ABSTRACT 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.

Post-glacial recolonisation 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 colonisation 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 contribute to understanding local adaptation in forest trees, with implications for predicting species' responses to climate change.

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.

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. ### Competing Interest Statement The authors have declared no competing interest. Nilsson-Ehle Endowments, 43255 Swedish Phytogeographic Society Formas, 2016-00780, 2024-02415

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.

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.

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 (similar to 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.

Autopolyploidy, the result of genome duplication within a single species, is widespread among plant lineages and believed to have played a major role in angiosperm evolution and diversification. Whole genome duplication often triggers significant morphological and ecological changes in autopolyploids vis-a-vis their diploid progenitors, which are induced by subtle changes in gene expression patterns, often of a stochastic nature. Recent results have nonetheless identified specific changes in meiotic, metabolic, and defense response pathways that seem to be commonly shared among autopolyploid species, hinting at convergent evolution. Notably, a set of 12 core meiotic genes, including several genes involved in meiotic crossover formation, has been found to undergo strong selective pressure in the aftermath of autopolyploidization. For the most part these findings have been based on the study of Arabidopsis arenosa and A. lyrata autotetraploids and the question has remained as to whether the evolutionary forces shaping the establishment and evolution of autopolyploidy in the Arabidopsis model system extend more broadly across angiosperms, an area where our knowledge is still limited. In order to address these questions, we conducted a comparative transcriptome analysis of Betula pubescens , a highly introgressed autotetraploid, and its diploid sister species, B. pendula , two birch species belonging to the Fagales order that diverged from Brassicales 120-140 Mya. Our results reveal significant changes in the expression patterns of B. pubescens in genes involved in secondary metabolic processes and the regulation of stress response to pathogens, in agreement with results obtained in other autopolyploid plant complexes. Allele-specific expression analysis identified 16 meiotic genes in B. pubescens with constrained expression patterns, strongly favoring alleles introgressed from B. humilis or B. nana , a set that includes 8 meiotic genes − ASY1 , ASY3 , PDS5B , PRD3 , SYN1 , SMC3, SHOC1 and SCC4 − previously found to be under selection in Arabidopsis autopolyploids. These results provide support to the hypothesis that whole genome duplication triggers similar genomic responses across flowering plants, and that the evolutionary path available to autopolyploids for regaining meiotic stability is highly conserved and dependent on a small group of core meiotic genes. ### Competing Interest Statement The authors have declared no competing interest.

Anopheles gambiae s.l . has been the target of intense insecticide treatment since the mid-20th century to try and control malaria. A substitution in the ace-1 locus has been rapidly selected for, allowing resistance to organophosphate and carbamate insecticides. Since then, two types of duplication of the ace-1 locus have been found in An. gambiae s.l . populations: homogeneous duplications that are composed of several resistance copies, or heterogeneous duplications that contain both resistance and susceptible copies. The substitution induces a trade-off between resistance in the presence of insecticides and disadvantages in their absence: the heterogeneous duplications allow the fixation of the intermediate heterozygote phenotype. So far, a single heterogeneous duplication has been described in An. gambiae s.l . populations (in contrast with the multiple duplicated alleles found in Culex pipiens mosquitoes). We used a new approach, combining long and short-read sequencing with Sanger sequencing to precisely identify and describe at least nine different heterogeneous duplications, in two populations of An. gambiae s.l . We show that these alleles share the same structure as the previously identified heterogeneous and homogeneous duplications, namely 203-kb tandem amplifications with conserved breakpoints. Our study sheds new light on the origin and maintenance of these alleles in An. gambiae s.l . populations, and their role in mosquito adaptation.

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, Ne, 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 Ne 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. European forest tree species experienced strong climatic fluctuations over Quaternary. In spite of these pronounced environmental changes, population genomic analyses reveal that major forest tree species managed to retain their evolutionary potential over the period.

Introgression allows polyploid species to acquire new genomic content from diploid progenitors or from other unrelated diploid or polyploid lineages, contributing to genetic diversity and facilitating adaptive allele discovery. In some cases, high levels of introgression elicit the replacement of large numbers of alleles inherited from the polyploid's ancestral species, profoundly reshaping the polyploid's genomic composition. In such complex polyploids, it is often difficult to determine which taxa were the progenitor species and which taxa provided additional introgressive blocks through subsequent hybridization. Here, we use population-level genomic data to reconstruct the phylogenetic history of Betula pubescens (downy birch), a tetraploid species often assumed to be of allopolyploid origin and which is known to hybridize with at least four other birch species. This was achieved by modeling polyploidization and introgression events under the multispecies coalescent and then using an approximate Bayesian computation rejection algorithm to evaluate and compare competing polyploidization models. We provide evidence that B. pubescens is the outcome of an autoploid genome doubling event in the common ancestor of B. pendula and its extant sister species, B. platyphylla, that took place approximately 178,000-188,000 generations ago. Extensive hybridization with B. pendula, B. nana, and B. humilis followed in the aftermath of autopolyploidization, with the relative contribution of each of these species to the B. pubescens genome varying markedly across the species' range. Functional analysis of B. pubescens loci containing alleles introgressed from B. nana identified multiple genes involved in climate adaptation, while loci containing alleles derived from B. humilis revealed several genes involved in the regulation of meiotic stability and pollen viability in plant species.

New mutations provide the raw material for evolution and adaptation. The distribution of fitness effects (DFE) describes the spectrum of effects of new mutations that can occur along a genome, and is, therefore, of vital interest in evolutionary biology. Recent work has uncovered striking similarities in the DFE between closely related species, prompting us to ask whether there is variation in the DFE among populations of the same species, or among species with different degrees of divergence, that is whether there is variation in the DFE at different levels of evolution. Using exome capture data from six tree species sampled across Europe we characterized the DFE for multiple species, and for each species, multiple populations, and investigated the factors potentially influencing the DFE, such as demography, population divergence, and genetic background. We find statistical support for the presence of variation in the DFE at the species level, even among relatively closely related species. However, we find very little difference at the population level, suggesting that differences in the DFE are primarily driven by deep features of species biology, and those evolutionarily recent events, such as demographic changes and local adaptation, have little impact.

