Understanding the demography of species over recent history (e.g., < 100 years) is critical in studies of ecology and evolution, but records of population history are rarely available. Large single nucleotide polymorphism datasets generated with restriction-site associated DNA sequencing (RADseq), in combination with demographic inference methods, are improving our ability to gain insights into the population history of both model and non-model species. However, to assess the performance of genetic methods it is important to compare their estimates of population history to known demography, in both simulation and empirical settings. Here, I used a simulation approach to examine the potential for RADseq datasets to accurately estimate effective population size (Ne) in Wright-Fisher populations over the course of stable and declining population trends, and distinguish stable from steadily declining populations over a contemporary time scale (20 generations). Overall, my results reveal that demographic inference using genome-wide data can be successfully applied to estimate Ne, and the detection of population-size declines. Next, I assess these methods in an empirical study from a wetland with 37 years of amphibian mark-recapture data to study the utility of genetically-based demographic inference on salamander species with documented population declines (Ambystoma talpoideum) and expansions (A. opacum). For both species, demographic model inference supported population size changes that corroborated mark-recapture data. To further validate these findings, I used individual-based population models of the pond-breeding salamander, Ambystoma opacum, with life-history parameters estimated from a long-term dataset, over a 50 year projection. My results demonstrate that genetically estimated Ne is positively correlated with census size in isolated and subdivided A. opacum populations. Finally, I investigated metapopulation patterns of genomic diversity in A. opacum and A. talpoideum and how migration may impact Ne estimation. I found strong patterns of subpopulation structuring, signatures of migration between subpopulations, and differences in Ne at the subpopulation level in both species. Overall, my findings suggest the ability of genomic data to reconstruct recent demographic changes, which can have important applications to conservation biology, and ultimately can help us elucidate the effects of environmental disturbances in the demography of endangered or declining species.

Ce projet vise à comprendre comment la structure génétique intra-spécifique d'espèces végétales tropicales emblématiques et de l’espèce humaine a été affectée par les variations spatio-temporelles de l’environnement actuel et passé. Nous avons développé une approche d’inférence génétique basée sur la théorie de la coalescence pour évaluer l’influence potentielle des changements climatiques passés sur l’évolution de la distribution géographique et de la diversité génétique neutre et/ou adaptative d’Amborella trichopoda Baill. en Nouvelle-Calédonie (espèce-sœur des angiospermes, données NGS et microsatellites), de Coffea canephora Pierre ex A. Froehn en Afrique tropicale (caféier Robusta, données NGS) et de populations européenne et africaine (Luhya, Kenya) d’humains anatomiquement modernes (données NGS issues du Projet 1000 Génomes). Nos travaux suggèrent que les fluctuations climatiques du Pleistocène tardif ont joué un rôle majeur sur l’évolution de la diversité génétique des espèces étudiées de milieux tropicaux et tempérés, avec une empreinte remarquable du Dernier Maximum Glaciaire (DMG, 21 000 ans avant le présent). Les contractions démographiques associées à la glaciation planétaire ont vraisemblablement conduit à la divergence entre les lignées génétiques d’Amborella et participé à l’accumulation des différences génétiques entre les lignées de C. canephora. Nos résultats suggèrent que les événements de glaciation planétaire ont probablement entraîné une différenciation génétique idiosyncratique dans les forêts tropicales humides mais l’intensité de cette réponse semble avoir varié entre espèces. Nous avons également identifié de nombreux événements passés de sélection dans les génomes de la population humaine européenne qui ont été vraisemblablement provoquées par les conditions environnementales au cours du DMG. Les adaptations phénotypiques associées ont probablement assuré le maintien de l’expansion démographique en dépit des pressions de sélection nouvelles auxquelles les populations étaient confrontées au cours du dernier âge glaciaire en Europe. / This project aims at understanding how the structure of the intra-specific genetic diversity in emblematic tropical plant species and in the human species was shaped by the spatiotemporal variation of current and past environments. We developed a genetic inference approach based on the coalescent theory to assess the potential impact of past climatic change onto the evolution of the geographic range and of the neutral and/or adaptive genetic diversity in Amborella trichopoda Baill. in New Caledonia (sister-species of all extant angiosperms, NGS and microsatellite datasets), in Coffea canephora Pierre ex A. Froehn in tropical Africa (Robusta coffee, NGS dataset) and in North-Western European and African (Luhya, Kenya) human populations (NGS dataset 1000 Genomes Project). We found that the climatic fluctuations of the Late Pleistocene influenced the evolution of genetic diversity in these species distributed in temperate and tropical environments. The environmental conditions during the Last Glacial Maximum (LGM, 21.000 years before present) appear as an important factor. The demographic contraction associated with the last global glaciation influenced the divergence between Amborella genetic lineages and contributed to the accumulation of genetic differences between C. canephora lineages. Our results suggest that global glaciation events likely drove idiosyncratic genetic differentiation in tropical rain forests but the intensity of this response varied between species. We also identified multiple events of selection in the genomes of the European human population which were likely triggered by the environmental conditions during the LGM. The associated phenotypic adaptations probably allowed the paleo-populations to maintain their demographic expansion despite the new kinds of selective pressure they faced during the last glacial age in Europe.