Christelle Tougard
email: christelle.tougard@umontpellier.fr

Will the genomics revolution finally solve the Salmo systematics?

Keywords: mitochondrial DNA, molecular phylogeny, next-generation sequencing technologies, nuclear DNA, Salmo trutta

On one hand, studies on Salmo biological variations during the last centuries have led to the morphological description of several Salmo species (>50). On the other hand, Salmo trutta is seen as a polymorphic species, i.e. including populations with different morphotypes and ecotypes, subdivided into nine genetically divergent evolutionary lineages. For 30 years, phylogeographic and phylogenetic investigations tried to solve the Salmo systematic problem using the mitochondrial control region, sometimes combined with other mitochondrial (e.g. protein coding region or rRNA genes) or nuclear (e.g. allozymes or microsatellites) markers.

With the advent of high throughput next-generation sequencing, complete mitogenomes were made available for Salmo phylogenetic studies. Even better, complete genome or chromosomes with annotations as well as genes of interest can now be loaded from public database. However, in the genomic era, some challenges still need to be addressed such as an appropriate taxon sampling or the identification of orthologous genes before having an accurate phylogeny. In the present review, I examine how traditional molecular markers contributed to our knowledge of trout systematics, and what we can expect from the genomics revolution.

Context

Salmonidae are the focus of much scientific attention, in particular the subfamily Salmoninae, with, at least, three species (Onchorhynchus mykiss (Walbaum, 1792), Salmo salar [START_REF] Linnaeus | Systema naturae. Salvius[END_REF]Salmo trutta Linnaeus, 1758) among the ten most studied fishes [START_REF] Hutching | Unintentional selection, unanticipated insights: introductions, stocking and the evolutionary ecology of fishes[END_REF][START_REF] Birnie-Gauvin | Overlooked aspects of the Salmo salar and Salmo trutta lifecycles[END_REF]. Despite this attention, some issues remain, however, unresolved, such as Salmo systematics. Problems started nearly 300 years ago when Linnaeus first classified Salmo trutta under different common and Latin names [START_REF] Linnaeus | Systema naturae. Salvius[END_REF]. Because of complex patterns of phenotypically distinct geographic forms and considerable life-history strategies [START_REF] Bernatchez | DNA sequence variation of the mitochondrial control region among geographically and morphologically remote European brown trout Salmo trutta populations[END_REF][START_REF] Elliott | Wild brown trout Salmo trutta: an important national and international resource[END_REF][START_REF] Kottelat | Hanbook of European freshwater fishes[END_REF][START_REF] Sanz | Phylogeographic history of brown trout: a review[END_REF], studies of Salmo biological variations during the last centuries have led to the morphological description of several Salmo species (or morphospecies; [START_REF] Cronquist | Once again, what is a species?[END_REF], from around 30 [START_REF] Kottelat | Hanbook of European freshwater fishes[END_REF]IUCN, 2022) to more than 50 [START_REF] Behnke | About trout[END_REF][START_REF] Froese | FishBase, The Global Database of Fishes[END_REF] depending on the source. Molecular data have, however, refuted the validity of some species, such as S. dentex (Heckel, 1851) [START_REF] Snoj | Resolving taxonomic uncertainties using molecular systematics: Salmo dentex and the Balkan trout community[END_REF] or S. platycephalus Behnke, 1968[START_REF] Sušnik | Phylogenetic position of Salmo (Platysalmo) platycephalus Behnke 1968 from south-central Turkey, evidenced by genetic data[END_REF], whereas they confirmed the reclassification of others in the genus Salmo, such as S. obtusirostris (Heckel, 1851) (Snoj et al., 2002) and S. ohridanus Steindachner, 1892 [START_REF] Phillips | Phylogenetic analysis of mitochondrial and nuclear sequences supports inclusion of Acantholingua ohridana in the genus Salmo[END_REF][START_REF] Sušnik | Genetic and morphological characterization of a Lake Ohrid endemic, Salmo (Acantholingua) ohridanus with the comparison to sympatric Salmo trutta[END_REF]. Indeed, most of the described (morpho)species have close phylogenetic relationships with S. trutta, and, for this reason, several taxonomic and phylogenetic studies consider S. trutta as a complex of species, except S. salar, S. obtusirostris and S. ohridanus (e.g. [START_REF] Patarnello | Cytochome b and 16S rRNA sequence variation in the Salmo trutta (Salmonidae, Teleostei) species complex[END_REF][START_REF] Lo Brutto | Genetic divergence between morphological forms of brown trout Salmo trutta L. in the Balkan region of Macedonia[END_REF][START_REF] Vera | Phylogeography, genetic structure, and conservation of the endangered Caspian brown trout, Salmo trutta caspius (Kessler, 1877), from Iran[END_REF][START_REF] Meraner | Nothing but a trace left? Autochthony and conservation status of Northern Adriatic Salmo trutta inferred from PCR multiplexing, mtDNA control region sequencing and microsatellite analysis[END_REF][START_REF] Gratton | The evolutionary jigsaw puzzle of the surviving trout (Salmo trutta L. complex) diversity in the Italian region. A multilocus Bayesian approach[END_REF]Tošić et al., 2014;[START_REF] Splendiani | Museum samples could help to reconstruct the original distribution of Salmo trutta complex in Italy[END_REF]. On the other hand, Salmo trutta is also seen as a polymorphic species, i.e. including populations with different morphotypes and ecotypes, subdivided into several genetically divergent evolutionary lineages [START_REF] Bernatchez | DNA sequence variation of the mitochondrial control region among geographically and morphologically remote European brown trout Salmo trutta populations[END_REF][START_REF] Bernatchez | The evolutionary history of brown trout (Salmo trutta L.) inferred from phylogeographic, nested clade, and mismatch analyses of mitochondrial DNA variation[END_REF][START_REF] Suárez | Evolution of the mitochondrial control region in Palaearctic brown trout (Salmo trutta) populations: the biogeographical role of the Iberian Peninsula[END_REF][START_REF] Sušnik | Genetic verification of native brown trout from the Persian Gulf (Catak Cay River, Tigris basin)[END_REF][START_REF] Bardakci | Phylogeography of the Turkish brown trout Salmo trutta L.: mitochondrial DNA PCR-RFLP variation[END_REF][START_REF] Vera | Maintenance of an endemic lineage of brown trout (Salmo trutta) within the Duero river basin[END_REF][START_REF] Snoj | Phylogeographic structure and demographic patterns of brown trout in North-West Africa[END_REF][START_REF] Tougard | Salmo macrostigma (Teleostei, Salmonidae): nothing more than a brown trout (S. trutta) lineage?[END_REF]. To avoid confusion, the term "trout" is here used to refer to both the S. trutta species complex and the evolutionary lineages.

