Sex-chromosome differentiation parallels postglacial range expansion in European tree frogs (Hyla arborea).

Occasional XY recombination is a proposed explanation for the sex-chromosome homomorphy in European tree frogs. Numerous laboratory crosses, however, failed to detect any event of male recombination, and a detailed survey of NW-European Hyla arborea populations identified male-specific alleles at sex-linked loci, pointing to the absence of XY recombination in their recent history. Here, we address this paradox in a phylogeographic framework by genotyping sex-linked microsatellite markers in populations and sibships from the entire species range. Contrasting with postglacial populations of NW Europe, which display complete absence of XY recombination and strong sex-chromosome differentiation, refugial populations of the southern Balkans and Adriatic coast show limited XY recombination and large overlaps in allele frequencies. Geographically and historically intermediate populations of the Pannonian Basin show intermediate patterns of XY differentiation. Even in populations where X and Y occasionally recombine, the genetic diversity of Y haplotypes is reduced below the levels expected from the fourfold drop in copy numbers. This study is the first in which X and Y haplotypes could be phased over the distribution range in a species with homomorphic sex chromosomes; it shows that XY-recombination patterns may differ strikingly between conspecific populations, and that recombination arrest may evolve rapidly (<5000 generations).

Anthropogenic disturbance as a driver of microspatial and microhabitat segregation of cytotypes of Centaurea stoebe and cytotype interactions in secondary contact zones.

BACKGROUND AND AIMS: In a mixed-ploidy population, strong frequency-dependent mating will lead to the elimination of the less common cytotype, unless prezygotic barriers enhance assortative mating. However, such barriers favouring cytotype coexistence have only rarely been explored. Here, an assessment is made of the mechanisms involved in formation of mixed-ploidy populations and coexistence of diploid plants and their closely related allotetraploid derivates from the Centaurea stoebe complex (Asteraceae). METHODS: An investigation was made of microspatial and microhabitat distribution, life-history and fitness traits, flowering phenology, genetic relatedness of cytotypes and intercytotype gene flow (cpDNA and microsatellites) in six mixed-ploidy populations in Central Europe. KEY RESULTS: Diploids and tetraploids were genetically differentiated, thus corroborating the secondary origin of contact zones. The cytotypes were spatially segregated at all sites studied, with tetraploids colonizing preferentially drier and open microhabitats created by human-induced disturbances. Conversely, they were rare in more natural microsites and microsites with denser vegetation despite their superior persistence ability (polycarpic life cycle). The seed set of tetraploid plants was strongly influenced by their frequency in mixed-ploidy populations. Triploid hybrids originated from bidirectional hybridizations were extremely rare and almost completely sterile, indicating a strong postzygotic barrier between cytotypes. CONCLUSIONS: The findings suggest that tetraploids are later immigrants into already established diploid populations and that anthropogenic activities creating open niches favouring propagule introductions were the major factor shaping the non-random distribution and habitat segregation of cytotypes at fine spatial scale. Establishment and spread of tetraploids was further facilitated by their superior persistence through the perennial life cycle. The results highlight the importance of non-adaptive spatio-temporal processes in explaining microhabitat and microspatial segregation of cytotypes.

An horizon scan of biogeography

The opportunity to reflect broadly on the accomplishments, prospects, and reach of a field may present itself relatively infrequently. Each biennial meeting of the International Biogeography Society showcases ideas solicited and developed largely during the preceding year, by individuals or teams from across the breadth of the discipline. Here, we highlight challenges, developments, and opportunities in biogeography that were summarized at or emerge from that biennial synthesis. We note the realized and potential impact of rapid data accumulation in several fields, a Renaissance for inter-disciplinary research, the importance of recognizing the evolution-ecology continuum across spatial and temporal scales and at different taxonomic, phylogenetic and functional levels, and re-exploration of classical assumptions and hypotheses using new tools. However, advances are taxonomically and geographically biased, key theoretical frameworks await development of tools for handling, or strategies for simplifying, the biological complexity seen in empirical systems. Current threats to biodiversity require unprecedented integration of knowledge and development of predictive capacity which may enable biogeography to unite its descriptive and hypothetico-deductive arms and establish a greater role within and outside academia

Chromosomal versus mitochondrial DNA evolution: tracking the evolutionary history of the southwestern european populations of the Sorex araneus group (Mammalia Insectivora)

