.14	1.33 (0.58) 21.33 (17.21)	1.74 (1.86) 24.00 (8.20)
	Back	509.87 (97.07)	2512.02 <0.01	0.33	0.68	---	13.00 (7.55)	---	11.77 (5.94)
	Upper	2308.20 (115.84)	8513.79 <0.01	0.54	0.42	9.33 (3.51) 161.00 (32.70) 1.57 (0.53) 27.26 (3.53)
	Mid	819.04 (73.30)	1295.23 <0.01	0.63	0.64	12.00 (4.36) 159.00 (53.33) 3.44 (0.40) 45.86 (5.15)

3

  Population structure of Millepora hydrocorals populations are foremost sustained by the growth of remnant colonies, local recruitment through sexual reproduction where wave energy is low and clonal propagation in high wave energy zones.

	Patch 1	17.4775	149.7673	35.40	66.47	0.97
	Patch 2	17.4759	149.7699	20.28	52.78	0.90
	Patch 3	17.4742	149.7726	26.91	58.98	0.59
	Fringing 1 17.4881	149.8967	331.05	564.65	0.79
	Fringing 2 17.4902	149.8676	323.32	561.96	0.84
	Fringing 3 17.4836	149.8165	40.07	1198.13	0.80
	Back 1	17.4838	149.8742	917.83	87.80	0.65
	Back 2	17.4834	149.8773	1074.67	65.50	0.81
	Back 3	17.4832	149.8805	927.40	37.72	0.76
	Upper 1	17.4820	149.8755	1110.26	84.56	6.09
	Upper 2	17.4818	149.8786	1176.29	93.45	5.95
	Upper 2	17.4822	149.8816	995.20	76.98	5.65
	Mid 1	17.4816	149.8755	1155.73	122.36	13.17
	Mid 2	17.4813	149.8785	1215.28	135.54	12.99
	Mid 3	17.4819	149.8817	1034.70	118.32	12.59

Table S2

 S2 Index describing the spatial distribution, recruitment and morphology for Millepora platyphylla across the five surveyed habitats.

				Spatial Distribution					Recruitment		Morphology
	Habitat	N	Density (n.m -2 ) Cover (%)	DI	ND	N Recruit Juvenile Adult Recruit	% Juvenile	Adult	Adult size (cm 2 )	Height
	Patch 1	62	0.02	0.61	1.60	39.81	---	8	51	---	13.56	86.44	4074.63	20.84
	Patch 2	68	0.02	0.29	2.35	34.13	3	12	53	4.41	17.65	77.94	1625.37	19.62
	Patch 3	59	0.02	0.60	1.82	35.60	---	14	48	---	22.58	77.42	3571.44	33.81
	Tot / Mean (SE)		0.02 (0.00)	0.50 (0.18) 1.92 (0.39) 36.51 (2.95)	3	34	152 1.47 (2.55) 17.93 (4.52) 80.60 (5.06) 3090.48 (1293.52) 24.76 (7.86)
	Fringing 1	78	0.03	0.27	3.05	15.83	---	14	64	---	17.95	82.05	1255.04	23.15
	Fringing 2	27	0.01	0.11	6.38	17.76	1	9	17	3.70	33.33	62.96	1912.57	30.41
	Fringing 3		0.07	0.82	3.10	9.34	1	41	154	1.52	20.71	77.78	1602.59	19.03
	Tot / Mean (SE)		0.04 (0.03)	0.40 (0.37) 4.18 (1.91) 14.31 (4.41)	2	64	235 1.74 (1.86) 24.00 (8.20) 74.26 (10.02) 1590.07 (328.94) 24.20 (5.76)
	Back 1		0.03	0.15	1.28	19.66	---	12	89	---	11.88	88.12	499.72	7.69
	Back 2		0.04	0.20	1.25	17.79	---	21	98	---	17.65	82.35	611.62	9.37
	Back 3		0.03	0.14	1.44	17.73	---	6	98	---	5.77	94.23	418.27	8.35
	Tot / Mean (SE)		0.03 (0.01)	0.16 (0.03) 1.32 (0.10) 18.39 (1.10)	---	39	285	---	11.77 (5.94) 88.23 (5.94)	509.87 (97.07)	8.47 (0.85)
	Upper 1		0.17	2.78	4.07	4.37	6	124	380	1.17	24.27	74.36	2189.29	9.26
	Upper 2		0.22	3.66	3.61	3.71	9	173	474	1.37	26.37	72.26	2314.60	7.55
	Upper 3		0.20	3.22	4.34	4.20	13	186	398	2.18	31.16	66.67	2420.71	6.26
	Tot / Mean (SE) 1761	0.20 (0.03)	3.22 (0.44) 4.01 (0.37) 4.09 (0.34)	28	483	1252 1.57 (0.53) 27.26 (3.53) 71.10 (3.98)	2308.20 (115.84)	7.69 (1.51)
	Mid 1		0.18	0.86	2.64	4.68	17	219	306	3.14	40.41	56.46	840.45	8.07
	Mid 2		0.08	0.26	2.20	8.38	9	117	105	3.90	50.65	45.45	737.43	6.11
	Mid 3		0.10	0.45	3.38	6.86	10	141	152	3.30	46.53	50.17	879.25	5.62
	Tot / Mean (SE) 1075	0.12 (0.05)	0.52 (0.31) 2.74 (0.59) 6.64 (1.86)	36	477	563 3.44 (0.40) 45.86 (5.15) 50.69 (5.52)	819.04 (73.30)	6.60 (1.30)

N, population size; DI, distribution index; ND, Neighborhood distance; Recruits, < 1 cm 2 ; Juveniles, 1-20 cm 2 . Values in bold were average per habitat and SE for variation among transects.

Table S3

 S3 Average percentages of adult colonies for M. platyphylla with encrusting, sheet tree and massive morphology across surveyed habitats.

					3
	Habitat Mid Slope Upper Slope Back Reef Fringing Reef Patch Reef	Encrusting 73.95 (1.10) 30.51 (3.21) 74.51 (5.21) 20.28 (8.30) 37.83 (9.41)	Sheet tree 6.63 (2.41) 69.49 (3.21) 9.25 (3.16) ----3.14 (3.14)	Massive 19.42 (1.77) 16.24 (2.06) 79.72 (8.30) 59.03 (9.91) ----	Population structure of Millepora hydrocorals
			CHAPTER 4

Genetic diversity and differentiation in Millepora species, as revealed by cross-species amplification of novel microsatellite loci

In press: Dubé CE, Planes S, Zhou Y, Berteaux-Lecellier V, Boissin E. Genetic diversity and differentiation in reef-building Millepora species, as revealed by cross-species amplification of fifteen novel microsatellite loci. PeerJ Genetic

diversity and differentiation in reef-building Millepora species, as revealed by cross-species amplification of fifteen novel microsatellite loci

	Caroline E. Dubé 1,2 , Serge Planes 1,2 , Yuxiang Zhou 1 , Véronique Berteaux-Lecellier 2 , Emilie
	Boissin 1,2
	1 EPHE, PSL Research University, UPVD-CNRS, USR 3278 CRIOBE, F-66860 Perpignan, FRANCE
	2 Laboratoire d'excellence "CORAIL", EPHE, PSL Research University, UPVD-CNRS, USR 3278
	CRIOBE, BP 1013, 98729 Papetoai, Moorea
	Corresponding Author:
	Caroline E Dubé
	Email address: caroline.dube.qc@gmail.com

  . There is currently no agreement regarding the number of Millepora species and no phylogenetic study investigating the genetic relationships among them (but see Ruiz-Ramos et al. 2014 for a species complex in the Caribbean). Although microsatellite loci have been identified in Millepora alcicornis (Ruiz-Ramos and Baums 2014), there was a lack of highly variable genetic markers for this genus until very recently (but see[START_REF] Heckenhauer | Isolation, characterization and cross amplification of eleven novel microsatellite loci for the hydrozoan coral Millepora[END_REF]. The development of new molecular Millepora reefs in French Polynesia. Secondly, we tested these new microsatellite loci for cross-species amplification in five other Millepora species: the branching Millepora intricata, Millepora dichotoma and Millepora tenera, the plate-like species Millepora complanata and the encrusting Millepora exaesa(Boshma 1948). Lastly, genetic distances based on the 16S mitochondrial gene were estimated among these species and M. platyphylla to identify the transferability success of these newly developed microsatellites across the Milleporidae.

	reef-building
	in
	differentiation
	and
	diversity
	Genetic

markers for Millepora species will increase our knowledge on the genetic diversity of a conspicuous reef-building organism across its geographic range. These microsatellite markers will enable further studies on the biological, ecological and evolutionary processes underlying the population persistence of Millepora hydrocorals.

