Pascal Milesi

Aim: Human land‐use has dramatically altered the amount, quality and connectivity of habitat for species worldwide. Understanding how these changes affect individual species is essential for predicting the overall consequences of land‐use change for biodiversity. Location: The Caribbean island of Puerto Rico. Forest cover on the island increased from about 18% to 45% from the late 1940's to the early 2000's. Methods: Using data on modelled geographic distributions and functional traits for 546 tree species, we evaluated how the gain of modelled potential suitable habitat (i.e., climatically‐suitable and forested) was related to species‐specific climatic associations and life‐history strategies. We estimated species‐specific potential suitable habitat (climatically suitable and forested) with species distribution models and data on land cover. We characterized each species' niche breadth (the range of environmental conditions it occupies) and niche position (the environmental conditions it prefers) to compare with the niche characteristics of reforested lands (i.e., those that changed from nonforest to forest land cover). Results: Species with relatively more potential suitable habitat in 1951 also had relatively larger gains in potential suitable habitat from 1951 to 2000. Species that tend to occur in conditions different from those common in reforested areas (i.e., associated with more ‘marginal’ habitats) gained relatively less potential suitable habitat and species with broad environmental niches gained more potential suitable habitat. Niche breadth was weakly associated with changes in connectivity among patches. Main Conclusions: Our results show that Puerto Rico's reforestation preferentially increased potential suitable habitat for species that (1) already had suitable habitat in the landscape and (2) tolerate a wide range of climatic conditions. Our findings illustrate how land‐use change in heterogeneous tropical landscapes can generate non‐uniform habitat gains across species, which may favour generalist over specialist species and potentially alter community composition.

Les mutations sont à l'origine des nombreux "variants" présents dans les populations naturelles. Les variants adaptatifs sont propagés par sélection naturelle. Cependant, une mutation bénéfique sur un trait peut affecter négativement d’autres traits (coût sélectif): un compromis émerge alors entre les avantages et les coûts qu’elle induit. Cette thèse vise à comprendre comment des modifications de l’environnement peuvent affecter les compromis évolutifs de différents types de mutations adaptatives (substitutions, duplications hétérogènes, amplifications). Chez les moustiques, l’utilisation d’insecticides organophosphorés (OPs) et carbamates (CXs) a sélectionné trois réponses adaptatives majeures : une amplification de gènes au locus Ester (codant pour des enzymes détoxicantes), une substitution au locus ace-1 (codant pour la cible des insecticides), et des duplications associant une copie sensible et une copie résistante du locus ace-1. Un premier axe de ma thèse a été de mieux comprendre le rôle de ces duplications hétérogènes (qui associent deux copies divergentes d’un même gène) dans l’adaptation. En caractérisant leurs compromis évolutifs nous avons montré qu'elles confèrent un phénotype proche de celui d’hétérozygotes standards. Toutefois, l’étude de leur distribution mondiale et des analyses en laboratoire ont révélé que ces duplications, avantageuses à l’état hétérozygote, sont majoritairement sublétales à l’état homozygote. Le second axe de cette thèse a été l’étude de l’influence des variations de pression de sélection sur la dynamique des allèles adaptatifs. Une étude d’évolution expérimentale a montré que des pressions de sélection intermédiaires pouvaient générer des situations de superdominance au locus ace-1, favorables à la sélection de duplications hétérogènes. Par ailleurs, l’analyse d’échantillons montpelliérains récoltés sur une trentaine d’années nous a permis de relier quantitativement les variations de la pression de sélection et les variations de la valeur sélective des différents allèles du locus Ester. Enfin, l’étude de trois zones géographiques (Mayotte, Martinique, et Montpellier) a permis de montrer que les différentes adaptations ne répondaient pas de la même façon à une modification environnementale majeure liée au retrait de la pression de sélection (interdiction des OPs et CXs en 2007) : alors que les allèles de résistance du locus ace-1 tendent à disparaitre, ceux du locus Ester se maintiennent en fréquence non négligeable dans les populations naturelles.

