Genomes provide windows into the evolutionary histories of species. The recent accessibility of genome-scale data in non-model organisms and the proliferation of powerful statistical models are now providing unprecedented opportunities to uncover evolutionary relationships and to test hypotheses about the processes that generate and maintain biodiversity. This dissertation work reveals shallow-scale species boundaries and population genetic structure in two imperiled groups of salamanders and demonstrates that the number and information content of genomic regions used in species delimitation exert strong effects on the resulting inferences. Genome scans are employed to test hypotheses about the mechanisms of genetic sex determination in cryptobranchid salamanders, suggesting a conserved system of female heterogamety in this group. At much deeper scales, phylogenetic analyses of hundreds of protein-coding genes across all major amphibian lineages are employed to reveal the backbone topology and evolutionary timescales of the amphibian tree of life, suggesting a new set of hypotheses for relationships among extant amphibians. Yet, genomic data on their own are no panacea for the thorniest questions in evolutionary biology, and this work also demonstrates the power of a model testing framework to dissect support for different phylogenetic and population genetic hypotheses across different regions of the genome.

Une forte structure génétique a été décrite dans la littérature parmi les populations européennes de la coque de lagune Cerastoderma glaucum. Cependant, les limites géographiques entre les grandes divisions génétiques varient d'un marqueur à l'autre et leur faible nombre ne permettait pas de tester réellement les échanges génétiques entre ces groupes. Le but principal de cette thèse était donc d'estimer la structure des populations de C. glaucum à l'aide de marqueurs, en considérant les rôles respectifs de la divergence passée et de la fragmentation de l'habitat. Pour atteindre ses objectifs, des populations des côtes atlantiques et méditerranéennes ont été étudiées en utilisant : i) des marqueurs génétiques classiques (un EPIC et des marqueurs microsatellites déjà publiés); ii) des séquences associées à des sites de restriction (“restriction associated DNA sequences”) ou RADseq. Alors que les marqueurs génétiques classiques ont révélé le caractère divergent des populations de Méditerranée orientale, l'approche RADseq a permis de reconstruire les relations phylogénétiques entre groupes au sein de l'espèce avec une résolution jamais encore ateinte. Trois lignées profondément divergentes ont ainsi été identifiée au sein de C. glaucum: une en Mer Egée – Mer Noire, une en Mer Ionienne et la dernière largement distribuée de la Méditerranée à la Baltique. Cette dernière lignée c'est par ailleurs sous divisée en entités isolées en Méditerranée Occidentale, en Atlantique, en Mer du Nord et an Baltique. Comparée à l'espèce soeur C. edule, qui profite d'un habitat moins fragmenté, C. glaucum présente une beaucoup plus forte différenciation génétique entre populations. Il semble donc que des incompatibilités génétiques, conséquences de l'isolement géographique et de l'adaptation locale, aient pu être à l'origine d'un complexe d'espèces. Ces résultats soulignent par ailleurs le rôle évolutif particulier de l'habitat lagunaire, accélérateur de la diversification génétique. / Previous studies found a high level of genetic structuring among the European populations of the lagoon cockle Cerastoderma glaucum. However, the geographic locations of the major genetic divisions differed among markers and the small number of genetic markers used lacked the power to test for gene flow between divergent clusters. Therefore, the main aim of this thesis was to assess the population structure of C. glaucum using new genetic markers in the light of the respective role of past divergence and habitat fragmentation. To reach these objectives, populations from the Atlantic and Mediterranean coasts have been investigated using: i) classical genetic markers (EPIC together with previously published microsatellites); ii) restriction-site associated DNA sequencing (RADseq). When the classical genetic markers revealed the divergent character of Eastern Mediterranean populations, the RADseq approach allowed inferring phylogenetic relationships with an unprecedented resolution. Three deeply divergent lineages were described within C. glaucum: one in the Aegean-Black Sea region, one in the Ionian Sea, and the last one widely distributed from the Western Mediterranean to the Baltic Sea. This last lineage underwent further diversification with isolated entities detected in Western Mediterranean, Atlantic, North Sea and Baltic Sea. Compared to the sister species C. edule, which thrives in a less fragmented habitat, C. glaucum displayed a much stronger genetic differentiation among populations. Consequently, it seems that genetic incompatibilities, which emerged as a by-product of geographic isolation together with local adaptation, led to the origin of a species complex. These results highlight the evolutionary role of lagoon habitats, where genetic diversification can proceed very quickly.