There is no phylogenetic study based on morphological characters and including all Salmo species. Attempts of molecular phylogeny were restricted to a limited number of Salmo species, while relationships between S. trutta evolutionary lineages are not fully resolved (e.g. [START_REF] Bernatchez | The evolutionary history of brown trout (Salmo trutta L.) inferred from phylogeographic, nested clade, and mismatch analyses of mitochondrial DNA variation[END_REF][START_REF] Cortey | Historical biogeography of Mediterranean trout[END_REF][START_REF] Pustovrh | Molecular phylogeny of Salmo of the western Balkans, based upon multiple nuclear loci[END_REF][START_REF] Sanz | Phylogeographic history of brown trout: a review[END_REF][START_REF] Tougard | Salmo macrostigma (Teleostei, Salmonidae): nothing more than a brown trout (S. trutta) lineage?[END_REF][START_REF] Guinand | Brown trout phylogenetics: a persistent mirage towards (too) many species[END_REF][START_REF] Hashemzadeh Segherloo | A genomic perspective on an old question: Salmo trouts or Salmo trutta (Teleostei: Salmonidae)?[END_REF]. In all cases, Salmo is a monophyletic genus with S. salar as the first offshoot of this group [START_REF] Crespi | Molecular systematics of Salmonidae: combined nuclear data yields a robust phylogeny[END_REF][START_REF] Crête-Lafrenière | Framing the Salmonidae family phylogenetic portrait: a more complete picture from increased taxon sampling[END_REF][START_REF] Shedko | Phylogeny of salmonids (Salmoniformes: Salmonidae) and its molecular dating: analysis of mtDNA data[END_REF][START_REF] Horreo | Revisiting the mitogenomic phylogeny of Salmoninae: new insights thanks to recent sequencing advances[END_REF][START_REF] Lecaudey | Inferring phylogenetic structure, hybridization and divergence times within Salmoninae (Teleostei: Salmonidae) using RAD-sequencing[END_REF]. From the molecular dating, this genus originated during the Miocene, between 16 and 10 Myr [START_REF] Crête-Lafrenière | Framing the Salmonidae family phylogenetic portrait: a more complete picture from increased taxon sampling[END_REF][START_REF] Shedko | Phylogeny of salmonids (Salmoniformes: Salmonidae) and its molecular dating: analysis of mtDNA data[END_REF][START_REF] Horreo | Revisiting the mitogenomic phylogeny of Salmoninae: new insights thanks to recent sequencing advances[END_REF][START_REF] Lecaudey | Inferring phylogenetic structure, hybridization and divergence times within Salmoninae (Teleostei: Salmonidae) using RAD-sequencing[END_REF]. In most phylogenetic studies, S. obtusirostris is the sister species of S. ohridanus, except in [START_REF] Pustovrh | Molecular phylogeny of Salmo of the western Balkans, based upon multiple nuclear loci[END_REF] where S. obtusirostris was found to be the sister species of S. trutta and S. marmoratus Cuvier, 1829. The clade including S. obtusirostris, S. ohridanus and trout is dated back to the Pliocene, around 5-4 Myr [START_REF] Crête-Lafrenière | Framing the Salmonidae family phylogenetic portrait: a more complete picture from increased taxon sampling[END_REF][START_REF] Pustovrh | Molecular phylogeny of Salmo of the western Balkans, based upon multiple nuclear loci[END_REF][START_REF] Lecaudey | Inferring phylogenetic structure, hybridization and divergence times within Salmoninae (Teleostei: Salmonidae) using RAD-sequencing[END_REF], while the trout age was estimated between 4 and 0.40 Myr [START_REF] Crête-Lafrenière | Framing the Salmonidae family phylogenetic portrait: a more complete picture from increased taxon sampling[END_REF][START_REF] Pustovrh | Molecular phylogeny of Salmo of the western Balkans, based upon multiple nuclear loci[END_REF][START_REF] Horreo | Revisiting the mitogenomic phylogeny of Salmoninae: new insights thanks to recent sequencing advances[END_REF][START_REF] Lecaudey | Inferring phylogenetic structure, hybridization and divergence times within Salmoninae (Teleostei: Salmonidae) using RAD-sequencing[END_REF]. This is more or less concordant with the fossil record since the oldest fossil remains of Salmo, found in Croatia, dated from the Middle or Upper Miocene (13 -5.33 Myr;[START_REF] Gorjanović-Kramberger | Palaeoichthyoložki prilozi (Collectae palaeoichthyologicae). Rad Jugoslavenske Akademije Znanosti i Umjetnosti[END_REF]Anđelković,1989), and those of S. trutta, found in Caucasus, dated from the Pliocene (~ 2 Myr) [START_REF] Vladimirov | The trout from the diatomite deposits of the Pliocene[END_REF][START_REF] Vladimirov | Armenian brook trout and its relations to other representatives of the genus Salmo[END_REF]. Several hypotheses were proposed in trying to understand the trout evolutionary history during the Pleistocene, and how it was impacted by the Quaternary climatic changes (e.g. [START_REF] Hamilton | Postglacial colonization of brown trout, Salmo trutta L.: Ldh-5 as a phylogeographic marker locus[END_REF][START_REF] García-Marín | Postglacial colonization of brown trout in Europe based on distribution of allozyme variants[END_REF][START_REF] Sanz | Divergence of brown trout (Salmo trutta) within glacial refugia[END_REF][START_REF] Bernatchez | The evolutionary history of brown trout (Salmo trutta L.) inferred from phylogeographic, nested clade, and mismatch analyses of mitochondrial DNA variation[END_REF][START_REF] Antunes | The role of nuclear genes in intraspecific evolutionary inference: genealogy of the transferrin gene in brown trout[END_REF][START_REF] Cortey | Historical biogeography of Mediterranean trout[END_REF][START_REF] Mckeown | Phylogeographic structure of brown trout Salmo trutta in Britain and Ireland: glacial refugia, postglacial colonization and origins of sympatric populations[END_REF][START_REF] Snoj | Phylogeographic structure and demographic patterns of brown trout in North-West Africa[END_REF][START_REF] Splendiani | The effects of paleoclimatic events on Mediterranean trout: preliminary evidences from ancient DNA[END_REF]. However, since phylogenetic relationships between evolutionary lineages are poorly resolved, and no phylogeny includes all Salmo species, this history can only be partial at best. Paradoxically, S. trutta, considered as one of the world's invasive species in countries (at least 24) where it was introduced, is imperiled in much of its native distribution, i.e. in Eurasia and North Africa [START_REF] Budy | Limitation and facilitation of one of the world's most invasive fish: an international comparison[END_REF][START_REF] Elliott | Preface[END_REF]. Among the 36 Salmo species listed in the International Union for Conservation of Nature, 18 are threatened or endangered, and one (S. pallaryi Pellegrin, 1924) considered extinct [START_REF] Crivelli | Salmo pallaryi. The IUCN Red List of Threatened Species[END_REF]IUCN 2022). Trout provides recreation and food to million of people and plays important roles in ecosystem functioning, but it is extremely sensitive to habitat disturbances induced by human activities (e.g. overfishing, pollution, dams, deforestation, agriculture, grazing, and mining) and climate change (Muhlfeld et al., 2018). Native trout diversity is also threatened by the massive stocking of domesticated strains that facilitates the spread of pathogens and parasites. By hydridization of native populations with specimens from hatcheries, stocking erodes genetic diversity or eliminates original local adaptations [START_REF] García-Marín | Proportions of native and introduced brown trout in adjacent fished and unfished Spanish rivers[END_REF][START_REF] Lobón-Cerviá | Princess of the streams: the brown trout Salmo trutta L. as aquatic royalty[END_REF]. Even if the genetic diversity of Salmo populations is relatively well understand, notably at the intra-basin level, concrete conservation strategies should take into account practices that do not erode and/or modify this natural diversity. Efforts to protect native trout morphological, ecological and genetic diversity should rely on appropriate local and/or global conservation and management strategies, and systematics is essential to biodiversity conservation by helping to set conservation priorities [START_REF] Wheeler | Systematics, overview[END_REF]. However, what must be done in the case of a messy systematics as in the trout case? Indeed, systematics discrepancies hamper our understanding of trout evolutionary history, and impede the development of appropriate strategies to protect natural diversity of native trout [START_REF] Bernatchez | DNA sequence variation of the mitochondrial control region among geographically and morphologically remote European brown trout Salmo trutta populations[END_REF][START_REF] Antunes | Complex evolutionary history in the brown trout: Insights on the recognition of conservation units[END_REF][START_REF] Fumagalli | Extreme genetic differentiation among the remnant populations of marble trout (Salmo marmoratus) in Slovenia[END_REF][START_REF] Snoj | Resolving taxonomic uncertainties using molecular systematics: Salmo dentex and the Balkan trout community[END_REF][START_REF] Crête-Lafrenière | Framing the Salmonidae family phylogenetic portrait: a more complete picture from increased taxon sampling[END_REF][START_REF] Gratton | Genetic differentiation and hybridization in two naturally occurring sympatric trout Salmo spp. forms from a small karstic lake[END_REF][START_REF] Ninua | Phylogeography and taxonomic status of trout and salmon from the Ponto-Caspian drainages, with inferences on European brown trout evolution and taxonomy[END_REF][START_REF] Hashemzadeh Segherloo | A genomic perspective on an old question: Salmo trouts or Salmo trutta (Teleostei: Salmonidae)?[END_REF]. Trout systematics thus needs urgently revision/clarification. This systematics was mostly investigated from a genetic standpoint, and the use of genetics in trout systematics has a long history (Fig. 1). In the present review, I examine how traditional molecular markers, and notably mitochondrial DNA (mtDNA), contributed to our knowledge of trout systematics, and what we can expect from the genomics revolution.