Post-glacial recolonization of Fennoscandia created secondary contact zones in many species, offering opportunities to study how gene flow and selection contribute to their establishment and maintenance. Here, we analyse genomic data from three boreal tree species— Picea abies , Betula pendula , and Pinus sylvestris —sampled along a latitudinal gradient in Sweden. Despite differences in colonization timing and dispersal ecology, all three species exhibit north–south genetic structuring aligned with environmental gradients. Most notably, the two main genetic clusters within each species overlap in a shared contact zone, corresponding to the climatic transition between Sweden’s two major environmental zones. The extent and structure of the contact zone differ among species: P. abies shows stronger genetic structure and moderate gene flow, B. pendula exhibits intermediate differentiation and gene flow, and P. sylvestris displays the weakest structure with stronger gene flow. All three species also show genomic signatures of local adaptation, with distinct underlying architectures. In P. abies , adaptive loci are broadly distributed across the genome, while, strikingly, they are mostly found within an inversion on chromosome 1 in B. pendula . In P. sylvestris , local adaptation likely relies on subtle allele frequency shifts across many loci with weak signals. These patterns align with theoretical expectations for polygenic local adaptation under varying migration regimes. Our comparative approach demonstrates how gene flow and selection jointly shape genomic landscapes in shared environments and contributes to understanding local adaptation in forest trees, with implications for predicting species’ responses to climate change.

Gene copy number variations (gCNVs) are structural variations that represent a significant source of genetic polymorphism. While single nucleotide polymorphisms (SNPs) have been the primary focus of population and quantitative genomics, recent studies indicated that gCNVs could also play an important role in adaptation notably because of their multiallelic and quantitative nature. In this study, we investigate the role of gCNVs in local adaptation along environmental gradients using extensive genomic datasets in Norway spruce ( Picea abies ) and Siberian spruce ( P. obovata ). We used a robust pipeline for the detection and quantification of gCNVs from short-read exome capture data and used haploid samples for validation. We showed that gCNVs are pervasive, representing approximately 11% of the protein coding genes and are notably enriched in genes involved in response to environmental stress, such as temperature tolerance, immune response, and metal ion regulation. Population genetic structure at gCNV was similar to that observed at SNPs. However, some gCNVs also display distinctive adaptive signatures not captured by SNPs. Finally, we conducted gCNV-based genotype-environment association (GEA) and genome-wide association studies (GWAS) to further evidence that gCNVs contribute to local adaptation patterns and to the control of quantitative traits.

Understanding how historical versus contemporary processes shape population genetic structure and diversity is important to design effective management actions for threatened species. We genotyped 1834 SNPs in 1120 individuals from 110 Scandinavian populations of the declining orchid Gymnadenia conopsea , in three different habitat types, to examine whether genetic structure was related to wind speed, terrain ruggedness, forest cover, and seasonality at the landscape scale, and whether genetic diversity increases with census population size and is higher in core habitats (fen and meadow) than in marginal, coastal habitats. We identified three genetic clusters and pronounced isolation by distance, consistent with two independent colonization routes after the last glacial maximum, followed by admixture. Effective population size was highest in the admixed cluster. Estimates of effective migration indicated reduced gene flow along the Atlantic coast, between coastal and inland populations, and among southern meadow populations. High landscape resistance to gene flow was associated with complex topography and pronounced seasonality. Genetic diversity increased with population size but did not vary among habitat types. Genetic diversity peaked in core habitats, i.e. southern meadows and inland fens along the Scandes Mountains. The lowest genetic diversity was found along the Atlantic coast and in a few scattered populations. Current genetic structure suggests a strong legacy of historical events, and the high genetic diversity documented in the main Scandinavian range indicates that current viability and future adaptation potential are high. To maintain genetic diversity and connectivity between genetic groups, it is particularly important to preserve southern meadow populations, which are currently in strong decline. Overall, our results illustrate how a declining species can help us understand the impact of historical and current processes, how landscape genetic data can inform proactive conservation, and how a slow genetic response to fragmentation can allow time to maintain genetic diversity through habitat restoration and management.