Microsatellites, also known as simple sequence repeats (SSRs) or short tandem repeats (STRs), have emerged as one of the most powerful genetic markers in population and evolutionary genetics

[START_REF] Selkoe | Microsatellites for ecologists: a practical guide to using and evaluating microsatellite markers[END_REF]

. Improvements in next generation sequencing techniques have provided new opportunities for microsatellite isolation in non-model organisms (i.e. with no genetic information available)

[START_REF] Zhang | The impact of next-generation sequencing on genomics[END_REF]

, with a good representativeness of loci across the genome

[START_REF] Martin | Representativeness of microsatellite distributions in genomes, as revealed by 454 GS-FLX titanium pyrosequencing[END_REF]

. Because microsatellites are codominant

[START_REF] Estoup | CT)n and (GT)n microsatellites: a new class of genetic markers for Salmo trutta L. (brown trout)[END_REF]

, highly polymorphic

[START_REF] Schlötterer | Evolutionary dynamics of microsatellite DNA[END_REF]

and transferable among closely related species

[START_REF] Cheng | Screening of new microsatellite DNA markers from the genome of Platyeriocheir formosa[END_REF]

, they are commonly used for a remarkable array of applications, such as inferring genetic diversity

[START_REF] Silva | Emerging patterns of genetic variation in the New Zeland endemic scallop Pecten novaezelandiae[END_REF][START_REF] Nakajima | Genetic differentiation and connectivity of morphological types of the broadcast-spawning Galaxea fascicularis in the Nansei Islands, Japan[END_REF]

) and population structure patterns

[START_REF] Noreen | Genetic diversity and connectivity in a brooding reef coral at the limit of its distribution[END_REF][START_REF] Boissin | Contemporary genetic structure and post-glacial demographic history of the black scorpionfish, Scorpaena porcus, in the Mediterranean and the Black Seas[END_REF]

, evaluating reproductive strategies

[START_REF] Baums | Marginal coral populations: the densest known aggregation of Pocillopora in the Galapagos Archipelago is of asexual origin[END_REF][START_REF] Ardehed | Complex spatial clonal structure in the macroalgae Fucus radicans with both sexual and asexual recruitment[END_REF]

and parentage screening

[START_REF] Mourier | Direct genetic evidence for reproductive philopatry and associated finescale migrations in female blacktip reef sharks (Carcharhinus melanopterus) in French Polynesia[END_REF][START_REF] Warner | Sperm dispersal distances estimated by parentage analysis in a brooding scleractinian coral[END_REF]

. Cross-species transferability has been successful in many species

[START_REF] Barbará | Cross-species transfer of nuclear microsatellite markers: potential and limitations[END_REF][START_REF] Reid | High-throughput microsatellite marker development in two sparid species and verification of their transferability in the family Sparidae[END_REF][START_REF] Maduna | Microsatellite crossspecies amplification and utility in southern African elasmobranchs: a valuable resource for fisheries management and conservation[END_REF][START_REF] Pirog | Isolation and characterization of eight microsatellite loci from Galeocerdo cuvier (tiger shark) and cross-amplification in Carcharhinus leucas, Carcharhinus brevipinna, Carcharhinus plumbeus and Sphyrna lewini[END_REF]

) allowing for genetic studies in closely related species. However, the few studies that have investigated the efficiency of cross-species transferability of microsatellite loci have demonstrated a negative correlation between the genetic distance and the amplification success

[START_REF] Carreras-Carbonell | Utility of pairwise mtDNA genetic distances for predicting cross-species microsatellite amplification and polymorphism success in fishes[END_REF][START_REF] Hendrix | Strong correlation between crossamplification success and genetic distance across all members of 'True Salamanders' (Amphibia: Salamandridae) revealed by Salamandra salamandra-specific microsatellite loci[END_REF][START_REF] Moodley | Evolutionary factors affecting the cross-species utility of newly developed microsatellite markers in seabirds[END_REF]

. This constraint can hamper accurate comparisons of genetic diversity among more distantly related species.

Here, we used 454 GS-FLX sequencing technology to develop an additional set of de novo microsatellite markers for Millepora platyphylla to first assess its genetic diversity on Moorea's 4

Table 4 .1

 4 Characterization of de novo microsatellite loci and genetic variation in the target species M. platyphylla collected in Moorea, French Polynesia. panel in which each locus was included; T A , primer temperature annealing; N, number of individuals with reliable amplification; Null, proportion of null alleles; LD, proportion of allele comparisons showing significant linkage disequilibrium (P < 0.05); Na, number of alleles; H O , observed heterozygosity; H E , expected heterozygosity; F IS , inbreeding coefficient. Significant values of F IS are indicated by bold values with * P < 0.05 and ** P < 0.001.

	Locus	Primer Sequence 5'-3'	Dye	MP Motif	T A (°C) # GenBank N	Size (bp) Null	LD	Na H O	H E	F IS
	Mill07	F: TAGTACATCGGGCATGAGCA	6-FAM	3	(CA) 16	57	KX670763	50 92-144	---	---	0.760 0.855 0.121*
		R: GTACTCTACGGCGTGTGCGT
	Mill27	R: CTTTCGTTTCCGATCATTCC	VIC	3	(TG) 10	57	KX670764	50 136-148	---	0.044	0.600 0.636 0.067
		R: TGCCAGAACTAAGTTATCACAGC
	Mill30	F: AGTTGGCTCTGAGTGCGAGT	NED	2	(TG) 11	57	KX670765	50 203-211	---	0.025	0.680 0.648 -0.039
		R: CCTCGGTTTATGGCTGAGAT
	Mill47	F: AAGCGTGTAATGCACTCAAAGA	NED	2	(GA) 8	57	KX670766	50 118-162	0.101 0.057 0.600 0.766 0.227**
		R: AACAGAAGTCGAACTGAGTCAAAA
	Mill52	F: CCCTGAGGCATCGAAATATAA	6-FAM	1	(AC) 9	60	KX670767	50 94-98	---	---	0.420 0.412 -0.010
		R: TGCAATTGATGGTATTTGCATT
	Mill56	F: TCTGCAGATTTTGCATCTCG	PET	1	(AGA) 6	60	KX670768	50 194	---	---	0	0	---
		R: TAGCAACAATGCTTCGCTGA
	Mill61	F: AAATGAACTCGCCCAAAAGA	PET	4	(CAA) 7	57	KX670769	50 163-166	---	0.048	0.480 0.467 0.044
		R: ACACTGTCGATTGTGTTCCAA
	Mill67	F: TTGCGAGTTTACTTACCAGGC	VIC	1	(TAGA) 6	60	KX670770	50 259-359	0.144 0.039 0.420 0.588 0.294**
		R: TGAAGCAAATGACAAGAGCAA
	Mill86	F: GCGCGAAAATAAATTAAGGAA	NED	4	(GTT) 5	57	KX670771	50 106	---	---	0	0	---
		R: TCCAATCTGAATTCCACCCT
	Mill91	F: CACTTTCGCCATTGTTGCTA	PET	4	(CAA) 6	57	KX670772	50 116	---	---	0	0	---
		R: AACGGAATTCGAATCATTGC
	Mill93	F: TGAAATTTTCCAGTGACATCAAA	6-FAM	2	(TGT) 7	57	KX670773	50 91-100	---	0.055	0.260 0.339 0.243
		R: GCTAATTATGAAATAGCAACTCCTAAA
	Mill94	F: GCATAAAGAATAAAGCAGAGGCA	6-FAM	3	(GAA) 7	57	KX670774	50 131-140	---	0.016	0.480 0.461 -0.032
		R: CAATTGTGGGGAAGTTCGTT
	Mill95	F: TCCATAGCTTCTGCCTCCTC	6-FAM	1	(TTG) 7	60	KX670775	50 123-138	---	0.022	0.320 0.304 -0.042
		R: GCTGATGATGCTGTCGAAGA
	Mill101 F: AGTCCTTCAATTGGTGGGTG	PET	2	(CAA) 6	57	KX670776	50 132-135	---	---	0.640 0.493 -0.289
		R: GAGATGATGACTGAGCAGCAG
	Mill103 F: TTAAAGCCAGAGACAGAGAGACA	VIC	3	(AG) 7	57	KX670777	50 94-100	---	0.017	0.700 0.621 -0.117
		R: ATCAACAGTTTCCCCTGTGC
	MP, multiplex

Table 4 .2

 4 Summary of genetic distances (GD) based on the 16S gene between the target species and otherMillepora species together with indices indicating microsatellite transferability and genetic diversity.

	Species	Locality N	MLG	Clonal MLG	P (ID)	GD	Amp (%)	Pol (%)	Null (%)	LD (%)	Na	Ho
	M. platyphylla Moorea	50	50	---	1.3E-6	---	100	80.0	13.3	9.1	3.462	0.411
	M. intricata	Papua	11	10	1	1.1E-6	0.048	73.3	60.0	---	12.1 3.909	0.405
	M. dichotoma Europa	30	24	4	4.1E-7	0.049	86.7	60.0	7.7	10.3 3.417	0.323
	M. tenera	Reunion	30	24	6	3.1E-7	0.049	80.0	73.3	58.3	23.0 4.833	0.439
	M. complanata Curaçao	30	30	---	1.3E-6	0.130	53.3	46.7	75.0	10.2 4.000	0.250
	M. exaesa	Reunion	14	14	---	3.9E-6	0.149	60.0	53.3	11.1	17.6 3.625	0.496

N, sample size; MLG, number of multilocus genotypes; Clonal MLG, number of multilocus genotypes with clonal replicates; P (ID) , Probability of Identity; Amp, percentage of loci amplified; Pol, percentage of polymorphic loci; Null, percentage of loci showing evidence of null alleles; LD, percentage of allele comparisons showing significant linkage disequilibrium (P < 0.05); Na, mean number of alleles; H O , mean observed heterozygosity. Na and Ho were estimated based on loci showing no evidence of null alleles and clonal replicates were removed from our dataset for these measures of genetic diversity.