PAST: mitochondrial DNA rise

Until the end of the 1980s, genetic discrimination of trout relied mostly on protein electrophoretic (allozyme) analyses (e.g. [START_REF] Ryman | Genetic changes in hatchery stocks of brown trout (Salmo trutta)[END_REF][START_REF] Ferguson | Allozyme evidence for reproductively isolated sympatric populations of brown trout Salmo trutta L. in Lough Melvin, Ireland[END_REF][START_REF] Vuorinen | Electrophoretic identification of Atlantic salmon (Salmo salar), brown trout (S. trutta), and their hybrids[END_REF][START_REF] Guyomard | Mise en évidence d'un flux génétique entre populations naturelles de truite fario et souche de repeuplement dans deux rivières de Corse[END_REF][START_REF] Skaala | Genetic differentiation between freshwater resident and anadromous brown trout, Salmo trutta, within watercourses[END_REF]. First investigations on trout systematics were performed with these markers, and refuted the classification of Greek trout populations into five subspecies [START_REF] Karakoukis | Genetic structure and differentiation among Greek brown trout (Salmo trutta L.) populations[END_REF]. Despite their usefulness in the delineation of genetically distinct salmonid populations, allozymes displayed a limited ability to identify existing genetic diversity by detecting only a part of amino acid substitutions and examining only coding regions of the genome [START_REF] Hynes | Mitochondrial DNA as a genetic marker for brown trout, Salmo trutta L., populations[END_REF]. Genetic diversity was thus studied in a population genetics context (genetic similarities between populations) rather than in a phylogenetic view (relationships among or within species with inference of their evolutionary history).

By the early 1990s, two molecular markers were proposed as new diagnostic markers to genetically differentiate salmonid species and populations: the eye-specific lactate dehydrogenase Ldh-5 nuclear locus [START_REF] Hamilton | Postglacial colonization of brown trout, Salmo trutta L.: Ldh-5 as a phylogeographic marker locus[END_REF], and the mitochondrial DNA [START_REF] Hynes | Mitochondrial DNA as a genetic marker for brown trout, Salmo trutta L., populations[END_REF]. The Ldh-5 locus, now called LDH-C1* locus, is polymorphic for two codominant alleles, Ldh-5 (100) or LDH-C1*100 and Ldh5 (90) or LDH-C1*90. The "100" or "ancestral" allele is present in several species of Salmonidae including southern European trout populations, while the "90" or "modern" allele is fixed for north-western European and hatchery trout populations [START_REF] Hamilton | Postglacial colonization of brown trout, Salmo trutta L.: Ldh-5 as a phylogeographic marker locus[END_REF]. Initially proposed to differentiate "ancestral" from "modern" populations in phylogeographic studies, this marker is today mostly used to differentiate natural populations from domesticated Atlantic strains or to detect and characterize introgression patterns between these populations [START_REF] Berrebi | Brown trout (Salmo trutta L.) high genetic diversity around the Tyrrhenian Sea as revealed by nuclear and mitochondrial markers[END_REF][START_REF] Rossi | Genetic identification of native populations of Mediterranean brown trout Salmo trutta L. complex (Osteichthyes: Salmonidae) in central Italy[END_REF][START_REF] Splendiani | The name of the trout: considerations on the taxonomic status of the Salmo trutta L., 1758 complex (Osteichthyes: Salmonidae) in Italy[END_REF][START_REF] Vera | Identification of an endemic Mediterranean brown trout mtDNA group within a highly perturbed aquatic system, the Llobregat River (NE Spain)[END_REF][START_REF] Kanjuh | Diversity of brown trout, Salmo trutta (Actinopterygii: Salmoniformes: Salmonidae), in the Danube river basin of Croatia revealed by mitochondrial DNA[END_REF]. [START_REF] Oleinik | The Lactate Dehydrogenase gene LDH-C1, a new molecular marker for phylogenetic analysis of salmonid fishes (Salmoniformes: Salmonidae)[END_REF] also tested this locus as phylogenetic marker in a study including 11 salmonid genera. If the genus Salmo was monophyletic, this locus failed to solve phylogenetic relationships between S. obtusirostris, S. ohridanus and S. trutta. Indeed, the most used molecular marker to date in trout phylogeographic and phylogenetic studies (116 out of 137; Table S1) is mtDNA (Fig. 1). Compared to nuclear DNA (nucDNA), mtDNA is a fast evolving and easy-to-isolate genome with a small size, simple constitution, and uniparental inheritance avoiding recombination and allowing matrilineal phylogeny inferences and molecular dating [START_REF] Hynes | Mitochondrial DNA as a genetic marker for brown trout, Salmo trutta L., populations[END_REF][START_REF] Meyer | Evolution of mitochondrial DNA in fishes[END_REF]. Comparison of mtDNA variations can be realised by restriction fragment length polymorphism (RFLP) analyses of mitochondrial fragments and/or by nucleotide sequences of mitochondrial partial or complete genes (e.g. [START_REF] Hansen | Genetic differentiation among Danish brown trout populations, as detected RFLP analysis of PCR amplified mitochondrial DNA segments[END_REF][START_REF] Osinov | Atlantic' and 'Danubian' phylogenetic groupings of brown trout Salmo trutta complex: Genetic divergence, evolution, and conservation[END_REF][START_REF] Machordom | Mitochondrial haplotype variation and phylogeography of Iberian brown trout populations[END_REF][START_REF] Weiss | Mitochondrial haplotype diversity among Portuguese brown trout Salmo trutta L. populations: relevance to the post-Pleistocene recolonization of northern Europe[END_REF][START_REF] Aurelle | Genetic structure of brown trout (Salmo trutta L.) populations from south-western France: data from mitochondrial control region variability[END_REF][START_REF] Bernatchez | The evolutionary history of brown trout (Salmo trutta L.) inferred from phylogeographic, nested clade, and mismatch analyses of mitochondrial DNA variation[END_REF][START_REF] Sell | Mitochondrial DNA differentiation between two forms of trout Salmo letnica, endemic to the Balkan Lake Ohrid, reflects their reproductive isolation[END_REF][START_REF] Bardakci | Phylogeography of the Turkish brown trout Salmo trutta L.: mitochondrial DNA PCR-RFLP variation[END_REF][START_REF] Splendiani | Phylogeographic inferences on the native brown trout mtDNA variation in central Italy[END_REF][START_REF] Apostolidis | Genetic structure and demographic history of brown trout (Salmo trutta) populations from southern Balkans[END_REF][START_REF] Cortey | Northern and Southern expansions of Atlantic brown trout (Salmo trutta) populations during the Pleistocene[END_REF][START_REF] Griffiths | Complete mitochondrial control region sequences indicate a distinct variety of brown trout Salmo trutta in the Aral Sea[END_REF][START_REF] Mckeown | Phylogeographic structure of brown trout Salmo trutta in Britain and Ireland: glacial refugia, postglacial colonization and origins of sympatric populations[END_REF][START_REF] Schenekar | Fine-scale phylogeographic contact zone in Austrian brown trout Salmo trutta reveals multiple waves of post-glacial colonization and a pre-dominance of natural versus anthropogenic admixture[END_REF].