The shrews of the Sorer araneus group have undergone a spectacular chromosome evolution. The karyotype of Sorer granarius is generally considered ancestral to those of Sorer coronatus and S. araneus. However, a sequence of 777 base pairs of the cytochrome b gene of the mitochondrial DNA (mtDNA) produces a quite different picture: S. granarius is closely related to the populations of S. araneus from the Pyrenees and from the northwestern Alps, whereas S. coronatus and S. araneus from Italy and the southern Alps represent two well-separated lineages. It is suggested that mtDNA and chromosomal evolution are in this case largely independant processes. Whereas mtDNA haplotypes are closely linked to the geographical history of the populations, chromosomal mutations were probably transmitted from one population to another. Available data suggest that the impressive chromosome polymorphism of this group is quite a recent phenomenon.

Contrasting diffusion of Quaternary gene pools across Europe: the case of the arctic-alpine Gentiana nivalis L. (Gentianaceae).

The fate of European arctic-alpine species during Pleistocene climatic oscillations still remains debated. Did these cold-adapted species invade much of the continental steppe or did they remain restricted to warmer slopes of inner mountain massifs? To examine this question, we investigated the phylogeography of Gentiana nivalis, a typical European arctic-alpine plant species. Genome fingerprinting analyses revealed that four genetic pools are actually unevenly distributed across the continent. One cluster covers almost all mountain massifs as well as northern areas, and thus coincides with a scenario of past distribution covering a large part of the European glacial steppe. In contrast, the three other lineages are strongly restricted spatially to western, central, and eastern Alps, respectively, thus arguing towards a scenario of in situ glacial survival. The coexistence of lineages with such contrasting demographic histories in Europe challenges our classical view of refugia and corroborates several hypotheses of biogeographers from the twentieth century.

Predicting present and future intra-specific genetic structure through niche hindcasting across 24 millennia.

Paleoclimatic reconstructions coupled with species distribution models and identification of extant spatial genetic structure have the potential to provide insights into the demographic events that shape the distribution of intra-specific genetic variation across time. Using the globeflower Trollius europaeus as a case-study, we combined (1) Amplified Fragment Length Polymorphisms, (2) suites of 1000-years stepwise hindcasted species distributions and (3) a model of diffusion through time over the last 24,000 years, to trace the spatial dynamics that most likely fits the species' current genetic structure. We show that the globeflower comprises four gene pools in Europe which, from the dry period preceding the Last Glacial Maximum, dispersed while tracking the conditions fitting its climatic niche. Among these four gene pools, two are predicted to experience drastic range retraction in the near future. Our interdisciplinary approach, applicable to virtually any taxon, is an advance in inferring how climate change impacts species' genetic structures.

Dugesia sicula (Platyhelminthes, Tricladida): the colonizing success of an asexual Planarian

Background Dugesia sicula is the only species of its genus not presenting an endemic or restricted distribution within the Mediterranean area. It mostly comprises fissiparous populations (asexual reproduction by body division and regeneration), most likely sexually sterile, and characterized by an extremely low genetic diversity interpreted as the consequence of a recent anthropic expansion. However, its fissiparous reproduction can result in an apparent lack of diversity within the species, since genetic variation within individuals can be as large as between them because most individuals within a population are clones. We have estimated haplotype and nucleotide diversity of cytochrome oxidase I within and among individuals along the species distribution of a broad sample of D. sicula, including asexual and the two only sexual populations known today; and predicted its potential distribution based on climatic variables. Our aim was to determine the centre of colonisation origin, whether the populations are recent, and whether the species is expanding. Results The species presents 3 most frequent haplotypes, differing in a maximum of 11 base pairs. As expected from their fissiparous mode of reproduction, in half of all the analysed localities many individuals have multiple heteroplasmic haplotypes. The distribution of haplotypes is not geographically structured; however, the distribution of haplotypes and heteroplasmic populations shows higher diversity in the central Mediterranean region. The potential distribution predicted by climatic variables based modelling shows a preference for coastal areas and fits well with the observed data. Conclusions The distribution and frequency of the most frequent haplotypes and the presence of heteroplasmic individuals allow us to gain an understanding of the recent history of the species, together with previous knowledge on its phylogenetic relationships and age: The species most probably originated in Africa and dispersed through the central Mediterranean. After one or multiple populations became triploid and fissiparous, the species colonized the Mediterranean basin, likely both by its own means and helped by human activities. Its present distribution practically fulfils its potential distribution as modelled with climatic variables. Its prevalence in coastal regions with higher water temperatures predicts a likely future expansion to northern and more interior areas following the increase in temperatures due to climate change.