  Assessment of the mtDNA genetic distances (GD) within the Millepora genus revealed that branching species, i.e. M. intricata, M. dichotoma and M. tenera, were more closely related (0.048-0.049) to our target species, with haplotypes shared between M. dichotoma and M. tenera (Table4.3 Millepora amplification also revealed a significant decrease of polymorphism with increasing mtDNA distance (r = -0.857, P = 0.029), with lower percentages of polymorphic loci for non-target species (≤ 73.3%, Table4.2). No relationship was found between the percentage of loci showing evidence of null alleles and genetic distance (r = 0.331, P = 0.521). The highest percentage was recorded for Nuclear (F ST ) and mitochondrial (p-distance) genetic distances among Millepora species.Values above the diagonal are the F ST calculated on the microsatellite dataset, values with P < 0.001 are in bold and the remaining values are NS. Values below the diagonal are genetic distances (p-distance) based on the mitochondrial 16S gene.

	locus increased significantly with increasing level of genetic distance (Fig. 4.1A, r = 0.214, P = 0.044). reef-building M. complanata (75.0%), while lowest for M. intricata (0%). The proportion of missing data per Table 4.3
		in
		differentiation
		and
		diversity
	and see Appendix S1 for the haplotype network). The plate-like M. complanata (0.130) and	Genetic
	encrusting M. exaesa (0.149) were more genetically distant from M. platyphylla. The mean
	amplification success for cross-species amplification was 70.7% (~11 loci out of 15) and the mean

polymorphism was 58.7% (~9 loci out of 15). Cross-species amplification decreased significantly with mtDNA genetic distance (r = -0.931, P = 0.007), with a reduced amplification success in the most divergent species, i.e. M. complanata (53.3%) and M. exaesa (60.0%), and higher for M. intricata (73.3%), M. tenera (80.0%) and M. dichotoma (86.7%) (Table

4

.2). Cross-species 4

  Table 4.3 and see Appendix S2 for the Bayesian clustering analysis). No significant genetic differentiation was observed for the closely related branching species (i.e. M. intricata, M. dichotoma and M. tenera). For all comparisons involving our target species M.

		M. platyphylla	M. intricata	M. dichotoma	M. tenera	M. exaesa
	M. platyphylla		0.343	0.373	0.339	0.167
	M. intricata	0.048		0.031	0.065	0.181
	M. dichotoma	0.049	0.051		0.062	0.221
	M. tenera	0.049	0.051	0.000		0.293
	M. exaesa	0.149	0.143	0.150	0.150

platyphylla, the lowest value of F ST (≤ 0.167) was recorded for the most divergent species M. exaesa. No relationship (r = 0.150, P = 0.679) was found between the nuclear (F ST from microsatellite data) and mitochondrial (p-distance from 16S) genetic distances.

Table S1

 S1 Symbiodinium strains used to identify coral specific loci.See http://www.nsm.buffalo.edu/Bio/burr/ for more details on the Symbiodinium strains.

	Culture ID	Host	Location	18S rDNA	Genotype
					(23S chloroplast rDNA)
	FLAP1	Aiptasia pallida	Florida	A	A193	4
	Cass KB8	Cassiopea sp.	Hawaii	A	A194
	Pe FLAP2 Mp A001 A014	Porites evermanni Aiptasia pallida Mastigia paupa Acropora sp. Porites australiensis	Hawaii Florida Palau Okinawa Okinawa	B B C D D	B184 B184 C180 D206 D206	in reef-building Millepora
	CCMP421 Pd	unknown Porites divaricata	New Zealand Florida	E F	E202 F178	differentiation
	Sin	Sinularia sp.	Guam	F	F179	and
						diversity
						Genetic

Table S2

 S2 Locations for Millepora spp. sampling.

	Species	Locality	Latitude (D.d) Longitude (D.d) Year
	M. platyphylla	Moorea	17.4816 S	149.8755 W	2013
	M. intricata	Papua New Guinea	4.9937 S	146.3299 E	2014
	M. dichotoma	Europa	20.3472 S	40.3667 E	2013
	M. tenera	Reunion	20.9029 S	55.3537 E	2009
	M. complanata	Curaçao	12.1202 N	68.9696 W	2014
	M. exaesa	Reunion	20.9029 S	55.3537 E	2009

Table S3

 S3 Cross-species transferability of fifteen microsatellite loci isolated from Millepora platyphylla (Moorea) in five others species of Millepora.

	Locus	T A (°C) Species	N	N amp Size (bp)	Null	LD	Na H O	H E	F IS
	Mill07 57	M. intricata	11	0	0	---	---	0	---	---	---
			M. dichotoma 30	8	96-102	---	8	4	0.000	0.688	1.000***
			M. tenera	30	0	0	---	---	0	---	---	---
			M. complanata 30	9	92-106	0.237	6	9	0.444	0.839	0.515***
			M. exaesa	14	0	0	---	---	0	---	---	---
	Mill27 57	M. intricata	11	11	156-188	---	4	15	0.900	0.920	0.052
			M. dichotoma 30	30	150-190	---	8	16	1.000	0.914	-0.073
			M. tenera	30	30	138-198	---	9	15	1.000	0.901	-0.089

  H O , observed heterozygosity; H E , expected heterozygosity; F IS , inbreeding coefficient. Significant values of F IS are indicated by bold values with * P < 0.05, ** P < 0.01 and *** P < 0.001. Clonal replicates were removed from our dataset for the measures of genetic diversity.

		complanata 30	25	101-194	0.410	4	7	0.08	0.7192 0.893***
		M. exaesa	14	0	0	---	---	0	---	---	---
	Mill93 57	M. intricata	11	11	91-103	---	5	4	0.500	0.655	0.359
		M. dichotoma 30	30	91-100	---	7	3	0.458	0.499	0.103
		M. tenera	30	29	94-97	0.291	7	2	0.174	0.454	0.630**
		M. complanata 30	0	0	---	---	0	---	---	---
		M. exaesa	14	8	91-97	---	2	3	1.000	0.555	-0.061
	Mill94 57	M. intricata	11	11	122-140	---	2	4	0.500	0.415	-0.176
		M. dichotoma 30	30	128-140	---	6	4	0.750	0.635	-0.161
		M. tenera	30	30	128-137	---	8	4	0.333	0.411	0.209
		M. complanata 30	25	128-140	0.224	4	5	0.292	0.673	0.581***
		M. exaesa	14	7	128-138	0.372	1	4	0.143	0.684	0.818*
	Mill95 63	M. intricata	11	11	123-126	---	2	2	0.500	0.455	0.000
		M. dichotoma 30	30	120-126	---	6	3	0.667	0.622	-0.051
		M. tenera	30	30	123-126	---	6	2	0.292	0.457	0.381
		M. complanata 30	28	120-171	0.186	5	7	0.357	0.576	0.396***
		M. exaesa	14	9	111-141	---	1	7	0.889	0.796	-0.058
	Mill101 57	M. intricata	11	11	132-138	---	---	3	0.100	0.185	0.500*
		M. dichotoma 30	30	135	---	---	1	0	0	---
		M. tenera	30	30	132-138	0.214	5	3	0.125	0.291	0.584***
		M. complanata 30	0	0	---	---	0	---	---	---
		M. exaesa	14	9	132-144	---	3	4	0.444	0.451	0.072
	Mill103 57	M. intricata	11	11	94-104	---	2	4	0.800	0.625	-0.151
		M. dichotoma 30	30	94-96	---	6	2	0.542	0.492	-0.079
		M. tenera	30	29	94-96	0.389	9	2	0.043	0.496	0.916***
		M. complanata 30	28	92-98	---	3	4	0.429	0.580	0.278*
		M. exaesa	14	9	94-98	---	1	3	0.222	0.364	0.439
	T A , primer temperature annealing; Sp, Species; N, sample size; N amp , number of individuals with reliable amplification;
	Null, proportion of null alleles; LD, proportion of allele comparisons showing significant linkage disequilibrium (P <
	0.05) ; Na, number of alleles;

Table 5 .1

 5 Proportion of clones with encrusting, sheet tree and massive morphology for six clonal lineages shared among habitats.

Table S1

 S1 Locations of each transect within the five surveyed habitats in Moorea, French Polynesia.

	Habitat	Latitude	Longitude Distance to	Distance to	Depth
		(°S)	(°W)	coast (m)	crest (m)	(m)
	Mid 1	17.4816	149.8755	1155.73	122.36	13.17
	Mid 2	17.4813	149.8785	1215.28	135.54	12.99
	Mid 3	17.4819	149.8817	1034.70	118.32	12.59
	Upper 1	17.4820	149.8755	1110.26	84.56	6.09
	Upper 2	17.4818	149.8786	1176.29	93.45	5.95
	Upper 2	17.4822	149.8816	995.20	76.98	5.65
	Back 1	17.4838	149.8742	917.83	87.80	0.65
	Back 2	17.4834	149.8773	1074.67	65.50	0.81
	Back 3	17.4832	149.8805	927.40	37.72	0.76
	Fringing 1	17.4881	149.8967	331.05	564.65	0.79
	Fringing 2	17.4902	149.8676	323.32	561.96	0.84
	Fringing 3	17.4836	149.8165	40.07	1198.13	0.80
	Patch 1	17.4775	149.7673	35.40	66.47	0.97
	Patch 2	17.4759	149.7699	20.28	52.78	0.90
	Patch 3	17.4742	149.7726	26.91	58.98	0.59

Table S2

 S2 Newly developed polymorphic microsatellite loci for M. platyphylla.