Craze for mitochondrial markers, and especially the control region (CR), is particularly linked to a study focused on the phylogeography of European S. trutta populations [START_REF] Bernatchez | DNA sequence variation of the mitochondrial control region among geographically and morphologically remote European brown trout Salmo trutta populations[END_REF]. Based on two CR fragments (310+330 base pairs, bp), this study was the first assessment of phylogenetic relationships between widely remote European populations (151 individuals from 24 populations). Identified haplotypes were distributed in five major mitochondrial evolutionary lineages: Adriatic (AD), Atlantic (AT), Danubian (DA), marmoratus or Marble (MA) and Mediterranean (ME) (see Fig. 2 for their distribution). These genetic lineages were not congruent with ecological and morphological differentiation [START_REF] Bernatchez | DNA sequence variation of the mitochondrial control region among geographically and morphologically remote European brown trout Salmo trutta populations[END_REF]. These preliminary results were later confirmed by [START_REF] Bernatchez | The evolutionary history of brown trout (Salmo trutta L.) inferred from phylogeographic, nested clade, and mismatch analyses of mitochondrial DNA variation[END_REF] in a study based on 1794 individuals from 174 populations. [START_REF] Bernatchez | The evolutionary history of brown trout (Salmo trutta L.) inferred from phylogeographic, nested clade, and mismatch analyses of mitochondrial DNA variation[END_REF] suggested that both Pleistocene glaciations and biological factors impacted the distribution of these major lineages as well as trout population structure. Since then, others evolutionary lineages, with a more restricted distribution (Fig. 2), were highlighted: the Duero lineage (DU) endemic of the north-western Iberian Peninsula [START_REF] Cortey | Northern and Southern expansions of Atlantic brown trout (Salmo trutta) populations during the Pleistocene[END_REF][START_REF] Vera | Maintenance of an endemic lineage of brown trout (Salmo trutta) within the Duero river basin[END_REF][START_REF] Vera | Phylogenetic diversity within the endemic brown trout Duero lineage: implications for conservation and management[END_REF]; the Tigris lineage (TI) endemic of the Çatak river in Turkey [START_REF] Sušnik | Genetic verification of native brown trout from the Persian Gulf (Catak Cay River, Tigris basin)[END_REF][START_REF] Bardakci | Phylogeography of the Turkish brown trout Salmo trutta L.: mitochondrial DNA PCR-RFLP variation[END_REF]; the Dades lineage endemic of the Drâa basin in Morocco [START_REF] Snoj | Phylogeographic structure and demographic patterns of brown trout in North-West Africa[END_REF]; the North-African lineage (NA) found in Morocco, Algeria, Sicily and maybe in Spain [START_REF] Tougard | Salmo macrostigma (Teleostei, Salmonidae): nothing more than a brown trout (S. trutta) lineage?[END_REF][START_REF] Splendiani | The name of the trout: considerations on the taxonomic status of the Salmo trutta L., 1758 complex (Osteichthyes: Salmonidae) in Italy[END_REF]. Mitochondrial DNA was also a valuable marker to estimate past trout genetic diversity from museum samples [START_REF] Giuffra | Mitochondrial control region and protein coding genes sequence variation among phenotypic forms of brown trout Salmo trutta from northern Italy[END_REF][START_REF] Lahnsteiner | Changes in phenotype and genotype of Austrian Salmo trutta populations during the last century[END_REF][START_REF] Splendiani | Museum samples could help to reconstruct the original distribution of Salmo trutta complex in Italy[END_REF] or even archeological remains [START_REF] Splendiani | The effects of paleoclimatic events on Mediterranean trout: preliminary evidences from ancient DNA[END_REF], notably because nucleic acids degrade over time, and mtDNA is available in much higher copy numbers per cell compared with single-copy nucDNA [START_REF] Höss | Neanderthal population genetics[END_REF][START_REF] Wandeler | Patterns of nuclear DNA degeneration over time -a case study in historic teeth samples[END_REF].

The mitochondrial control region is thus considered as a reference to identify trout lineages or species (Table S2). However, this highly variable marker does not allow, alone, to get resolved trout phylogenetic relationships. Other mitochondrial markers, such as protein coding (cytochrome b, or cytochrome c oxidase, ATPase and NADH dehydrogenase subunits) and/or rRNA (12S and 16S) genes, have been proposed as alternatives (e.g. [START_REF] Giuffra | Mitochondrial control region and protein coding genes sequence variation among phenotypic forms of brown trout Salmo trutta from northern Italy[END_REF][START_REF] Patarnello | Cytochome b and 16S rRNA sequence variation in the Salmo trutta (Salmonidae, Teleostei) species complex[END_REF][START_REF] Machordom | Mitochondrial haplotype variation and phylogeography of Iberian brown trout populations[END_REF][START_REF] Dudu | Molecular analysis of Romanian salmonid species based on 16S rRNA and 12S rRNA sequences[END_REF][START_REF] Lo Brutto | Genetic divergence between morphological forms of brown trout Salmo trutta L. in the Balkan region of Macedonia[END_REF][START_REF] Dudu | Mitochondrial 16S and 12S rRNA sequence analysis in four salmonid species from Romania[END_REF][START_REF] Crête-Lafrenière | Framing the Salmonidae family phylogenetic portrait: a more complete picture from increased taxon sampling[END_REF][START_REF] Shedko | Phylogeny of salmonids (Salmoniformes: Salmonidae) and its molecular dating: analysis of mtDNA data[END_REF][START_REF] Rezaei | Studies on cytochrome c oxidase subunit II gene in Salmo trutta caspius[END_REF][START_REF] Turan | A new species of trout from the northern drainages of Euphrates River, Turkey (Salmoniformes: Salmonidae)[END_REF]. Some phylogenetic studies have involved also nucDNA such as allozymes (e.g. [START_REF] Bernatchez | Genetic diversity of trout (genus Salmo) from its most eastern native range based on mitochondrial DNA and nuclear gene variation[END_REF][START_REF] Riffel | Allozyme variability of brown trout (Salmo trutta L.) populations across the Rhenanian-Danubian watershed in southwest Germany[END_REF][START_REF] Apostolidis | Genetic divergence and phylogenetic relationships among Salmo trutta L. (brown trout) populations from Greece and other European countries[END_REF][START_REF] Antunes | Genetic characterization of Portuguese brown trout (Salmo trutta L.) and comparison with other European populations[END_REF][START_REF] Bouza | Allozymic evidence of parapatric differenciation of brown trout (Salmo trutta L.) within an Atlantic river basin of the Iberian Peninsula[END_REF][START_REF] Cagigas | Phylogeographical lineages in brown trout (Salmo trutta): investigating microgeographical differentiation between native populations from Northern Spain[END_REF], microsatellites (e.g. [START_REF] Sušnik | Reticulate evolution: ancient introgression of the Adriatic brown trout mtDNA in softmouth trout Salmo obtusirostris (Teleostei: Salmonidae)[END_REF][START_REF] Snoj | Phylogeographic structure and demographic patterns of brown trout in North-West Africa[END_REF][START_REF] Kohout | Genetic diversity and phylogenetic origin of brown trout Salmo trutta populations in eastern Balkans[END_REF][START_REF] Gratton | The evolutionary jigsaw puzzle of the surviving trout (Salmo trutta L. complex) diversity in the Italian region. A multilocus Bayesian approach[END_REF][START_REF] Marić | Phylogeography of stream-dwelling trout in the Republic of Macedonia and a molecular genetic basis for revision of the taxonomy proposed by S. Karaman[END_REF] or nuclear genes (e.g. transferin in [START_REF] Antunes | The role of nuclear genes in intraspecific evolutionary inference: genealogy of the transferrin gene in brown trout[END_REF] internal transcribed spacer 1 or ITS1 in [START_REF] Presa | Phylogeographic congruence between mtDNA and rDNA ITS markers in brown trout[END_REF][START_REF] Turan | Two new species of trouts, resident and migratory, sympatric in streams of northern Anatolia (Salmoniformes: Salmonidae)[END_REF][START_REF] Vera | Phylogeography, genetic structure, and conservation of the endangered Caspian brown trout, Salmo trutta caspius (Kessler, 1877), from Iran[END_REF]; C intron of growth hormone 2 or GH2C in [START_REF] Razpet | Genetic variation among trout in the river Neretva basin, Bosnia and Herzegovina[END_REF]somatolactin in Snoj et al., 2010;recombination activating gene 1 or RAG1 in [START_REF] Shedko | Phylogeny of salmonids (Salmoniformes: Salmonidae) and its molecular dating: analysis of nuclear RAG1 gene[END_REF]. For both mitochondrial and nuclear alternatives, few studies were, however, fully freed from the CR reference. Even the genomic study of Hashemzadeh Segherloo et al. ( 2021) based on 15,169 single nucleotide polymorphisms markers (SNPs) includes CR sequences. Recently, Pustovrh et al. (2011a[START_REF] Pustovrh | Molecular phylogeny of Salmo of the western Balkans, based upon multiple nuclear loci[END_REF] and [START_REF] Snoj | Nuclear DNA reveals multiple waves of colonisation, reticulate evolution and a large impact of stocking on trout in north-west Africa[END_REF] performed phylogenetic analyses based exclusively on nuclear loci. These studies contradicted mtDNA observations. Among the 7000 to 8000 bp of the final alignments, few variations are, however, informative sites (70, 196 and 286, respectively), and this low number of information could provide insufficient phylogenetic signal, and thus false phylogenetic inference [START_REF] Philippe | The pitfalls of molecular phylogeny based on four species, as illustrated by the Cetacea/Artiodactyla relationships[END_REF][START_REF] Wiens | Missing data, incomplete taxa, and phylogenetic accuracy[END_REF][START_REF] Phillipe | Phylogenomics of Eukaryotes: impact of missing data on large alignments[END_REF] as suggested, for instance, by the lack of resolution at several nodes of the trees and the trichotomy linking S. obtusirostris, S. marmoratus and S. trutta in Pustovrh et al. (2011a[START_REF] Pustovrh | Molecular phylogeny of Salmo of the western Balkans, based upon multiple nuclear loci[END_REF].