Evolutionary and dispersal history of Eurasian house mice Mus musculus clarified by more extensive geographic sampling of mitochondrial DNA.

We examined the sequence variation of mitochondrial DNA control region and cytochrome b gene of the house mouse (Mus musculus sensu lato) drawn from ca. 200 localities, with 286 new samples drawn primarily from previously unsampled portions of their Eurasian distribution and with the objective of further clarifying evolutionary episodes of this species before and after the onset of human-mediated long-distance dispersals. Phylogenetic analysis of the expanded data detected five equally distinct clades, with geographic ranges of northern Eurasia (musculus, MUS), India and Southeast Asia (castaneus, CAS), Nepal (unspecified, NEP), western Europe (domesticus, DOM) and Yemen (gentilulus). Our results confirm previous suggestions of Southwestern Asia as the likely place of origin of M. musculus and the region of Iran, Afghanistan, Pakistan, and northern India, specifically as the ancestral homeland of CAS. The divergence of the subspecies lineages and of internal sublineage differentiation within CAS were estimated to be 0.37-0.47 and 0.14-0.23 million years ago (mya), respectively, assuming a split of M. musculus and Mus spretus at 1.7 mya. Of the four CAS sublineages detected, only one extends to eastern parts of India, Southeast Asia, Indonesia, Philippines, South China, Northeast China, Primorye, Sakhalin and Japan, implying a dramatic range expansion of CAS out of its homeland during an evolutionary short time, perhaps associated with the spread of agricultural practices. Multiple and non-coincident eastward dispersal events of MUS sublineages to distant geographic areas, such as northern China, Russia and Korea, are inferred, with the possibility of several different routes.

The odd couple: contrasting phylogeographic patterns in two sympatric sibling species of woodlouse-­‐hunter spiders in the Canary Islands

Comparative phylogeography seeks for commonalities in the spatial demographic history of sympatric organisms to characterize the mechanisms that shaped such patterns. The unveiling of incongruent phylogeographic patterns in co-occurring species, on the other hand, may hint to overlooked differences in their life histories or microhabitat preferences. The woodlouse-hunter spiders of the genus Dysdera have undergone a major diversi cation on the Canary Islands. The species pair Dysdera alegranzaensis and Dysdera nesiotes are endemic to the island of Lanzarote and nearby islets, where they co-occur at most of their known localities. The two species stand in sharp contrast to other sympatric endemic Dysdera in showing no evidence of somatic (non-genitalic) differentiation. Phylogenetic and population genetic analyses of mitochondrial cox1 sequences from an exhaustive sample of D. alegranzaensis and D. nesiotes specimens, and additional mitochondrial (16S, L1, nad1) and nuclear genes (28S, H3) were analysed to reveal their phylogeographic patterns and clarify their phylogenetic relationships. Relaxed molecular clock models using ve calibration points were further used to estimate divergence times between species and populations. Striking differences in phylogeography and population structure between the two species were observed. Dysdera nesiotes displayed a metapopulation-like structure, while D. alegranzaensis was characterized by a weaker geographical structure but greater genetic divergences among its main haplotype lineages, suggesting more complex population dynamics. Our study con rms that co-distributed sibling species may exhibit contrasting phylogeographic patterns in the absence of somatic differentiation. Further ecological studies, however, will be necessary to clarify whether the contrasting phylogeographies may hint at an overlooked niche partitioning between the two species. In addition, further comparisons with available phylogeographic data of other eastern Canarian Dysdera endemics con rm the key role of lava ows in structuring local populations in oceanic islands and identify localities that acted as refugia during volcanic eruptions

The Imprint of Geologic History on Within‐Island Diversification of Woodlouse-­Hunter Spiders (Araneae, Dysderidae) in the Canary Islands.