	Locus			GenBank	T A	Size (bp)	Na
	name	Primer Sequence 5'-3'	Motif	accession	(°C)	range
	Mill07 F: TAGTACATCGGGCATGAGCA	(CA) 16	KX670763	63	92-144
		R: GTACTCTACGGCGTGTGCGT
	Mill27 R: CTTTCGTTTCCGATCATTCC	(TG) 10	KX670764	55	136-148
		R: TGCCAGAACTAAGTTATCACAGC
	Mill30 F: AGTTGGCTCTGAGTGCGAGT	(TG) 11	KX670765	57	203-211
		R: CCTCGGTTTATGGCTGAGAT
	Mill47 F: AAGCGTGTAATGCACTCAAAGA	(GA) 8	KX670766	53	118-162
		R: AACAGAAGTCGAACTGAGTCAAAA
	Mill52 F: CCCTGAGGCATCGAAATATAA	(AC) 9	KX670767	57	94-98
		R: TGCAATTGATGGTATTTGCATT
	Mill61 F: AAATGAACTCGCCCAAAAGA R: ACACTGTCGATTGTGTTCCAA	(CAA) 7	KX670769	57	163-166	5
	Mill67 F: TTGCGAGTTTACTTACCAGGC R: TGAAGCAAATGACAAGAGCAA Mill93 F: TGAAATTTTCCAGTGACATCAAA R: GCTAATTATGAAATAGCAACTCCTAAA Mill94 F: GCATAAAGAATAAAGCAGAGGCA Mill95 F: TCCATAGCTTCTGCCTCCTC R: GCTGATGATGCTGTCGAAGA R: CAATTGTGGGGAAGTTCGTT	(TAGA) 6 KX670770 (GAA) 7 KX670774 (TTG) 7 KX670775 (TGT) 7 KX670773	53 55 53 57	259-359 131-140 123-138 91-100	demonstrate phenotypic plasticity
	Mill101 F: AGTCCTTCAATTGGTGGGTG R: GAGATGATGACTGAGCAGCAG	(CAA) 6	KX670776	53	132-135	clones
	Mill103 F: TTAAAGCCAGAGACAGAGAGACA	(AG) 7	KX670777	53	94-100	coral
		R: ATCAACAGTTTCCCCTGTGC					Fire
	T A , Annealing temperature (°C); Na, Number of alleles per locus.

Table S3

 S3 Index describing sexual and clonal diversity for M. platyphylla across the five surveyed habitats.N, number of genotyped samples; G SR , number of lineages with single ramet; G MR , number of lineages with multiple ramets; Clone, proportion of clones; P SEX , probability that clones arisen from sex; R, clonal richness; D*, Simpson' diversity index; ED*, clonal evenness; MAX, maximum number of ramets per lineage; CR, clonal subrange (m). Bold values are average per habitat and ± SE for variation among transects

	Habitat	N	G SR G MR	Clone	R	D*	ED*	MAX	CR (m)
					(% of N)
	Mid 1	542 147 48	0.73	0.36	0.98	0.95	53	25.89
	Mid 2	230 131 22	0.43	0.66	0.99	0.90	14	31.54
	Mid 3	303 128 28	0.58	0.51	0.98	0.93	21	31.33
	Tot / Mean	1075 406 98	0.58 ± 0.15 0.51 ± 0.15 0.98 ± 0.01 0.93 ± 0.03		29.59 ± 3.20
	Upper 1	510 57	53	0.89	0.21	0.97	0.96	54	32.83
	Upper 2	656 73	55	0.89	0.19	0.96	0.94	71	54.69
	Upper 3	595 75	54	0.87	0.22	0.94	0.91	125	31.36
	Tot / Mean	1761 205 162 0.88 ± 0.01 0.21 ± 0.02 0.96 ± 0.02 0.94 ± 0.03		39.63 ± 13.07
	Back 1	101 26	28	0.74	0.53	0.97	0.89	12	78.20
	Back 2	119	29	33	0.76	0.52	0.97	0.90	15	108.69
	Back 3	104 34	25	0.67	0.56	0.98	0.94	7	75.91
	Tot / Mean	324 89	86	0.72 ± 0.05 0.54 ± 0.02 0.97 ± 0.01 0.91 ± 0.03		87.60 ± 18.30
	Fringing 1	78	3	7	0.96	0.12	0.76	0.78	34	28.61
	Fringing 2	27	1	3	0.96	0.12	0.34	0.22	22	111.40
	Fringing 3	197	2	12	0.99	0.07	0.79	0.83	81	28.98
	Tot / Mean	302	6	22	0.

97 ± 0.02 0.10 ± 0.03 0.63 ± 0.25 0.61 ± 0.04 56.33 ± 47.70

	Table S4 Average numbers (N ± SE) and percentages (% ± SE) of colonies for M. platyphylla with
	encrusting, sheet tree and massive morphology within each surveyed habitat.
	N					Colonies of M. platyphylla
	Habitat			Encrusting		Sheet tree		Massive
	Mid			82.67 ± 50.62		12.67 ± 15.14		33.33 ± 15.37
	Upper			74.67 ± 10.97		249.67 ± 38.53		----
	Back			59.00 ± 8.54		7.67 ± 5.13		15.33 ± 2.89
	Fringing			12.67 ± 14.57		----		49.67 ± 39.07
	Patch			8.67 ± 1.53		1.00 ± 1.73		29.33 ± 8.74
											5
	%					Colonies of M. platyphylla
	Habitat			Encrusting		Sheet tree		Massive		plasticity
	Mid Upper			64.43 ± 3.13 23.28 ± 5.08		7.55 ± 5.47 76.72 ± 5.08		28.01 ± 6.09 ----	phenotypic
	Patch 1 Patch 2 Patch 3 Back Fringing Patch	62 68 59	8 6 13	12 6 12 71.91 ± 9.90 0.87 0.91 0.78 15.54 ± 8.38 23.08 ± 7.10	0.31 0.16 0.41	0.94 0.77 0.95 9.38 ± 6.39 ----2.50 ± 4.33	0.93 0.75 0.92	8 25 7 18.71 ± 3.56 84.46 ± 8.38 74.42 ± 9.14	216.80 112.08 99.19	demonstrate
	Tot / Mean	189 27	30	0.85 ± 0.07 0.29 ± 0.13 0.89 ± 0.10 0.87 ± 0.10	142.69 ± 64.50	clones
											coral
											Fire

Table S5

 S5 Average numbers (N ± SE) and percentages (% ± SE) of single and clonal ramets for M. platyphylla with each morphology within each surveyed habitat.

	N		Single ramet			Clonal ramet
	Habitat	Encrusting	Sheet-tree	Massive	Encrusting	Sheet-tree	Massive
	Mid	18.00 ± 3.64	1.33 ± 1.52	5.33 ± 0.58	64.67 ± 48.21	11.33 ± 13.65	28.00 ± 15.87
	Upper	8.00 ± 3.60	22.00 ± 3.60	----	66.67 ± 7.37 227.67 ± 36.23	----
	Back	18.33 ± 7.09	1.66 ± 2.89	3.00 ± 2.00	40.67 ± 1.53	6.00 ± 3.60	12.33 ± 1.53
	Fringing	----	----	2.00 ± 1.00	12.67 ± 14.57	----	47.67 ± 38.63
	Patch	----	----	6.67 ± 3.05	8.67 ± 1.53	1.00 ± 1.73	22.67 ± 6.51
								5
	% Habitat	Encrusting	Single Ramet Sheet-tree	Massive	Encrusting	Single Ramet Sheet-tree	Massive	plasticity
	Mid Upper Back Fringing Patch	72.70 ± 6.76 26.67 ± 12.02 77.86 ± 18.15 --------	4.90 ± 5.41 73.33 ± 12.02 8.33 ± 14.43 --------	22.40 ± 9.52 ----13.81 ± 9.57 100 ± 0.00 100 ± 0.00	61.99 ± 2.00 40.78 ± 7.44 69.15 ± 6.26 16.17 ± 8.25 27.74 ± 8.28	8.39 ± 5.03 54.93 ± 7.44 9.94 ± 5.64 ----2.78 ± 4.81	29.61 ± 5.80 20.90 ± 2.13 83.83 ± 28.23 69.48 ± 9.59 ----	demonstrate phenotypic
								clones
								coral
								Fire

Table 6 .2

 6 Summary results of parentage analysis in Millepora platyphylla within the entire reef area (9000 m 2 ). Characteristics of parents contributing to self-recruitment and comparisons between clonal and single genotype parents are given: number of potential parents surveyed in the study area; number of parents assigned to an offspring within the surveyed area with their mean colony size (cm²), standard error (SE) and median; total number of assigned offspring and mean number of assigned offspring to one single parent with standard error (SE), maximum and median. All values are presented at the genet level (i.e. without clonal replicates). Estimates of offspring dispersal within the study area are shown: mean distance between the parent and their assigned offspring with standard error (SE), minimum, maximum and median.