Over the years, molecular diagnostic protocols were designed to allow rapid trout identification, either from SNPs (CR SNPs in Apostolodis et al., 2007;nucDNA SNPs in Pustovrh et al., 2011b;[START_REF] Casanova | Genomic hatchery introgression in brown trout (Salmo trutta L.): development of a diagnostic SNP panel for monitoring the impacted Mediterranean Rivers[END_REF] or pyrosequencing assay [START_REF] Keller | A pyrosequencing assay for the rapid discrimination of mitochondrial lineages in the Salmo trutta complex[END_REF].

Both approaches did not receive, however, the expected success. As illustrated by the numerous references cited above, genetic trout identification is mostly done through mtDNA or nucDNA sequences, and the combination or concatenation of these markers provided better inferences on trout systematics as in the following examples: inclusion of Acantholingua ohridana (cytochrome b, ITS1 and GH2C sequences; [START_REF] Phillips | Phylogenetic analysis of mitochondrial and nuclear sequences supports inclusion of Acantholingua ohridana in the genus Salmo[END_REF] and Salmothymus obtusirostris (CR, cytochrome b and LDH-C1* sequences; [START_REF] Snoj | The taxonomic status of the "sea trout" from the north Adriatic Sea, as revealed by mitochondrial and nuclear DNA analysis[END_REF] in the genus Salmo (S. ohridanus and S. obtusirostris, respectively); reclassification of Salmo (Platysalmo) platycephalus in a lower taxonomic category (CR, cytochrome b and ITS1 sequences; [START_REF] Sušnik | Phylogenetic position of Salmo (Platysalmo) platycephalus Behnke 1968 from south-central Turkey, evidenced by genetic data[END_REF].

With the advent of high throughput next-generation sequencing (NGS), complete mitochondrial genomes (or mitogenomes) were made available for Salmo phylogenetic studies [START_REF] Horreo | Revisiting the mitogenomic phylogeny of Salmoninae: new insights thanks to recent sequencing advances[END_REF]. Compared to S. salar [START_REF] Hurst | The complete mitochondrial DNA sequence of the Atlantic salmon, Salmo salar[END_REF], it is very recently that first S. trutta mitogenomes were published. One (KT634053) was obtained in a more classical way with amplification by PCR and Sanger sequencing of overlapping mtDNA fragments [START_REF] Li | The complete mitochondrial genome of Salmo trutta fario Linnaeus (Salmoniformes, Salmoninae)[END_REF], while the other (KT633607) was obtained through shotgun libraries subjected to Illumina Miseq sequencing [START_REF] Sahoo | The complete mitogenome of brown trout (Salmo trutta fario) and its phylogeny[END_REF]. Since then, mitogenomes were produced for several trouts (S. macrostigma (Duméril, 1858), S. ischchan Kessler, 1877, S. trutta fario Linnaeus, 1858 and S. trutta caspius Kessler, 1877) from modern (Rezaei & Akhshabi, 2017;Rezaei et al., 2017) or museum [START_REF] Levin | High-throughput sequencing of the mitochondrial genomes from archived fish scales: an example of the endangered putative species flock of Sevan trout Salmo ischchan[END_REF][START_REF] Levin | Caucasian treasure: genomics sheds light on the evolution of half-extinct Sevan trout, Salmo ischchan, species flock[END_REF]Nedoluzhko et al., 2018aNedoluzhko et al., , 2018b;;[START_REF] Tougard | Salmo macrostigma (Teleostei, Salmonidae): nothing more than a brown trout (S. trutta) lineage?[END_REF] samples. More than any other technology, NGS has also made thousand of loci and SNPs available through the whole trout genome. For instance, Restriction-site Associated DNA sequencing markers (RADseq) or double digest RADseq (ddRADseq) were recently used to screen for genetic variations in Atlantic and Mediterranean populations [START_REF] Leitwein | Genome-wide nucleotide diversity of hatchery-reared Atlantic and Mediterranean strains of brown trout Salmo trutta compared to wild Mediterranean populations[END_REF][START_REF] Leitwein | A dense brown trout (Salmo trutta) linkage map reveals recent chromosomal rearrangements in the Salmo genus and the impact of selection on linked neutral diversity. G3: Genes, Genomes[END_REF][START_REF] Saint-Pé | Development of a large SNPs resource and a low-density SNP array for brown trout (Salmo trutta) population genetics[END_REF], while RADseq and Genotyping-by-Sequencing methods were recently used to investigate phylogenetic relationships among Salmoninae and some Salmo species, respectively [START_REF] Lecaudey | Inferring phylogenetic structure, hybridization and divergence times within Salmoninae (Teleostei: Salmonidae) using RAD-sequencing[END_REF][START_REF] Hashemzadeh Segherloo | A genomic perspective on an old question: Salmo trouts or Salmo trutta (Teleostei: Salmonidae)?[END_REF].