Geological processes and ecological adaptation are major drivers of diversification on oceanic islands. Although diversification in these islands is often interpreted as resulting from dispersal or island hopping rather than vicariance, this may not be the case in islands with complex geological histories. The island of Tenerife, in the Canary Islands, emerged in the late Miocene as 3 precursor islands that were subsequently connected and reisolated by volcanic cycles. The spider Dysdera verneaui is endemic to the island of Tenerife, where it is widely distributed throughout most island habitats, providing an excellent model to investigate the role of physical barriers and ecological adaptation in shaping within-island diversity. Here, we present evidence that the phylogeographic patterns of this species trace back to the independent emergence of the protoislands. Molecular markers (mitochondrial genes cox1, 16S, and nad1 and the nuclear genes ITS-2 and 28S) analyzed from 100 specimens (including a thorough sampling of D. verneaui populations and additional outgroups) identify 2 distinct evolutionary lineages that correspond to 2 precursor islands, each with diagnostic genital characters indicative of separate species status. Episodic introgression events between these 2 main evolutionary lineages explain the observed incongruence between mitochondrial and nuclear markers, probably as a result of the homogenization of their ITS-2 sequence types. The most widespread lineage exhibits a complex population structure, which is compatible with either secondary contact, following connection of deeply divergent lineages, or alternatively, a back colonization from 1 precursor island to another.

The Imprint of Geologic History on Within‐Island Diversification of Woodlouse-­Hunter Spiders (Araneae, Dysderidae) in the Canary Islands.

Geological processes and ecological adaptation are major drivers of diversification on oceanic islands. Although diversification in these islands is often interpreted as resulting from dispersal or island hopping rather than vicariance, this may not be the case in islands with complex geological histories. The island of Tenerife, in the Canary Islands, emerged in the late Miocene as 3 precursor islands that were subsequently connected and reisolated by volcanic cycles. The spider Dysdera verneaui is endemic to the island of Tenerife, where it is widely distributed throughout most island habitats, providing an excellent model to investigate the role of physical barriers and ecological adaptation in shaping within-island diversity. Here, we present evidence that the phylogeographic patterns of this species trace back to the independent emergence of the protoislands. Molecular markers (mitochondrial genes cox1, 16S, and nad1 and the nuclear genes ITS-2 and 28S) analyzed from 100 specimens (including a thorough sampling of D. verneaui populations and additional outgroups) identify 2 distinct evolutionary lineages that correspond to 2 precursor islands, each with diagnostic genital characters indicative of separate species status. Episodic introgression events between these 2 main evolutionary lineages explain the observed incongruence between mitochondrial and nuclear markers, probably as a result of the homogenization of their ITS-2 sequence types. The most widespread lineage exhibits a complex population structure, which is compatible with either secondary contact, following connection of deeply divergent lineages, or alternatively, a back colonization from 1 precursor island to another.

The Imprint of Geologic History on Within‐Island Diversification of Woodlouse-­Hunter Spiders (Araneae, Dysderidae) in the Canary Islands.

Geological processes and ecological adaptation are major drivers of diversification on oceanic islands. Although diversification in these islands is often interpreted as resulting from dispersal or island hopping rather than vicariance, this may not be the case in islands with complex geological histories. The island of Tenerife, in the Canary Islands, emerged in the late Miocene as 3 precursor islands that were subsequently connected and reisolated by volcanic cycles. The spider Dysdera verneaui is endemic to the island of Tenerife, where it is widely distributed throughout most island habitats, providing an excellent model to investigate the role of physical barriers and ecological adaptation in shaping within-island diversity. Here, we present evidence that the phylogeographic patterns of this species trace back to the independent emergence of the protoislands. Molecular markers (mitochondrial genes cox1, 16S, and nad1 and the nuclear genes ITS-2 and 28S) analyzed from 100 specimens (including a thorough sampling of D. verneaui populations and additional outgroups) identify 2 distinct evolutionary lineages that correspond to 2 precursor islands, each with diagnostic genital characters indicative of separate species status. Episodic introgression events between these 2 main evolutionary lineages explain the observed incongruence between mitochondrial and nuclear markers, probably as a result of the homogenization of their ITS-2 sequence types. The most widespread lineage exhibits a complex population structure, which is compatible with either secondary contact, following connection of deeply divergent lineages, or alternatively, a back colonization from 1 precursor island to another.