	Parent	Parent	Parent
	total	clonal genotype	single genotype

Table S1

 S1 Summary statistics for the twelve microsatellite loci analyzed in this study.N: number of colonies successfully genotyped; N A : number of alleles; H O : observed heterozygosity; H E : expected heterozygosity; F IS :[START_REF] Weir | Estimating F-statistics for the analysis of population structure[END_REF] inbreeding coefficient; Null: frequency of null alleles; LD: percentage of pair of loci showing significant linkage disequilibrium (P < 0.05); P ID : Probability of idendity P EX : probability of exclusion given one missing parent genotype. Significant values of FIS are indicated by bold values with * P < 0.05 and ** P < 0.001 and the mean P ID and P EX in red represents the additive estimate for all loci.

		Mill07	Mill27	Mill30	Mill47	Mill52	Mill61	Mill67	Mill93	Mill94	Mill95	Mill101 Mill103
	N	3148	3157	3154	3145	3159	3160	3132	3142	3159	3157	3157	3154
	N A	25	6	4	14	2	2	17	4	5	5	2	4
	H O	0.7951	0.710	0.668	0.625	0.000	0.321	0.376	0.362	0.444	0.314	0.468	0.650
	H E	0.890	0.642	0.660	0.722	0.192	0.484	0.483	0.417	0.448	0.320	0.488	0.581
	F IS	0.107**	-0.105	-0.013	0.134**	1.000**	0.337**	0.220**	0.133**	0.008	0.019	0.040*	-0.119
	Null	0.032	---	---	0.092	0.079	0.135	0.093	0.087	---	---	---	---
	LD	63.64	27.27	36.36	18.18	18.18	36.36	9.09	9.09	54.55	9.09	18.18	27.27
	P ID	3.8E-1	8.5E-2	1.0E-2	3.1E-3	1.5E-3	3.0E-4	6.5E-6	2.6E-6	4.4E-7	3.0E-7	1.1E-	4.5E-8
	P EX	0.12	0.28	0.52	0.58	0.6	0.68	0.89	0.9	0.92	0.92	0.93	0.94

Table S2

 S2 Dispersal distance of offspring that were assigned to parent pairs within the study area and the geographic distance between the mother and father.

	Offspring	Parents	Offspring dispersal (m)	Distance parents (m)
	MDT3-R4	UPT1-R304	387.63	601.32
		MDT3-L143	215.32
	MDT3-L118	MDT1-L96	768.65	98.06
		MDT1-L185	670.61
	MDT1-L229	MDT3-R16	465.14	165.75
		UPT2-R267	310.00
	UPT3-R168	UPT3-L226	33.90	3.94
		UPT3-L209	32.52
	MDT1-L95	MDT3-L162	836.40	45.53
		MDT3-R81	791.02
	MDT1-R153	MDT3-R79	687.50	429.00
		UPT2-R153	266.46
	UPT3-R253	UPT3-L226	5.21	3.94
		UPT3-L209	1.30
	BRT2-R34	UPT2-R327	188.28	177.78
		BRT2-L48	63.75
	UPT2-R99	UPT3-L101	433.31	178.41
		MDT3-R7	268.54
	MDT1-L113	MDT2-R35	285.53	255.15
		MDT1-R102	30.38
	UPT1-R99	UPT3-L38	645.35	603.45
		BRT1-R41	179.91
	MDT2-R38	BRT3-L35	536.17	891.74
		MDT1-R30	376.60
	MDT1-R81	MDT2-R35	304.51	255.21
		MDT1-R102	49.30

Table S3

 S3 Dispersal patterns of juvenile cohorts within four local families (P1, P2, P3 and P4). Several indices are indicated as follows: the number of potential parents (ramet level); the number of juveniles that were full siblings or half siblings; the mean dispersal distance of assigned offspring with standard error (SE), minimum, maximum and median values; and the mean dispersal distance between assigned offspring and their parent with standard error (SE), minimum, maximum and median values. Total dispersal distances were estimated at the genet level, i.e. the biggest parent in each of the local pedigree was retained for dispersal estimates. See Fig.6.2 for location of parents and assigned offspring in the four local families.

		P1	P2	P3	P4	Total
	# potential parents	1	1	2	23	27
	# full-sibs	2	---	---	---	2
	# half-sibs	5	5	5	5	20
	Mean dispersal distance of assigned offspring (m)	364.47	99.39	426.34	20.37	257.16
	SE	326.66	62.96	253.07	12.81	285.84
	Min	6.42	10.38	12.62	0.70	0.70
	Max	768.25	221.21	881.11	33.18	881.11
	Median	132.90	88.59	371.16	24.68	102.92
	Mean dispersal distance parent-offspring (m)	333.34	362.61	402.54	29.14	309.00
	SE	56.18	81.96	262.75	30.51	223.12
	Min	234.76	267.00	110.40	0.07	0.07
	Max	400.74	488.21	770.72	104.70	770.72
	Median	361.30	341.23	262.48	25.05	309.85

  data 1 ). Studies relating the occurrence of intracolonial genotypic variability to habitat specific environmental conditions and reproductive strategies (i.e. at both ramet and genet levels) remain largely unavailable (but see[START_REF] Reusch | Widespread genetic mosaicism in the marine angiosperm Zostera marina is correlated with clonal reproduction[END_REF][START_REF] Rinkevich | Venturing in coral larval chimerism: a compact functional domain with fostered genotypic diversity[END_REF]). Here, using microsatellite markers, we investigated the occurrence of chimeras and mosaic colonies within populations of the hydrocoral M. platyphylla in five reef habitats in Moorea, French Polynesia; the mid slope, upper slope, back reef, fringing reef and patch

1 Dubé CE et al. Fire coral clones demonstrate phenotypic plasticity among reef habitats.

Table 7 .1

 7 Sampling pattern among the five surveyed habitats. Number of colonies (# Col), number of replicates within a single colony (# Repl), total number of samples (# Sam), number of detected multilocus genotypes (# Gen), number of clones in sampled colonies (# Clon), percentage of genetically heterogeneous colonies (% Het), number of colonies displaying massive (M), encrusting (E) or sheet tree (ST) morphology and mean colony size are given for the 51 colonies sampled. The number of colonies sampled belonging to a clonal (asexual reproduction) or single genotypes (sexual reproduction) according to an exhaustive sampling and genotyping of M. platyphylla colonies (performed byDubé et al. unpublished data 1 ) are also shown.

	Habitat # Col # Repl # Sam # Gen # Clon % Het Morphology (N) Colony # Clonal	# Single
								M	E	ST size (cm²) lineages genotypes
	Patch	10	5	50	17	1	60.0	10	---	---	11 272	8	2
	Fringing 10	5	50	12	1	20.0	10	---	---	8 976	7	3
	Back	8	5	40	7	1	---	2	---	6	4 289	8	---
	Upper	13	5	65	17	1	46.2	---	2	11	29 749	13	---
	Mid	10	5	50	12	0	20.0	3	4	3	18 459	9	1

  al. unpublished data 2 ), hence limiting the colony 7 .e. growth and age). This limitation in size can hamper the potential for the accumulation of mutations in adult corals. However, mosaicism was found in colonies of various sizes (> 800 as high as 63,500 cm 2 ), while some of the largest colonies sampled were genetically homogeneous. In partially clonal organisms, such variability in the accumulation of mutations among size classes can be related to recently small fragmented ramets that might have accumulated mutations before their fragmentation. This highlights the importance of aging clonal lineage (as described inDevlin- Durante et al. 2016) rather than estimating colony size to better understand the mechanisms behind mosaicism in reef-building corals, such as fire corals.

	in M.
	genotypic variability
	Intracolonial

platyphylla size (i

Table 1

 1

	platyphylla
	in M.
	genotypic variability
	Intracolonial

,

Dubé et al. unpublished data 1

). For the 51 sampled colonies of M. platyphylla that were subjected to multiple samplings, the most common genotype was retained as the main genotype (i.e. single genotype). All additional 7

  , age determination remains challenging in clonal organisms. Devlin-Durante and colleagues (2016) have recently demonstrated that the accumulation of somatic mutations within a clone correlates with genet age. Such technique based on the genetic divergence of microsatellite markers could be used to estimate the age of the 328 clonal lineages identified in this thesis. Such data are important to relate investment in clonal reproduction to environmental disturbances, such as El Niño events and cyclones, and also provide further insights into the history of M. platyphylla spread on Moorea's reefs.

Table S1

 S1 Index of genetic diversity in Millepora platyphylla in Moorea, French Polunesia. Na, number of alleles; H O , observed heterozygosity; H E , expected heterozygosity; F IS , inbreeding coefficient. Significant values of F IS are indicated by bold values with * P < 0.05, ** P < 0.01 and *** P < 0.001.