PRESENT: new hope through next-generation sequencing

Despite 30 years of trout phylogeographic and phylogenetic investigations, no consensus was found between morphological and genetic approaches about trout systematics. In fact, no molecular phylogeny has yet included specimens from all trout (morpho)species and/or covering the whole geographic distribution of S. trutta evolutionary lineages. Some studies underlined, however, relationships between one of the nine trout lineages from CR -sometimes combined with other mtDNA or nucDNA markers -with some trout (morpho)species (e.g. Lo [START_REF] Lo Brutto | Genetic divergence between morphological forms of brown trout Salmo trutta L. in the Balkan region of Macedonia[END_REF][START_REF] Kalayci | Genetic and molecular evidence that the brown trout Salmo trutta belonging to the Danubian lineage are a single biological species[END_REF][START_REF] Tougard | Salmo macrostigma (Teleostei, Salmonidae): nothing more than a brown trout (S. trutta) lineage?[END_REF][START_REF] Hashemzadeh Segherloo | A genomic perspective on an old question: Salmo trouts or Salmo trutta (Teleostei: Salmonidae)?[END_REF]Table S2). Moreover, it should be noted that higher morphological diversity is associated to southern lineages compared to the AT lineage, but this diversity is not congruent with genetic diversity known for each evolutionary lineage. The AT and DA lineages have an extended distribution (Fig. 2) associated to a higher haplotype diversity [START_REF] Sanz | Phylogeographic history of brown trout: a review[END_REF] compared to the AD, Dades, DU, MA, ME, TI and NA lineages. This unequally distributed diversity could be one of the reasons why phylogenetic relationships between lineages remain poorly solved. However, it seems more likely that currently used mtDNA (control region or cytochrome b) and/or nucDNA markers are not sufficiently informative. Informative sites in these markers represent a weak proportion of the genetic variation, compared, for instance, to the whole mitochondrial genome (Fig. 3).

As already mentioned, NGS technologies are promising to study trout phylogeny.

Through these technologies, the whole annotated genome of Salmo trutta was recently made available from the National Center for Biotechnology Information (https://www.ncbi.nlm.nih.gov/genome/31807). Complete genome or chromosomes with annotations as well as genes of interest can now be loaded, and used to identify more appropriate markers (e.g. [START_REF] Sass | Revisiting the Zingiberales: using multiplexed exon capture to resolve ancient and recent phylogenetic splits in a charismatic plant lineage[END_REF][START_REF] Hughes | Comprehensive phylogeny of ray-finned fishes (Actinopterygii) based on transciptomic and genomic data[END_REF][START_REF] Cloutier | Wholegenome analyses resolve the phylogeny of flightless birds (Palaeognathae) in the presence of an empirical anomaly zone[END_REF][START_REF] Hansen | The genome sequence of the brown trout, Salmo trutta Linneaus 1758 (version 1; peer review: 3 approved)[END_REF] to get an accurate trout phylogeny, and to understand morphological character evolution such as colour pattern, a key character in trout description and identification.

FUTURE: challenges to face

Without clear phylogenetic consensus, it is unrealistic to draw conclusions on the trout evolutionary history. It seems that genomics methods can provide qualitatively and quantitatively new types of information that cannot be achieved using traditional methods, and our ability to reconstruct evolutionary histories from (phylo)genomic analyses will thus help us to define conservation units. However, if technical processes of NGS technologies are increasingly better mastered, practical and analytical issues remain challenging such as taxon sampling, identification of orthologous genes, bioinformatics, and data storage.

Sampling choice is a crucial step in phylogenetic studies. First, stocking programs may conceal Salmo natural genetic patterns. In Morocco, for instance, Salmo populations with higher levels of genetic diversity were those affected by stocking programs [START_REF] Perea | Influence of historical and human factors on genetic structure and diversity patterns in peripheral populations: Implications for the conservation of Moroccan trout[END_REF]. Then, it may lead to contradictory evolutionary assumptions as in the studies of (2011). Therefore, in phylogenetic studies, especially those discussing specific status, and for more relevant comparisons, it would be recommended to include, in the molecular dataset, sequences of specimens from the evolutionary lineages, some genetically valid species such as S. obtusirostris and S. ohridanus and/or type specimens (e.g. holotype, syntype, lectotype) to check the taxa validity, and thus to strengthen phylogenetic and/or systematic inferences.

A diversity of NGS technologies exists to produce data suitable for phylogenomic studies (e.g. [START_REF] Díaz-Arce | RADseq derived genome-wide nuclear markers resolve the phylogeny of tunas[END_REF][START_REF] Dong | Genome wide identification, phylogeny, and expression of Aquaporin genes in common carp (Cyprinus carpio)[END_REF][START_REF] Hughes | Comprehensive phylogeny of ray-finned fishes (Actinopterygii) based on transciptomic and genomic data[END_REF][START_REF] Parhi | Diagnosis of mitogenome for robust phylogeny: a case of Cyprinifomes fish group[END_REF]. One main question then arises: will it be possible to easily identify orthologous genes since the common ancestor of all Salmonidae experienced a whole genome duplication no later than 88 Myr, resulting in an autotetraploid genome [START_REF] Moghadam | Whole genome duplication: challenges and considerations associated with sequence orthology assignment in Salmoninae[END_REF][START_REF] Alexandrou | Genome duplication and multiple evolutionary origins of complex migratory behaviour in Salmonidae[END_REF][START_REF] Macqueen | A well-constrained estimate for the timing of the salmonid whole genome duplication reveals major decoupling from species diversification[END_REF] [START_REF] Linnaeus | Systema naturae. Salvius[END_REF]) [START_REF] Samy | SalmoBase: an integrated molecular data resource for salmonid species[END_REF]. Guidelines for de novo or graph-based inference methods for orthologous gene identification were also proposed, and several pipelines are available for automating this procedure (see [START_REF] Kapli | Phylogenetic tree building in the genomic age[END_REF].

Phylogenomic reconstruction methods are of two kinds: methods based on wholegenome features (such as SNPs), and methods based on primary sequences (such as mitogenomes). First methods are, however, sensitive to hidden paralogy, horizontal gene transfert or tree reconstruction artifacts [START_REF] Delsuc | Phylogenomics and the reconstruction of the tree of life[END_REF][START_REF] Delsuc | Phylogenomics and the reconstruction of the tree of life[END_REF]. For these reasons, the second methods, having already a substantial methodological background, are thus currently preferred and recommended [START_REF] Delsuc | Phylogenomics and the reconstruction of the tree of life[END_REF][START_REF] Delsuc | Phylogenomics and the reconstruction of the tree of life[END_REF][START_REF] Kapli | Phylogenetic tree building in the genomic age[END_REF]. These latter phylogenomic methods have, however, also their own sets of problems related to phylogenomic dataset construction and inference. Although NGS technologies have greatly improved sequence quality, they also led to the amplification of data errors that are manually intractable because of the amount of data generated (Philippe et al., 2017). Despite the development of numerous custom scripts, no consensus has yet been found regarding the quality controls that should be included in phylogenomic dataset construction (Philippe et al., 2017). A special care should be then brought to the data assembly to avoid frameshift errors (sequencing or annotation errors) for protein-coding genes, and/or contaminant sequences (commensals/symbionts, parasites, gut contents in animals, environmental sources or experimental errors) (Philippe et al., 2017;[START_REF] Kapli | Phylogenetic tree building in the genomic age[END_REF]. Contaminants can be identified and excluded based on the GC content of sequences, read coverage and taxonomy of sequence similarity matches [START_REF] Kapli | Phylogenetic tree building in the genomic age[END_REF]. Data alignment is also a challenging task since alignment errors would hamper phylogenetic inferences. It is thus crucial to identify the homologous nucleotides or amino-acid residues at every position of the sequences (Philippe et al., 2017;[START_REF] Kapli | Phylogenetic tree building in the genomic age[END_REF]. Alignment methods can be classified into several categories, and for each category, a panel of softwares is available (for a review, see Philippe et al., 2017;[START_REF] Kapli | Phylogenetic tree building in the genomic age[END_REF]. Lastly, the choice of phylogenetic reconstruction methods constitutes one of the most essential criteria to avoid phylogenomic result inconsistency. Character-based methods, and in particular the probabilistic maximum likelihood and Bayesian methods, are based on an explicitly evolutionary model of sequences [START_REF] Delsuc | Phylogenomics and the reconstruction of the tree of life[END_REF][START_REF] Kapli | Phylogenetic tree building in the genomic age[END_REF]. The use of the most complex models will thus reduce the probability of inconsistency, except when sequences evolve heterogeneously and are not identically distributed [START_REF] Kolaczkowski | Performance of maximum parsimony and likelihood phylogenetics when evolution is heterogeneous[END_REF][START_REF] Delsuc | Phylogenomics and the reconstruction of the tree of life[END_REF]. Research on more realistic models of sequence evolution is a work-in-process [START_REF] Delsuc | Phylogenomics and the reconstruction of the tree of life[END_REF]Philippe et al., 2017). Detailed guidelines and a phylogenomic pipeline recently proposed by [START_REF] Kapli | Phylogenetic tree building in the genomic age[END_REF] could easily be applied to trout phylogenomic studies.