Phylogéographie des principales vipères européennes (Vipera ammodytes, V. aspis et V. berus), structuration génétique et multipaternité chez Vipera berus

Résumé: Les vipères du genre Vipera sont des serpents venimeux distribués dans la totalité du Paléarctique. Malgré cette répartition considérable, elles sont extrêmement menacées, leur déclin étant principalement dû à la destruction et à la fragmentation de leur habitat ainsi qu'à la persécution humaine. Afin d'apporter de nouveaux éléments dans le contexte de la protection de ce groupe de reptiles, nous avons utilisé durant ce travail de thèse différents marqueurs moléculaires pour étudier la structuration génétique à petite et à large échelle chez trois espèces appartenant au genre Vipera. La première étude, une phylogéographie moléculaire de la vipère ammodytes (Vipera ammodytes), a montré dans l'ensemble de l'aire de répartition une forte structuration génétique provenant d'isolements antérieures au Pléistocène. La présence d'un nombre important de clades dans le centre des Balkans suggère que cette région a fourni de nombreux refuges isolés durant les glaciations. Ces dernières ont également eu un impact considérable sur la diversité génétique au sein de la majorité des clades, suite à d'importants goulots d'étranglement durant le Pléistocène. L'étude de la phylogéographie de la vipère aspic (Vipera aspis) a montré une différenciation génétique entre les populations présentes de chaque côté des Alpes, mais également une forte structuration interne avec la mise en évidence d'un refuge en France. Cette étude est la première à établir clairement l'utilisation d'un refuge français pour un vertébré terrestre. La troisième partie de cette thèse a étudié la phylogéographie de la vipère péliade (Vipera berus), espèce cible de ce travail. En plus de la mise en évidence d'un groupe génétique inattendu (localisé dans le nord de l'Italie, le sud de l'Autriche, le nord de la Slovénie et l'extrême sud-est de la Suisse), la variabilité génétique au sein du groupe nordique (comprenant les animaux de l'entier de l'aire de répartition de l'espèce à l'exception des individus du groupe italien et les animaux provenant des Balkans) est suffisamment importante pour conclure à l'utilisation de refuges glaciaires nordiques durant les dernières glaciations, en complément des refuges habituellement décrits pour la majorité des espèces animales (soit les péninsules ibérique, italienne et balakanique). Ces résultats nous ont conduit à effectuer une étude morphologique (quatrième partie) comparant les vipères péliades du "clade italien" et du "clade nordique" décrits ci-dessus. Seules de petites différences morphologiques ont pu être mises en évidence, malgré une séparation de ces groupes estimée à plus d'un million d'années. Une étude à plus petite échelle, centrée sur le Massif jurassien et certaines populations alpines et françaises, a été entreprise afin d'estimer leur diversité génétique et d'évaluer la structuration génétique entre les populations à l'aide de marqueurs microsatellites (cinquième partie). Une importante structuration a été observée entre les populations distantes de plus de 3 kilomètres, la structuration entre les populations plus proches étant plus limitée. De plus, une diversité génétique plus faible dans les populations jurassiennes et alpines comparativement aux populations du massif central et de la côte atlantique a été constatée, probablement due à une perte de diversité génétique lors de la recolonisation post-glaciaire. La sixième étude s'est intéressée au succès reproducteur des mâles de vipères péliades en conditions naturelles. Une corrélation entre la taille des mâles et leur succès reproducteur a été relevée, les individus de plus grande taille ayant un succès reproducteur plus élevé. Le taux de multipaternité a aussi été investigué, démontrant que la proportion de pontes issues de plusieurs pères est élevée (69%) malgré la faible densité de vipères observée sur le site étudié. Finalement, aucun lien entre le nombre de pères au sein d'une ponte et la mortalité des jeunes à la naissance n'a pu être mis en évidence, contrastant avec des travaux précédents. En conclusion, l'observation de la structuration très marquée chez les vipères péliades devrait permettre d'affiner les méthodes de protection de l'espèce dans le massif jurassien. A plus large échelle, l'importante structuration génétique observée chez les vipères ammodytes, aspic et péliade résultant de l'utilisation de nombreux refuges glaciaires, complémentaires aux refuges habituellement utilisés par les espèces animales, démontre