	Habitats	Transects Na		Ramet level	Genet level
				Ho	He	F IS	Ho	He	F IS
	Patch Reef	T1	4.33	0.544 0.538 -0.011	0.518 0.549 0.058
		T2	4.00	0.489 0.459 -0.065	0.467 0.534 0.132*
		T3	4.17	0.483 0.548 0.120***	0.481 0.544 0.118**
	Fringing Reef	T1	3.83	0.416 0.390 -0.066	0.425 0.527 0.202**
		T2	2.75	0.472 0.332 -0.436	0.417 0.503 0.195
		T3	4.17	0.602 0.543 -0.10	0.559 0.576 0.030
	Back Reef	T1	5.08	0.487 0.513 0.051**	0.498 0.533 0.067**
		T2	4.92	0.479 0.513 0.066***	0.507 0.530 0.045*
		T3	5.17	0.481 0.542 0.113***	0.495 0.547 0.096***
	Upper Slope	T1 T2	5.33 5.92	0.522 0.536 0.026** 0.492 0.511 0.038***	0.485 0.534 0.092*** 0.504 0.543 0.072***	Directions
	Mid Slope	T3 T1 T2 T3	5.67 6.17 6.17 5.83	0.415 0.506 0.180*** 0.531 0.552 0.038*** 0.518 0.545 0.049*** 0.580 0.554 -0.048	0.465 0.534 0.133*** 0.584 0.563 -0.038* 0.520 0.555 0.063*** 0.505 0.542 0.069***	Conclusions and New
							8

Dubé CE et al. Fire coral clones demonstrate phenotypic plasticity among reef habitats.

Dubé CE et al. Population structure of the hydrocoral M. platyphylla in habitats experiencing different flow regimes.

Dubé CE et al. Dispersal limitations and sibling aggregations in Millepora hydrocorals.

Acknowledgements

We thank A Merciere for support on the field. We additionally thank three anonymous reviewers and the editor for comments that greatly improved this manuscript. CED and EB are financially supported by the Fonds Québécois de Recherche sur la Nature et les Technologies (FQRNT) and the Marie Curie fellowship MC-CIG-618480, respectively.

Acknowledgements

We are grateful to F Lerouvreur and M Besson who contributed to the fieldwork and E Boissin for valuable discussion. We also thank the CRIOBE staff for technical and logistic support.

Acknowledgements

We are grateful to Alexandre Mercière, Maggy Nugues, Nicky Gravier-Bonnet, Chloé Bourmaud, Julia Leung, Suzie Mills and Ricardo Beldade who contributed to sample collection, Nathalie Tolou for technical advice and Jeanine Almany for English improvements on the manuscript. We are also grateful to Mary Alice Coffroth and her laboratory for providing us cultured Symbiodinium strains.

We also thank Iliana Baums and one anonymous reviewer for their thoughtful comments on the manuscript.

Acknowledgements

We are grateful to A. Mercière for field support and help with statistical analyses. We also thank F. Lerouvreur and M. Besson who contributed to the fieldwork and V. Berteaux-Lecellier for valuable discussions. The figures were developed collaboratively with D. Tracey. C.E.D. is supported by a graduate scholarship from the Fonds Québécois de Recherche sur la Nature et les Technologies. E.B. and J.A.M. were supported by European Commission Marie Curie Actions fellowships

Acknowledgements

We are grateful to Alexandre Mercière for field support and help with statistical analyses. We also thank Franck Lerouvreur and Marc Besson who contributed to the fieldwork and Jeanine Almany for English improvements on the manuscript.

Acknowledgements

We are grateful to Alexandre Mercière who contributed to sample collection and Jeanine Almany for English improvements on the manuscript. C.E.D. is supported by a graduate scholarship from the Fonds Québécois de Recherche sur la Nature et les Technologies. E.B. is supported by European Marie Curie Postdoctoral fellowship MC-CIG-618480.

9

References

the last four years. His love and support were a source of strength to accomplish this thesis.

This Research received funding from the Fonds Québécois de Recherche sur la Nature et les Technologies for a graduate scholarship.

Supporting Information

Table S1 Locations of each transect surveyed in the five habitats. Each pie represents one 16S haplotype (with its area proportional to the number of individuals in which it was detected). The lengths of the grey lines connecting the 16S haplotypes are proportional to the number of mutations separating them with the number of mutations shown in red on each line. This haplotype network was reconstructed using the median joining algorithm (Bandelt et al.1999) Assignment analyses based on Bayesian clustering analysis using STRUCTURE [START_REF] Pritchard | Inference of population structure using multilocus genotype data[END_REF] for five of the six studied species: (1) M. platyphylla, (2) M. exaesa, (3) M. intricata, (4) M. dichotoma and ( 5) M. tenera. The x-axis shows species identification and y-axis shows the cluster membership (K=2). Initial STRUCTURE runs were used to determine the most likely number of clusters (K). Runs were performed with the default setting, a burn-in period of 50000, 50000 MCMC repeats and 10 iterations per K. The results were uploaded to STRUCTURE HARVESTER [START_REF] Earl | STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method[END_REF] and the most likely K was retained for a second run in STRUCTURE with a burn-in period of 500000, 500000 MCMC repeats, 10 iterations and uniform prior setting. Table S6 Genetic differentiation for M. platyphylla populations between the five surveyed habitats.

The estimator of Weir and Cockerham' F ST was estimated among transects of each surveyed habitat using GENETIX v.4.05.2 [START_REF] Belkhir | GENETIX 4.05 Logiciel sous Windows pour la Génétique des Poplulations[END_REF]. Values were calculated on a data set where only one of each lineage was retained (i.e. colonies of sexual origin). * P < 0.05, ** P < 0.01, *** P < 0.001 and all other values are NS.

Genetic diversity and microsatellite panel

All twelve loci were polymorphic over the 3610 colonies analyzed, with a mean observed and expected heterozygosity of 0.478 and 0.527, respectively, and 7.50 alleles per locus on average.

Seven loci showed significant deficiencies in heterozygotes compared to HWE (F IS : 0.040-1.000) (Table S1). Null alleles occurred at low frequencies at six loci (< 0.006; Table S1), while a high frequency of null alleles was found only at Mill61 (> 0.1). The combined probability of exclusion, P (EX) , for the microsatellite marker panel was 0.94, revealing its high reliability for parentage assignments (Table S1), so all loci were retained to infer sibship and parentage relationships.

Parentage analyses and recruitment

Parentage analyses assigned 58% of all juvenile samples (216 of 375) to parents that were sampled within the study area (i.e. self-recruits, Table 6.1). 76% of these assigned juveniles (165 of 216)

were found within the mid slope. Only 7% (25 of 375) had at least one parent located in one of the other habitats surveyed, suggesting more limited inter-habitat connectivity. Among the 603 parents sampled in the entire study area (genet level), only 96 of them were contributing to self-recruitment in M. platyphylla population (Fig. S2). 42 parents were unique genotypes (i.e. assumed to be the result of sexual reproduction with one single ramet), while the other 54 belonged to repeated MLGs (i.e. clonal lineages) with a mean number of 12 ramets (i.e. potential parents) per MLG (range: 2-65). Of the 216 identified parent-offspring pairs, 203 were assigned to single parents and only 13

were to parent pairs. Although the sex of individuals was not identified in this study, distance research has shown limited dispersal ability of their sexual propagules (i.e. medusoids and planula larvae). Only medusoids can swim by pulsation of their bell, while eggs are negatively buoyant and slowly sink after being released [START_REF] Soong | Synchronised release of medusae from three species of hydrozoan fire corals[END_REF] and larvae crawl once they reach the reef substratum [START_REF] Bourmaud | Mass spawning events, seasonality and reproductive features in Milleporids (Cnidaria, Hydrozoa) from Reunion Island[END_REF]. Such early life history traits are most likely rising opportunities for self-recruitment in populations of fire corals, while the local dispersal among reef habitats must rely on the passive dispersal of their sexual propagules through water circulation patterns.

Dispersal of early life stages with reef currents

In Moorea, alongshore and cross-reef transports are known to affect recruitment of larvae and population connectivity among habitats within a single reef, both in corals [START_REF] Edmunds | Landscape-scale variation in coral recruitment in Moorea, French Polynesia[END_REF][START_REF] Leichter | Biological and physical interactions on a tropical island coral reef: Transport and retention processes on Moorea, French Polynesia[END_REF]) and fishes [START_REF] Beldade | Larger female fish contribute disproportionately more to self-replenishment[END_REF][START_REF] Bernardi | Full-sibs in cohorts of newly settled coral reef fishes[END_REF]. The low connectivity among adjacent habitats indicates that cross-reef transport from the fore reef towards the lagoon (e.g. [START_REF] Hench | Episodic circulation and exchange in a wave-driven coral reef and lagoon system[END_REF][START_REF] Monismith | Wave transformation and wavedriven flow across a steep coral reef[END_REF] is not the major factor determining the dispersal of offspring in M. platyphylla at Moorea. In contrast, for some scleractinian corals, this physical process seems to have a strong influence on their recruitment patterns on Moorea's reefs [START_REF] Edmunds | Landscape-scale variation in coral recruitment in Moorea, French Polynesia[END_REF]). However, these conclusions were based only on field surveys, no population genetic approaches or parentage analyses were performed. The dispersal of offspring crossing the reef matrix is therefore a question warranting further investigation in scleractinian species. For fire corals, cross-reef dispersal and subsequent recruitment patterns could be the result of a continuous supply of asexual fragments (Fig. S2, see Dubé et al. unpublished data 1 ). Considering that M.

platyphylla heavily relies on clonal reproduction in Moorea, fragmentation process, although more important during period of big swells and storms, can provide a means to connect populations among adjacent habitats rather than sexual reproduction.