Last but not least, the raw data generated, considered part of the "Big Data science", and all steps from data assembly to phylogenetic inference need huge storage requirements [START_REF] Giribet | New animal phylogeny: future challenges for animal phylogeny in the age of phylogenomics[END_REF]. Although some public databases allow to store raw data, assemblies or data matrices, satisfactory repositories are still lacking [START_REF] Giribet | New animal phylogeny: future challenges for animal phylogeny in the age of phylogenomics[END_REF]. Moreover, these amounts of generated genomic data and the complexity in evolutionary models come at a high computational cost [START_REF] Giribet | New animal phylogeny: future challenges for animal phylogeny in the age of phylogenomics[END_REF]. For instance, most heuristic searches with probabilistic methods will be nearly impossible with more than 200 species [START_REF] Delsuc | Phylogenomics and the reconstruction of the tree of life[END_REF]. Faster and more efficient algorithms are thus required to overcome the current and upcoming size of phylogenomic datasets [START_REF] Giribet | New animal phylogeny: future challenges for animal phylogeny in the age of phylogenomics[END_REF].

Nevertheless, genomics, thanks to a much larger number of loci available, has increased our ability to evaluate the degree of genetic isolation of populations and to detect introgression in many species. For this reason, genomic data can play an important role in species delimitation under many species concepts [START_REF] Rannala | Species Delimitation[END_REF]. In order to propose clear and objective definition of species, powerful methods, such as coalescentbased species delimitation [START_REF] Fujita | Coalescentbased species delimitation in an integrative taxonomy[END_REF], were developed. Because species can show low genetic divergence but high divergence in other traits, the whole process of lineage diversification cannot be explained by these methods alone [START_REF] Fujita | Coalescentbased species delimitation in an integrative taxonomy[END_REF][START_REF] Cicero | Integrative taxonomy and geographic sampling underlie successful species delimitation[END_REF]. Some authors advocate that studies aimed at delimiting species are best framed in a more integrative context, by taking into account, notably, morphological and ecological characters as well as life-history traits of taxa across their distribution and habitats [START_REF] Fujita | Coalescentbased species delimitation in an integrative taxonomy[END_REF][START_REF] Cicero | Integrative taxonomy and geographic sampling underlie successful species delimitation[END_REF]. Indeed, when the taxa in question are of conservation concern, it is important to use multiple lines of evidence into taxonomic decision, even if this evidence can now, in theory, be provided by genomic data (for some examples, see [START_REF] Stanton | More grist for the mill? Species delimitation in the genomic era and its implications for conservation[END_REF]. Trout systematics will thus benefit from a more integrative view of the taxonomy.

Implications and prospective directions

In conservation biology, taxa identification (taxonomy) and the understanding of their evolutionary relationships (systematics) is fundamental to design efficient biodiversity conservation priorities and management strategies [START_REF] Allendorf | Units of conservation[END_REF]. In taxonomy and systematics, the central and fundamental unit is the species. Therefore, conservation strategies have long been focused on species. In order to protect trout biodiversity, some authors suggested thus to maintain species names for some trout populations despite discrepancies between morphology and genetics. For instance, S. letnica (Karaman, 1924) populations of the Lake Ohrid in the Balkans represent a monophyletic group inside the AD lineage, whereas differences in morphology, intralacustrine distribution, ecology and the season of spawning were observed between populations [START_REF] Sell | Mitochondrial DNA differentiation between two forms of trout Salmo letnica, endemic to the Balkan Lake Ohrid, reflects their reproductive isolation[END_REF]Sušnik et al., 2007). In order to preserve the Lake Ohrid biodiversity, [START_REF] Sušnik | Reticulate evolution: ancient introgression of the Adriatic brown trout mtDNA in softmouth trout Salmo obtusirostris (Teleostei: Salmonidae)[END_REF] recommended, however, to keep the taxonomic epithet S. letnica for the endemic Ohrid trout.

At a larger geographic scale, S. marmoratus, characterized by a marbled-colour pattern, is supposed to inhabit northern and southern parts of the Adriatic Sea drainage, and it is often associated to the mitochondrial MA lineage [START_REF] Sanz | Phylogeographic history of brown trout: a review[END_REF]. However, the marble-colour pattern was also found in some trouts from Norway [START_REF] Skaala | Biochemical genetic variability and taxonomy of a marmorated salmonid in River Otra, Norway[END_REF], while MA haplotypes were identified in Central Italy as well as in French, Turkish or Greek populations (Fig. 2). These cases are just some examples among some others underlying the urgent need to revise the trout systematics in an integrative view. In this purpose, it will be crucial to consider all types of diversity (morphology, ecology, genetics, life-history traits, and so on), but also to choose appropriate morphological and genetic/genomic proxies, and taxon sampling (including type specimens) to describe a part of these diversities.

On the one hand, because species is a fundamental unit in conservation and, on the other hand, because less attention has been focused on the definition and delimitation of conservation units from intraspecific diversity, numerous known subspecies are elevated to the species rank for conservation purposes [START_REF] Isaac | Taxonomic inflation: its influence on macroecology and conservation[END_REF][START_REF] Berrebi | Genetic diversity and conservation of the Prespa trout in the Balkans[END_REF][START_REF] Zachos | Species inflation and taxonomic artefacts-A critical comment on recent trends in mammalian classification[END_REF]. Subspecies seem, however, also relevant in biodiversity conservation, with many taxa listed under the International Union for the Conservation of Nature Red List criteria [START_REF] Gippoliti | The problem of subspecies and biased taxonomy in conservation lists: the case of mammals[END_REF][START_REF] Braby | The subspecies concept in butterflies: has its application in taxonomy and conservation biology outlived its usefulness?[END_REF]IUCN, 2022), and recognized as a taxonomic unit by the International Code of Nomenclature (Article 5.2; https://www.iczn.org/the-code/the-code-online/; [START_REF] Braby | The subspecies concept in butterflies: has its application in taxonomy and conservation biology outlived its usefulness?[END_REF]. The utility of subspecies in taxonomy and conservation biology has been debated for decades, notably, because subspecies are not defined conceptually with objective criteria allowing their delimitation [START_REF] Braby | The subspecies concept in butterflies: has its application in taxonomy and conservation biology outlived its usefulness?[END_REF]. Moreover, discrepancies exist, at the subspecies level, between molecular and phenotypic characters [START_REF] Phillimore | Are subspecies useful in evolutionary and conservation biology?[END_REF][START_REF] Cicero | Integrative taxonomy and geographic sampling underlie successful species delimitation[END_REF]. Other intraspecific conservation units -e.g., the evolutionary significant units (ESU; [START_REF] Ryder | Species conservation and systematics: the dilemma of subspecies[END_REF][START_REF] Waples | Pacific salmon, Onchorhynchus spp., and the definition of "species" under endangered species act[END_REF][START_REF] Dizon | Rethinking the stock concept: a phylogeographic approach[END_REF][START_REF] Moritz | Defining 'Evolutionarily Significant Units' for conservation[END_REF][START_REF] Crandall | Considering evolutionary processes in conservation biology[END_REF], the operational conservation units (OCU; [START_REF] Doadrio | Allozymic variation of the endangered killifish Aphanius iberus and its application to conservation[END_REF] or the management units (MU; [START_REF] Taylor | First policy the science: why management unit based solely on genetic criteria cannot work[END_REF] -have been proposed. Several definitions exist to define an ESU, but the most popular one is that proposed by [START_REF] Moritz | Defining 'Evolutionarily Significant Units' for conservation[END_REF]: an ESU can be defined as populations that are monophyletic for mtDNA and showing significant divergence in nucDNA allele