La domestication est un modèle idéal pour étudier les processus évolutifs car elle implique des événements d'adaptation récents avec une sélection forte. Les champignons sont de bons organismes modèles pour étudier la domestication et plus généralement l’adaptation, grâce à leurs petits génomes et leur facilité de manipulation. Ils sont utilisés depuis longtemps pour la transformation alimentaire, par exemple P. camemberti et P. roqueforti pour la fabrication du fromage, et la levure Saccharomyces pour la fermentation du vin et de la bière. Chez ces champignons, des caractéristiques bénéfiques ont été acquises pour la transformation alimentaire, et les transferts horizontaux de gènes se sont révélés être un moyen essentiel d’adaptation rapide dans l’environnement alimentaire. Ici, j’ai étudié principalement l’adaptation de deux espèces de Penicillium relativement distantes phylogénétiquement - P. nalgiovense et P. salamii, toutes deux utilisées pour la maturation de la viande séchée. J’ai étudié si ces champignons ont été domestiqués, c’est-à-dire si les populations alimentaires se sont adaptées à l’environnement de la viande séchée, et s’il y a eu une différenciation génétique par rapport à d’autres populations; j’ai aussi recherché si des traces génomiques d’adaptation pouvaient être détectées. En analysant des génomes complets, j’ai trouvé peu de diversité génétique et de structure de population chez P. salamii et encore moins chez P. nalgiovense. Des expériences ont montré que les populations de P. salamii et P. nalgiovense provenant de viande séchée présentaient des taux de protéolyse et de lipolyse plus faibles et des couleurs différentes de celles des populations de viande non séchée. De plus, nous avons trouvé des transferts de gènes horizontaux partagés par P. salamii et P. nalgiovense et absents chez d’autres espèces de Penicillium. En résumé, ces résultats indiquent une évolution convergente et une adaptation des populations de P. salamii et P. nalgiovense à la viande séchée. J'ai également étudié les conséquences de la domestication chez le champignon utilisé pour la production de fromages bleus, P. roqueforti, montrant une faible fertilité des souches fromagères par rapport aux souches non fromagères. Les résultats de la thèse soulignent donc l'importance des transferts de gènes horizontaux pour une adaptation rapide chez les champignons et renforcent l'idée que les champignons domestiqués pour la production de nourriture sont de bons modèles pour étudier l'adaptation et l'évolution. / Domestication is an ideal model to study evolutionary processes due to the recent adaptation events and strong selection it implies. Fungi in particular are good model organisms to study domestication and more generally adaptation, with their small genomes and experimental tractability. Fungi have been used for food production, e.g., P. camemberti and P. roqueforti for cheesemaking, and Saccharomyces yeast for wine and beer fermentation. In these fungi, beneficial traits have been acquired for food production, and horizontal gene transfers (HGTs) have been shown to be a major way to rapid adaptation in food environment. Here, I mainly studied the adaptation of food Penicillium fungi using two distantly related Penicillium species - P. nalgiovense and P. salamii, both used for dry-cured meat maturation, to assess whether these fungi have been domesticated, i.e., whether food populations adapted to the dry-cured meat environment, whether were genetically differentiated from other populations, and whether we could find genomic footprints of adaptive events. Using genome sequencing, we found little diversity and population structure in P. salamii and even less in P. nalgiovense. Experiments showed that both P. salamii and P. nalgiovense dry-cured meat populations had lower proteolysis and lipolysis rates and different colors from non-dry-cured meat populations. Furthermore, we found HGTs shared by P. salamii and P. nalgiovense while lacking in other Penicillium species. Altogether, these results indicate convergence evolution and adaptation in P. salamii and P. nalgiovense dry-cured meat populations, as was previously found in cheese Penicillium fungi. I also studied the consequences of domestication in the blue cheese fungus P. roqueforti, showing lower fertility of cheese strains compared to non-cheese strains. The results of the thesis thus point out the importance of HGTs for rapid adaptation in fungi and reinforce the view that fungi are ideal models to study adaptation and evolution.