In this study, dispersal patterns within local families revealed that currents that run along the reef help to disperse sexual propagules on the fore reef. Such water circulation results in the settlement of larvae parallel to the reef in alignment with the location of their parents. Our data also suggest that gamete and/or larval supply from unsampled colony within the study population (between our transects and habitats, Fig. 6.2) are potentially contributing to the local replenishment. These findings indicate a potential for dispersal at longer distances (> 1km), whereas most of the larvae settled near the parental source (i.e. 0 to 300 m, with high proportion between 0 to 10 m). As previously described in Caribbean reefs (Paris and Cohen 2004)

Abstract

In recent years, intracolonial genotypic variability has been described in many colonial marine organisms. This genetic variability can arise from mosaicism (somatic mutations) and/or chimerism (allogenic fusion of genetically distinct individuals). Both processes provide an important source of genetic variation and raise questions on their implications regarding the adaptive capacity of threatened species, such as corals. We investigated intracolonial genotypic variability using microsatellite markers in the fire coral Millepora platyphylla in five habitats in Moorea, French

Polynesia. We aimed to determine whether chimerism and mosaicism are related to habitats, reproductive modes (asexual/sexual) and/or colony morphology. Our results show that intracolonial genetic variability is common (31.4%) in M. platyphylla with important variations in its frequency among habitats (0-60%). Mosaicism is responsible for most of the deviating genotypes (87.5%), while chimerism is rarer. Nearly all mosaic colonies were detected in individuals belonging to clonal lineages indicating that asexual reproduction increases the accumulation of somatic mutations, while there was no effect from their morphology. In addition to increasing genotypic diversity in highly clonal organisms, like M. platyphylla, intracolonial genetic variability results in more versatile phenotypic traits. Such variability presents what might well be a potential mechanism for adaptation under environmental changes.

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Intracolonial genotypic variability in M. platyphylla

Introduction

Understanding evolutionary strategies in species largely relies on the concept of individuality, where each individual represents the unit on which selection pressures occur [START_REF] Williams | Adaptation and Natural Selection[END_REF]). An individual is intrinsically defined as reproductive, physiologically autonomous, genetically unique and homogeneous [START_REF] Michod | Darwinian Dynamics: Evolutionary Transitions in Fitness and Individuality[END_REF][START_REF] Santelices | How many kinds of individual are there?[END_REF]), but there are many studies that question this definition (reviewed in Pineda-Krch and Lehtilä 2004). It has been recognized that for colonies of social insects, physiological unity is not respected because individuals cooperate with others to form a "superorganism", acting as though the colony was one single individual [START_REF] Hölldobler | The Superorganism: TheBeauty, Elegance, and Strangeness of Insect Societies[END_REF]. Furthermore, asexual reproduction is common in natural populations of countless plants and animals, where individuals are not genetically unique [START_REF] Avise | Clonality: The Genetics, Ecology, and Evolution of Sexual Abstinence in Vertebrate Animals[END_REF]. The occurrence of genetic heterogeneity within a single individual has also been documented in populations of protists, fungi, plants and animals (Pineda-Krch and Lehtilä 2004) and is now considered a common phenomenon.

There are two main processes that can lead to intra-individual genetic variability: mosaicism and chimerism. Mosaicism is the outcome of intrinsic genetic changes caused, among other processes, by somatic mutations [START_REF] Santelices | Mosaicism and chimerism as components of intraorganismal genetic heterogeneity[END_REF]). In contrast, chimerism originates from allogenic fusion and requires specific environmental conditions and species' life history traits [START_REF] Rinkevich | Chimeras in colonial invertebrates: a synergistic symbiosis or somatic-and germ-cell parasitism?[END_REF]. Chimerism is much rarer in natural populations due to allorecognition systems. This process mostly occurs in seaweeds and colonial marine organisms with a dispersive pelagic phase, e.g. sponges, hydroids, bryozoans, ascidians and corals [START_REF] Sommerfeldt | Intracolonial genetic variation: ecological and evolutionary aspects. Chimerism following fusion in a clonal ascidian (Urochordata)[END_REF][START_REF] Rinkevich | Allorecognition and xenorecognition in reef corals: a decade of interactions[END_REF][START_REF] Santelices | Mosaicism and chimerism as components of intraorganismal genetic heterogeneity[END_REF][START_REF] Gonzalez-Bernat | Fertilisation, embryogenesis and larval development in the tropical intertidal sand dollar Arachnoides placenta in response to reduced seawater pH[END_REF]. Mosaicism, by contrast, is a widespread mechanism of many clonal plants and animals with long life-spans [START_REF] Strassmann | Genetic conflicts and intercellular heterogeneity[END_REF][START_REF] Reusch | Widespread genetic mosaicism in the marine angiosperm Zostera marina is correlated with clonal reproduction[END_REF][START_REF] Van Oppen | Novel genetic diversity through somatic mutations: fuel for adaptation of reef corals?[END_REF]. Chimeras and mosaic organisms can lead to both evolutionary benefits and disadvantages. Theoretically, intra-individual genetic variability promotes disruptive internal conflicts threatening an organism's ability to function, e.g. developmental instability [START_REF] Stebbins | Gene action and morphogenesis in plants[END_REF][START_REF] Møller | Asymmetry, developmental stability and evolution[END_REF] or intra-individual competition [START_REF] Ne | Life history plasticity in chimaeras of the colonial ascidian Botryllus schlosseri[END_REF][START_REF] Folse | Direct benefits of genetic mosaicism and intraorganismal selection: modeling coevolution between a long-lived tree and a short-lived herbivore[END_REF]. However, the co-occurrence of many different genotypes within an individual also generates additional genotypic variation in populations, which can benefit the potential for adaptation [START_REF] Frankham | Genetics and extinction[END_REF][START_REF] Bonin | Population Adaptive Index: a new method to help measure intraspecific genetic diversity and prioritize populations for conservation[END_REF][START_REF] Funk | Harnessing genomics for delineating conservation units[END_REF]. This greater genotypic variability results in more versatile phenotypic traits (e.g. investigations have demonstrated that genotypic heterogeneity is widespread in species of scleractinian corals [START_REF] Maier | Intracolonial genetic variation in the scleractinian coral Seriatopora hystrix[END_REF]Puill-Stephan et al. 2012a;[START_REF] Schweinsberg | Transfer of intracolonial genetic variability through gametes in Acropora hyacinthus corals[END_REF][START_REF] Schweinsberg | More than one genotype: How common is intracolonial genetic variability in scleractinian corals?[END_REF].

Evolutionary and ecological implications

Considering the common occurrence of mosaicism in M. platyphylla, this process might have important implications for adaptation as this species heavily relies on clonal reproduction in Moorea. Clonal genets can accumulate allelic mutations that become functionally variable under strong selection pressures and these mutations can be spread in the population via both sexual and asexual reproduction [START_REF] Lashai | The dynamic clonal genome and its adaptive potential[END_REF][START_REF] Pouchkina-Stantcheve | Functional divergence of former alleles in an ancient asexual invertebrate[END_REF]). Such mutation dynamics can result into more versatile phenotypic traits and potentially compensate the reduced genotypic diversity usually associated with clonal reproduction [START_REF] Sniegowski | Beneficial mutations and the dynamics of adaptation in asexual populations[END_REF].

However, further investigations are needed to ensure that M. platyphylla have no clear separation of somatic and germ cells, and that mutations can be spread via the next sexual generation. Even if chimerism is less common is the study population, this process also contribute in creating novel genotypic diversity required for adaptation. It is thus imperative to expand studies of intracolonial genetic variability based on neutral microsatellite markers to include functional genes that underpin coral physiology, which often correlates with adaptive advantages.