frequencies. An OCU is rather a continuous area limited by geographic boundaries, and inhabited by one or more populations sharing the same genetic pattern [START_REF] Doadrio | Allozymic variation of the endangered killifish Aphanius iberus and its application to conservation[END_REF], while a MU is for populations of conspecific individuals among which the degree of connectivity is sufficiently low so that each population should be monitored and managed separately [START_REF] Palsbøll | Identification of management units using population genetic data[END_REF]. Some of these units were, in fact, already suggested to manage and conserve natural diversity of Iberian trout populations [START_REF] Machordom | Mitochondrial haplotype variation and phylogeography of Iberian brown trout populations[END_REF][START_REF] Almodóvar | Introgression variability among Iberian brown trout Evolutionary Significant Units: the influence of local management and environmental features[END_REF]. Even if the definition of most of these conservation units relies on genetic/genomic data, other types of information (e.g. life history traits, habitat type, phenotype, gene flow pattern, genomic clusters) are proposed to define conservation units [START_REF] Allendorf | Units of conservation[END_REF][START_REF] Hashemzadeh Segherloo | A genomic perspective on an old question: Salmo trouts or Salmo trutta (Teleostei: Salmonidae)?[END_REF]. In the near future, genomic approaches could be really appropriate to estimate the level of vulnerability of Salmo native populations as well as the extant of threats acting on them.

I cannot agree more with [START_REF] Kottelat | Hanbook of European freshwater fishes[END_REF] when they say that, despite the innumerable studies on trout, this interest has resulted in very little data usable in the taxonomic framework, unfortunately still today. To cite [START_REF] Kottelat | Hanbook of European freshwater fishes[END_REF], it is thus more than time that the "hordes" of geneticists and taxonomists studying trout start working together to better preserve natural diversity of trout in its native distribution. This will be probably allowed in a near future thanks to the combination of NGS technologies, a more integrative approach of the trout systematics and the appropriate definition of conservation units.

AD

  [START_REF] Doadrio | Two new species of Atlantic trout (Actinopterygii, Salmonidae) from Morocco[END_REF] and[START_REF] Tougard | Salmo macrostigma (Teleostei, Salmonidae): nothing more than a brown trout (S. trutta) lineage?[END_REF] focused on Moroccan populations. In[START_REF] Doadrio | Two new species of Atlantic trout (Actinopterygii, Salmonidae) from Morocco[END_REF], specimens only from Moroccan populations were taken into account, and no type specimen was included in the molecular dataset, while[START_REF] Tougard | Salmo macrostigma (Teleostei, Salmonidae): nothing more than a brown trout (S. trutta) lineage?[END_REF] included in their molecular dataset sequences from[START_REF] Doadrio | Two new species of Atlantic trout (Actinopterygii, Salmonidae) from Morocco[END_REF] and specimens belonging to the nine evolutionary lineages, valid species (S. orhidanus and S. obtusirostris), as well as one syntype of S. macrostigma. Conclusions of both studies were not congruent:[START_REF] Doadrio | Two new species of Atlantic trout (Actinopterygii, Salmonidae) from Morocco[END_REF] considered populations of the Lake Isli and the Drâa basin as distinct species (S.viridis[START_REF] Doadrio | Two new species of Atlantic trout (Actinopterygii, Salmonidae) from Morocco[END_REF] S. multipunctata Doadrio et al., 2015, respectively); Tougard et al. (2018) identified a new evolutionary lineage (NA) including specimens from Algeria (notably S. macrostigma syntype), Sicily and all Moroccan populations, except the Drâa basin population that was already considered a different lineage (Dades) by Snoj et al.

Acknowledgements

The present review is a follow-up to a presentation done as invited speaker at the "Associazione Italiana Ittilogi Acque Dolci" thematic congress that took place in Cagliari (Sardinia, Italy) in September 2019. For this reason, I would like to thanks the organizers, Andrea Sabatini and Francesco Palmas (Università degli Studi di Cagliari, Sardinia, Italy) for their kind invitation and their warm welcome. I am also grateful to Bruno Guinand (Institut des Sciences de l'Evolution de Montpellier, France) who encouraged me to write this review.

Thanks are also expressed to Andrea Splendiani and Vicenzo Caputo Barucchi (Università Politecnica delle Marche, Ancona, Italy), Aleš Snoj (University of Ljubljana, Slovenia) and Jose-Luis García-Marín (Universitat de Girona, Spain) who provided some trout tissue samples. I also warmly thank Andrea Splendiani and two anonymous reviewers for their helpful comments on the manuscript.

Funding

The French Government (CNRS) supported this study. The funder had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Data availability

Mitogenome sequences that support the findings of this study are openly available in GenBank at https://www.ncbi.nlm.nih.gov/genbank/ under the accession numbers MW632104 to MW632113.

Ethics declarations

Conflict of interest

There is no conflict of interest concerning the manuscript.

Ethical approval

New DNA sequences were obtained from DNA stored at -20 °C or fin clips stored in ethanol 96% and collected in the frame of previous studies. Therefore, no specific permissions were required for locations and activities involved in this study.

Figure legend

Fig. 1 Number of publications dealing with trout systematics found in public reference databases (Web of Sciences, Google Scholar, PubMed) in December 2021 using the words "Salmo" and "phylogeny", "systematics" or "diversity". A reference was considered when, at least, two Salmo species or S. trutta evolutionary lineages were included in the studied dataset, and phylogenetic relationships were represented by a tree or a network. The list of references considered is in Table S1. MtDNA, mitochondrial DNA; nucDNA, nuclear DNA; NGS, next-generation sequencing technologies. S1. (B), the concatenation of these two mitochondrial regions (C) and the complete mitogenome (D) using PhyML v3 [START_REF] Guindon | New algorithms and methods to estimate maximum-likelihood phylogenies: Assessing the performance of PhyML 3.0[END_REF]. Informative sites (IS) are indicated in brackets. Numbers at nodes are for bootstrap percentages (BP≥50%). Black circles indicate nodes with BP = 100%. White circles are for node with BP < 50%. Acquisition of new molecular data was done according to [START_REF] Tougard | Salmo macrostigma (Teleostei, Salmonidae): nothing more than a brown trout (S. trutta) lineage?[END_REF]. Sample list and information related to phylogenetic analyses are in Table S3. AD, Adriatic; AT, Atlantic. DA, Danubian; DU, Duero; MA, marble; ME, Mediterranean; NA, North African.

Supplementary information

Table S1 Detailed list of references taken into account for Figures 1 and2.

Table S2 Relationships between evolutionary lineages and morphospecies based on genetic studies.

Table S3 Details on models of sequence evolution and sampling (accession number, locality and reference) used for phylogenetic reconstruction with PhyML v3 [START_REF] Guindon | New algorithms and methods to estimate maximum-likelihood phylogenies: Assessing the performance of PhyML 3.0[END_REF].

Years Nb of publications