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<p dir="ltr">In a rapidly changing world, human actions and natural events are reshaping ecosystems and presenting new challenges for conservation efforts. Within this context, unraveling the recent ecosystem transformations and their implications on a fine scale is required. The impacts of such changes are not always sudden but often gradual and sometimes as a result of historical events. With the recent advancement in technologies, the resolution of information by genome sequences spans from millions of years ago (hindcasting) to future generations (forecasting). Aquatic ecosystems pose their own challenges when it comes to ecosystem changes and the types of data required to assess impact and help inform conservation efforts. My dissertation comprises three chapters focused on using genomic techniques to generate data valuable for the conservation and management of aquatic ecosystems. Each of the three chapters is a distinct manuscript in terms of scientific publications, where Chapter 1 has already been published, Chapter 2 has been submitted to a journal, revised, and is now awaiting publication, and Chapter 3 is in preparation for submission to a peer-reviewed journal. In Chapter 1, dietary DNA from harvested North American river otter (<i>Lontra canadensis</i>)<i> </i>was used to determine whether metabarcoding of stomach content could be used to identify fish prey species consumed. In Chapter 2, DNA sequencing of endangered pupfish species in the Tularosa Basin of New Mexico was studied; before my work, it was nominally comprised of a single species, the White Sands pupfish (<i>Cyprinodon tularosa</i>). The results indicate a rapid speciation event occurred within about the last ~5000 years, driven primarily by genetic drift. Chapter 3 extends Chapter 2 by assessing the dynamics of genomic diversity over space and time while evaluating the short-term evolutionary dynamics (~18 generations) of the two native pupfish populations. This temporal study aimed to determine if the extraordinarily rapid evolution over the last ~5000 years (observed in Chapter 2) could be detected over timescales more relevant to conservation and management efforts. Overall, this dissertation used genomic sequence data from metabarcoding of the COI gene region in the otter stomach content as well as pool sequencing and whole genome resequencing of pupfish to provide key biological insights into the conservation of these aquatic species. This dissertation also provides insights into avenues for further study and highlights the significant role that conservation genomics can play in the future. The findings presented in the three chapters are discussed within the context of species’ conservation and management.</p>

Only 40 years ago, just three individuals made the journey from Finland/Russia to found the current wolf population in the southwest of Sweden. This population, that to this date descends from less than 10 founders, has a substantial increased extinction risk due to inbreeding. Several previous studies have used SNPs to monitor the level of inbreeding and homozygosity in the population, as well as measure immigration and the inflow of new genetic material. This study uses both short- and long-read data to discover structural variants (SVs) and small indels in the population, so that they may be used to extend the analyses and provide more insight into the current state of the Scandinavian wolf population. After the calling of the SVs, strict filtering and manual curation were applied to the data, thereby removing many false positive calls and increasing confidence in the remaining SVs. Short-read and long-read SV-callers found 31,800 and 57,821 SVs respectively, with relatively little overlap between the two sets. By far, the most common SV-types were deletions and insertions, at about 30,000 each with varying length ranging from a 50 base pairs to several tens of Mbp. Analyses on the data, such as PCAs and parent-offspring trio analyses, reveal high-confidence calls and consistent results between SV-types and SV-callers, as well as a low estimated genotyping error rate. PCAs performed on the SVs resembled those performed on SNPs, which strengthens the credibility of the identified variants. Finally, this study suggests several alternative steps for possible improvement to the dataset, along with some proposals for subsequent research topics that may use the variants discovered in this study.