Methods

Sampling

Between April and December 2013 field surveys were conducted on the north shore of Moorea,

French Polynesia, at three different locations (Tiahura, Papetoai and Temae) across five reef habitats; two in the fore reef: mid slope (13 m depth) and upper slope (6 m depth), and three in the lagoon (< 1 m depth): back reef, fringing reef and patch reef (Fig. 7.1). From these surveys a total of 3651 colonies of M. platyphylla were collected, whereby 51 colonies were selected in the five habitats to determine whether intracolonial genetic variability is a common phenomenon in fire corals (Table 7.1). All fire coral colonies were subjected to a multiple sampling, where five tissue samples were taken from each colony with four samples taken from the edges of the colony and one additional from the middle. This sampling pattern was previously used to detect genetically heterogeneous individuals in some coral species [START_REF] Schweinsberg | More than one genotype: How common is intracolonial genetic variability in scleractinian corals?[END_REF]. All colonies had a minimum size of 100 cm to ensure sexual maturity and showed no visual evidence of fusion between two or more individuals (i.e. various morphologies and colors within a single colony, and no interaction zone). To determine whether the colony morphology influences the prevalence of intracolonial genetic variability, we classified each colony as one of these three morphologies: 1) massive: solid colonies, roughly hemispherical in shape, 2) encrusting: thin colonies growing against the substratum or 3) sheet tree: encrusting bases with vertical bladelike outgrowths (see [START_REF] Jackson | Morphological strategies of sessile animals[END_REF]). We also estimated mean colony size (cm²) from 2D photographs of each colony 2001). In contrast, a greater number of locus and allelic differences was expected in chimeras, i.e.

when two genetically distinct colonies merged. Based on the stepwise mutation model of microsatellite markers [START_REF] Selkoe | Microsatellites for ecologists: a practical guide to using and evaluating microsatellite markers[END_REF], we estimated the number of repeat units that were added or subtracted during a mutation event. Divergent alleles from the main genotype caused by multiple mutation step and large allele differences are most likely due to chimerism rather than somatic mutations. The size of the mutation step (in repeat units) were identified over all loci for each deviating genotype and averaged per habitat (percentage of mutational-step). Bayesian clustering analyses have been used to identify chimeras based on their cluster assignment probability, i.e. chimeras have to include genotypes that differ from the main genotype and are belonging to a different cluster [START_REF] Maier | Intracolonial genetic variation in the scleractinian coral Seriatopora hystrix[END_REF][START_REF] Schweinsberg | More than one genotype: How common is intracolonial genetic variability in scleractinian corals?[END_REF].

Here, mosaic individuals and chimeras were identified based on a Bayesian clustering analysis using STRUCTURE [START_REF] Pritchard | Inference of population structure using multilocus genotype data[END_REF]. Clustering analyses were performed to ensure nonbiased detection of deviating genotypes following the protocol used in [START_REF] Schweinsberg | More than one genotype: How common is intracolonial genetic variability in scleractinian corals?[END_REF].

Initial STRUCTURE runs were used to determine the most likely number of clusters (K) in each population of M. platyphylla, i.e. within the five reef habitats: mid slope, upper slope, back reef, fringing reef and patch reef. Runs were performed with the default setting, a burn-in period of 50 000, 50 000 MCMC repeats and 10 iterations per K. The results were uploaded to STRUCTURE HARVESTER [START_REF] Earl | STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method[END_REF] and the most likely K was retained for a second run in STRUCTURE with a burn-in period of 500 000, 500 000 MCMC repeats, 10 iterations and uniform prior setting. The results were once more uploaded to STRUCTURE HARVESTER and the resulting merge dataset was analyzed to estimate cluster assignment. Following the framework of [START_REF] Schweinsberg | More than one genotype: How common is intracolonial genetic variability in scleractinian corals?[END_REF], deviating genotypes that differed with more than 60% in their cluster assignment probability compared to the most common colony genotypes were identified as chimeras. All other deviating genotypes were considered as mosaic colonies. [START_REF] Correa | Understanding diversity in coral-algal symbiosis: a cluster-based approach to interpreting fine-scale genetic variation in the genus Symbiodinium[END_REF][START_REF] Littman | Responses of coral-associated bacterial communities to heat stress differ with Symbiodinium type on the same coral host[END_REF]) and thermal tolerance of coral hosts [START_REF] Rowan | Coral bleaching: thermal adaptation in reef coral symbionts[END_REF][START_REF] Berkelmans | The role of zooxanthellae in the thermal tolerance of corals: a 'nugget of hope'for coral reefs in an era of climate change[END_REF][START_REF] Howells | Coral thermal tolerance shaped by local adaptation of photosymbionts[END_REF]. Although not much is known with respect to Symbiodinium composition in hydrocorals, we performed preliminary tests in healthy and partially bleached colonies of M. platyphylla via PCRs amplification of the 28S gene for four clades (A, B, C and D). Clade A and D were present in both healthy and partially bleached colonies, while the clade C was present only in the healthy ones. In scleractinian corals, there is also evidence of temporal changes in the relative abundance of sensitive or more tolerant symbiont that correlate with distinct environmental settings, also referred to as 'shuffling' (reviewed in [START_REF] Baker | Flexibility and specificity in coral-algal symbiosis: diversity, ecology, and biogeography of Symbiodinium[END_REF]. Such variations in response to environmental changes or stress events are often accompanied by physiological changes of the coral host [START_REF] Berkelmans | The role of zooxanthellae in the thermal tolerance of corals: a 'nugget of hope'for coral reefs in an era of climate change[END_REF], a means for adaptive plasticity [START_REF] Kitano | Self-extending symbiosis: a mechanism for increasing robustness through evolution[END_REF]. Furthermore, microbes also provide critical functions within the host, including the passage and fixation of nitrogen and carbon, the production of secondary metabolites and antimicrobial compounds, mucus production and acquisition of nutrients [START_REF] Knowlton | Multispecies microbial mutualisms on coral reefs: the host as a habitat[END_REF][START_REF] Lesser | Are infectious diseases really killing corals? Alternative interpretations of the experimental and ecological data[END_REF][START_REF] Wegley | Metagenomic analysis of the microbial community associated with the coral Porites astreoides[END_REF][START_REF] Raina | Coral-associated bacteria and their role in the biogeochemical cycling of sulfur[END_REF][START_REF] Fiore | Nitrogen fixation and nitrogen transformations in marine symbioses[END_REF]. Considering that microbes confer immunity and support host metabolic demands it is crucial to gather more information into how coral-associated microbial communities are impacted by variation in environmental conditions, which can further benefit our understanding of acclimatization process in coral reefs.

Supporting Information

Recent advancements in DNA sequencing technology have enabled a new understanding of the role of symbiotic microorganisms (i.e. microbiome) in the adaptive response of corals to environmental changes (Pedrόs-Aliό 2006;[START_REF] Bik | Sequencing our way towards understanding global eukaryotic biodiversity[END_REF]. Many studies have demonstrated that changes in the microbiome assembly contribute to phenotypic plasticity [START_REF] Reshef | The coral probiotic hypothesis[END_REF][START_REF] Jones | A community change in the algal endosymbionts of a scleractinian coral following a natural bleaching event: field evidence of acclimatization[END_REF][START_REF] Lajeunesse | Outbreak and persistence of opportunistic symbiotic dinoflagellates during the 2005 Caribbean mass coral 'bleaching' event[END_REF]). As reef-building corals must acclimatize and adapt to rapid and unpredictable environmental changes, such phenotypic plasticity facilitates a more rapid response to environmental change than possible through natural selection and likely a key process for the persistence of many species [START_REF] Charmantier | Adaptive phenotypic plasticity in response to climate change in a wild bird population[END_REF][START_REF] Chevin | Adaptation, plasticity, and extinction in a changing environment: towards a predictive theory[END_REF]. However, plasticity is constrained by host-specific affinities for particular types of Symbiodinium and microbes and by the environmental availability of microorganisms diversity [START_REF] Manning | Diversity in populations of free-living Symbiodinium from a Caribbean and Pacific reef[END_REF][START_REF] Abrego | Onset of algal endosymbiont specificity varies among closely related species of Acropora corals during early ontogeny[END_REF]. Furthermore, symbiotic partners can also influence the adaptive capacity of corals through physiological and genetic adaptation to prevailing conditions [START_REF] Robison | Differential impacts of photoacclimation and thermal stress on the photobiology of four different phylotypes of Symbiodinium (pyrrhophyta)[END_REF][START_REF] Howells | Coral thermal tolerance shaped by local adaptation of photosymbionts[END_REF]. To date, the flexibility of the association between corals and microorganisms has been demonstrated using transplant experiments and/or coral colonies exposed to contrasting environmental conditions [START_REF] Bongaerts | Genetic divergence across habitats in the widespread coral Seriatopora hystrix and its associated Symbiodinium[END_REF][START_REF] Correa | Disaster taxa in microbially mediated metazoans: how endosymbionts and environmental catastrophes influence the adaptive capacity of reef corals[END_REF] A total of 3651 colonies of the fire coral Millepora platyphylla was measured, georeferenced and collected in 5 different habitats in Moorea to evaluate the biological and ecological context of the population maintenance and renewal. This thesis has demonstrated that the population structure of this species varies greatly between lagoonal and fore reef habitats. Using newly developed microsatellite markers, we have shown that M. platyphylla relies heavily on clonal reproduction via fragmentation (80%) and that the fragments are distributed in perfect alignment with wave energy dispersal. Clonal lineages with clones shared among habitats revealed the ability of a single genotype to express different phenotypes depending on its exposure to swell wave energy. Surprisingly, M. platyphylla invests in a vulnerable morphology to wave-induced breakage in high energy reef habitats. Furthermore, parentage analysis revealed a high contribution from self-seeding (58%), limited dispersal of sexual propagules and sibling aggregations. At last, we have demonstrated intracolonial genotypic variability, mostly from somatic mutations (mosaicism), which creates novel genetic diversity within the population. The interaction of these processes generates a high level of genetic and phenotypic variation within the population and allows for local replenishment and the persistence of this fire coral species in Moorea, a marginal habitat. These life history strategies thus increase the adaptive potential and resilience of M. platyphylla in response to rapid and unpredictable environmental changes.

Keywords: Millepora, Reproduction, Phenotypic plasticity, Dispersion, Genetic diversity, Adaptive potential