l'intérêt de l'analyse phylogéographique des reptiles pour la compréhension des phénomènes de colonisation et d' extinction des populations durant la fin du Tertiaire et le Quaternaire. La mise en évidence chez les différentes espèces de vipères étudiées de nombreux groupes génétiques distincts (ESUs) devrait conduire à des modifications de la taxonomie ainsi qu'au statut de protection de ces espèces. Abstract: The vipers of the genus Vipera are venomous snakes widespread throughout the Palaearctic regions. Despite a large distribution area, several species are extremely threatened, especially due to the destruction and fragmentation of their habitats, as well as by human persecution. In order to increase the knowledge on these species and to improve their protection, several molecular markers have been used to investigate the genetic structure on small and large scales, within three species of the genus Vipera. The first study, a molecular phylogeography of the nose-horned viper (Vipera ammodytes), showed a considerable structuring throughout the distribution area, due to isolation into refugia before the Pleistocene. A high number of clades in the centre of the Balkans suggests that this region harboured numerous isolated glacial refugia during the last glaciation. Moreover, low genetic diversity within several clades implies that most populations of nose-horned vipers have suffered bottlenecks during the Pleistocene. The study of the phylogeography of the asp viper (Vipera aspis) showed genetic differentiation between populations on each side of the Alps, as well as considerable internal genetic structure, suggesting the use of a glacial refugium in France. This study is the first to establish firmly the occurrence of a French refugia for a terrestrial vertebrate. The third part of this work involved a phylogeographic study of the adder (Vipera berus), the target species of this thesis. Three clades were revealed: a Balkan clade (corresponding to the subspecies V. b. sachalinensis), an unexpected Italian clade (limited to northern Italy, southern Austria, northern Slovenia and southeasternmost corner of Switzerland) and a Northern clade clade (including adders of the whole distribution area excepted animals from the Balkan and the Italian clades). The genetic variability within the Northern clade is sufficiently high to conclude that a northern glacial refugia during the last glaciation, in addition to those refugia already described for the main species (Iberian, Italian and Balkan peninsula). These results motivated a morphological study (part four) comparing the adders from the Italian and the Northern clades describe above. Only small morphological differences have been found, despite the split between these two clades have taken place more than 1 million years ago. A study on a local scale, focused on the Jura Mountains, on a few populations in the Alps and France was, performed to estimate the genetic diversity and the genetic structure between populations using microsatellite markers (part five). Considerable structure was observed between populations separated by more than 3 kilometres, whereas the structure between closer populations is less marked. Moreover, lower genetic diversity in the populations from Jura Mountains and Alps was noticed compared to populations from Massif Central of Atlantic coast. Such loss of genetic variation probably followed post-glacial recolonisation. The sixth study focused on the reproductive success of male adders in the wild. A positive correlation between body length and reproductive success was observed. Multiple paternity was also observed in most of clutches (69%) despite the low density of adders in the study area. Finally, no relationship was found between the number of fathers in a clutch and the survival of offspring at birth, contradicting previous studies. To conclude, the observation of a significant genetic structure in Vipera berus will enable recommendations to be made to improve protection of this species in the Jura Mountain. On a larger scale, the considerable genetic structure found within Vipera ammdoytes, V. aspis and V. berus, resulting from isolation in additional glacial refugia to those already described for other species, demonstrates the relevance of phylogeographic studies of reptiles to better understand the colonisation and disappearance during the last Tertiary and the Quaternary. The observation of several groups of evolutionary significant units (ESUs) within the three studied species might lead to a revision of the taxonomy, as well as their conservation status.