The effect of past environmental changes on the demography and genetic diversity of natural populations remains a contentious issue and has rarely been investigated across multiple, phylogenetically distant species. Here, we perform comparative population genomic analyses and demographic inferences for seven widely distributed and ecologically contrasting European forest tree species based on concerted sampling of 164 populations across their natural ranges. For all seven species, the effective population size, N_e, increased or remained stable over many glacial cycles and up to 15 million years in the most extreme cases. Surprisingly, the drastic environmental changes associated with the Pleistocene glacial cycles have had little impact on the level of genetic diversity of dominant forest tree species, despite major shifts in their geographic ranges. Based on their trajectories of N_e over time, the seven tree species can be divided into three major groups, highlighting the importance of life history and range size in determining synchronous variation in genetic diversity over time. Altogether, our results indicate that forest trees have been able to retain their evolutionary potential over very long periods of time despite strong environmental changes.

Closely related species often use the same genes to adapt to similar environments. However, we know little about why such genes possess increased adaptive potential and whether this is conserved across deeper evolutionary lineages. Adaptation to climate presents a natural laboratory to test these ideas, as even distantly related species must contend with similar stresses. Here, we re-analyse genomic data from thousands of individuals from 25 plant species as diverged as lodgepole pine and Arabidopsis (~300 Myr). We test for genetic repeatability based on within-species associations between allele frequencies in genes and variation in 21 climate variables. Our results demonstrate significant statistical evidence for genetic repeatability across deep time that is not expected under randomness, identifying a suite of 108 gene families (orthogroups) and gene functions that repeatedly drive local adaptation to climate. This set includes many orthogroups with well-known functions in abiotic stress response. Using gene co-expression networks to quantify pleiotropy, we find that orthogroups with stronger evidence for repeatability exhibit greater network centrality and broader expression across tissues (higher pleiotropy), contrary to the ‘cost of complexity’ theory. These gene families may be important in helping wild and crop species cope with future climate change, representing important candidates for future study.

Most tree species underwent cycles of contraction and expansion during the Quaternary. These cycles led to an ancient and complex genetic structure that has since been affected by extensive gene flow and by strong local adaptation. The extent to which hybridization played a role in this multi‐layered genetic structure is important to be investigated. To study the effect of hybridization on the joint population genetic structure of two dominant species of the Eurasian boreal forest, Picea abies and P. obovata, we used targeted resequencing and obtained around 480 K nuclear SNPs and 87 chloroplast SNPs in 542 individuals sampled across most of their distribution ranges. Despite extensive gene flow and a clear pattern of Isolation‐by‐Distance, distinct genetic clusters emerged, indicating the presence of barriers and corridors to migration. Two cryptic refugia located in the large hybrid zone between the two species played a critical role in shaping their current distributions. The two species repeatedly hybridized during the Pleistocene and the direction of introgression depended on latitude. Our study suggests that hybridization helped both species to overcome main shifts in their distribution ranges during glacial cycles and highlights the importance of considering whole species complex instead of separate entities to retrieve complex demographic histories.

Current global climate change is expected to affect biodiversity negatively at all scales leading to mass biodiversity loss. Many studies have shown that the distribution of allele frequencies across a species' range is often influenced by specific genetic loci associated with local environmental variables. This association reflects local adaptation and allele changes at those loci could thereby contribute to the evolutionary response to climate change. However, predicting how species will adapt to climate change from this type of data alone remains challenging. In the present study, we combined exome capture sequences and environmental niche reconstruction, to test multiple methods for assessing local adaptation and climate resilience in two widely distributed conifers, Norway spruce and Siberian spruce. Both species are keystone species of the boreal forest and share a vast hybrid zone. We show that local adaptation in conifers can be detected through allele frequency variation, population‐level ecological preferences, and historical niche movement. Moreover, we integrated genetic and ecological information into genetic offset predictive models to show that hybridization plays a central role in expanding the niche breadth of the two conifer species and may help both species to cope better with future changing climates. This joint genetic and ecological analysis also identified spruce populations that are at risk under current climate change.