Sex-chromosome evolution of Palearctic tree frogs in space and time

Sexual reproduction is nearly universal in eukaryotes and genetic determination of sex prevails among animals. The astonishing diversity of sex-determining systems and sex chromosomes is yet bewildering. Some taxonomic groups possess conserved and dimorphic sex chromosomes, involving a functional copy (e.g. mammals' X, birds' Z) and a degenerated copy (mammals' Y, birds' W), implying that sex- chromosomes are expected to decay. In contrast, others like amphibians, reptiles and fishes yet maintained undifferentiated sex chromosomes. Why such different evolutionary trajectories? In this thesis, we empirically test and characterize the main hypotheses proposed to prevent the genetic decay of sex chromosomes, namely occasional X-Y recombination and frequent sex-chromosome transitions, using the Palearctic radiation of Hyla tree frogs as a model system. We take a phylogeographic and phylogenetic approach to relate sex-chromosome recombination, differentiation, and transitions in a spatial and temporal framework. By reconstructing the recent evolutionary history of the widespread European tree frog H. arborea, we showed that sex chromosomes can recombine in males, preventing their differentiation, a situation that potentially evolves rapidly. At the scale of the entire radiation, X-Y recombination combines with frequent transitions to prevent sex-chromosome degeneration in Hyla: we traced several turnovers of sex-determining system within the last 10My. These rapid changes seem less random than usually assumed: we gathered evidences that one chromosome pair is a sex expert, carrying genes with key role in animal sex determination, and which probably specialized through frequent reuse as a sex chromosome in Hyla and other amphibians. Finally, we took advantage of secondary contact zones between closely-related Hyla lineages to evaluate the consequences of sex chromosome homomorphy on the genetics of speciation. In comparison with other systems, the evolution of sex chromosomes in Hyla emphasized the existence of consistent evolutionary patterns within the chaotic diversity of flexibility of cold-blooded vertebrates' sex-determining systems, and provides insights into the evolution of recombination. Beyond sex-chromosome evolution, this work also significantly contributed to speciation, phylogeography and applied conservation research. -- La reproduction sexuée est quasi-universelle chez les eucaryotes et le sexe est le plus souvent déterminé génétiquement au sein du règne animal. L'incroyable diversité des systèmes de reproduction et des chromosomes sexuels est particulièrement étonnante. Certains groupes taxonomiques possèdent des chromosomes sexuels dimorphiques et très conservés, avec une copie entièrement fonctionnelle (ex : le X des mammifères, le Z des oiseaux) et une copie dégénérée (ex : le Y des mammifères, le W des oiseaux), suggérant que les chromosomes sexuels sont voués à se détériorer. Cependant les chromosomes sexuels d'autres groupes tels que les amphibiens, les reptiles et les poissons sont pour la plupart indifférenciés. Comment expliquer des trajectoires évolutives si différentes? Au cours de cette thèse, nous avons étudié empiriquement les processus évolutifs pouvant maintenir les chromosomes sexuels intacts, à savoir la recombinaison X-Y occasionnel ainsi que les substitutions fréquentes de chromosomes sexuels, en utilisant les rainettes Paléarctiques du genre Hyla comme modèle d'étude. Nous avons adopté une approche phylogéographique et phylogénétique pour appréhender les événements de recombinaison, de différenciation et de transitions de chromosomes sexuels dans un contexte spatio-temporel. En retraçant l'histoire évolutive récente de la rainette verte H. arborea, nous avons mis en évidence que les chromosomes sexuels pouvaient recombiner chez les mâles, empêchant ainsi leur différenciation, et que ce processus avait le potentiel d'évoluer très rapidement. A l'échelle plus globale de la radiation, il apparait que les phénomènes de recombinaison X-Y soient également accompagnés de substitutions de chromosomes sexuels, et participent de concert au maintien de chromosomes sexuels intacts dans les populations: le système de détermination du sexe des rainettes a changé plusieurs fois au cours des 10 derniers millions d'années. Ces transitions fréquentes ne semblent pas aléatoires: nous avons identifié une paire de chromosomes qui présente des caractéristiques présageant d'une spécialisation dans le déterminisme du sexe (notamment car elle possède des gènes importants pour cette fonction), et qui a été réutilisée plusieurs fois comme tel chez les rainettes ainsi que d'autres amphibiens. Enfin, nous avons étudié l'hybridation entre différentes espèces dans leurs zones de contact, afin d'évaluer si l'absence de différenciation entre X et Y jouaient un rôle dans les processus génétiques de spéciation. Outre son intérêt pour la compréhension de l'évolution des chromosomes sexuels, ce travail contribue de manière significative à d'autres domaines de recherche tels que la spéciation, la phylogéographie, ainsi que la biologie de la conservation.

Genetic consequences of population expansions and contractions in the common hippopotamus (Hippopotamus amphibius) since the Late Pleistocene.

Over the past two decades, an increasing amount of phylogeographic work has substantially improved our understanding of African biogeography, in particular the role played by Pleistocene pluvial-drought cycles on terrestrial vertebrates. However, still little is known on the evolutionary history of semi-aquatic animals, which faced tremendous challenges imposed by unpredictable availability of water resources. In this study, we investigate the Late Pleistocene history of the common hippopotamus (Hippopotamus amphibius), using mitochondrial and nuclear DNA sequence variation and range-wide sampling. We documented a global demographic and spatial expansion approximately 0.1-0.3 Myr ago, most likely associated with an episode of massive drainage overflow. These events presumably enabled a historical continent-wide gene flow among hippopotamus populations, and hence, no clear continental-scale genetic structuring remains. Nevertheless, present-day hippopotamus populations are genetically disconnected, probably as a result of the mid-Holocene aridification and contemporary anthropogenic pressures. This unique pattern contrasts with the biogeographic paradigms established for savannah-adapted ungulate mammals and should be further investigated in other water-associated taxa. Our study has important consequences for the conservation of the hippo, an emblematic but threatened species that requires specific protection to curtail its long-term decline.