A. gambiae s.l. has been the target of intense insecticide treatment since the mid-XXth century to try and control malaria, and a substitution in the ace-1 locus allowing resistance to organophosphate and carbamates insecticides has been rapidly selected for. Since then, several duplications of the ace-1 locus have been found in A. gambiae s.l. populations. They associate either several resistance copies (homogeneous duplications) or both resistance and susceptible copies (heterogeneous duplications). Heterogeneous duplications confer an intermediate trade-off between resistance in presence of insecticide and disadvantage in their absence. So far, and in striking contrast with C. pipiens mosquitoes, a single heterogeneous duplication had been describe in A. gambiae populations. We use an innovative approach, combining information from long and short read sequencing with Sanger sequencing to precisely identify and describe at least nine different heterogeneous duplications in A. gambiae. We further show that these alleles share the exact same structure than the previously identified heterogeneous and homogeneous duplications, namely 203-kb tandem amplifications with conserved breakpoints. Our study sheds a new light on the origin and maintenance of these alleles in A. gambiae populations, and pushes one step further the striking evolutionary convergence with C. pipiens mosquitoes.

AbstractA. gambiae s.l.has been the target of intense insecticide treatment since the mid-XXth century to try and control malaria, and a substitution in theace-1locus allowing resistance to organophosphate and carbamates insecticides has been rapidly selected for. Since then, several duplications of the ace-1 locus have been found in A. gambiae s.l. populations. They associate either several resistance copies (homogeneous duplications) or both resistance and susceptible copies (heterogeneous duplications). Heterogeneous duplications confer an intermediate trade-off between resistance in presence of insecticide and disadvantage in their absence. So far, and in striking contrast withC. pipiensmosquitoes, a single heterogeneous duplication had been describe in A. gambiae populations. We use an innovative approach, combining information from long and short read sequencing with Sanger sequencing to precisely identify and describe at least nine different heterogeneous duplications in A. gambiae. We further show that these alleles share the exact same structure than the previously identified heterogeneous and homogeneous duplications, namely 203-kb tandem amplifications with conserved breakpoints. Our study sheds a new light on the origin and maintenance of these alleles in A. gambiae populations, and pushes one step further the striking evolutionary convergence withC. pipiensmosquitoes.

Phylogenetic analysis of polyploid hybrid species has long posed a formidable challenge as it requires the ability to distinguish between alleles of different ancestral origins in order to disentangle their individual evolutionary history. This problem has been previously addressed by conceiving phylogenies as reticulate networks, using a two-step phasing strategy that first identifies and segregates homoeologous loci and then, during a second phasing step, assigns each gene copy to one of the subgenomes of an allopolyploid species. Here, we propose an alternative approach, one that preserves the core idea behind phasing-to produce separate nucleotide sequences that capture the reticulate evolutionary history of a polyploid-while vastly simplifying its implementation by reducing a complex multistage procedure to a single phasing step. While most current methods used for phylogenetic reconstruction of polyploid species require sequencing reads to be pre-phased using experimental or computational methods-usually an expensive, complex, and/or time-consuming endeavor-phasing executed using our algorithm is performed directly on the multiple-sequence alignment (MSA), a key change that allows for the simultaneous segregation and sorting of gene copies. We introduce the concept of genomic polarization that, when applied to an allopolyploid species, produces nucleotide sequences that capture the fraction of a polyploid genome that deviates from that of a reference sequence, usually one of the other species present in the MSA. We show that if the reference sequence is one of the parental species, the polarized polyploid sequence has a close resemblance (high pairwise sequence identity) to the second parental species. This knowledge is harnessed to build a new heuristic algorithm where, by replacing the allopolyploid genomic sequence in the MSA by its polarized version, it is possible to identify the phylogenetic position of the polyploid's ancestral parents in an iterative process. The proposed methodology can be used with long-read and short-read high-throughput sequencing data and requires only one representative individual for each species to be included in the phylogenetic analysis. In its current form, it can be used in the analysis of phylogenies containing tetraploid and diploid species. We test the newly developed method extensively using simulated data in order to evaluate its accuracy. We show empirically that the use of polarized genomic sequences allows for the correct identification of both parental species of an allotetraploid with up to 97% certainty in phylogenies with moderate levels of incomplete lineage sorting (ILS) and 87% in phylogenies containing high levels of ILS. We then apply the polarization protocol to reconstruct the reticulate histories of Arabidopsis kamchatica and Arabidopsis suecica, two allopolyploids whose ancestry has been well documented. [Allopolyploidy; Arabidopsis; genomic polarization; homoeologs; incomplete lineage sorting; phasing; polyploid phylogenetics; reticulate evolution.].

Closely-related species often use the same genes to adapt to similar environments 1,2 . However, we know little about why such genes possess increased adaptive potential, and whether this is conserved across deeper evolutionary time. Classic theory suggests a “cost of complexity”: adaptation should occur via genes affecting fewer traits to reduce deleterious side-effects (i.e. lower pleiotropy) 3 . Adaptation to climate presents a natural laboratory to test this theory, as even distantly-related species must contend with similar stresses 4 . Here, we re-analyse genomic data from thousands of individuals from 25 plant species to identify a suite of 108 genes enriched for signatures of repeated local adaptation to climate. This set includes many genes with well-known functions in abiotic stress response, identifying key genes that repeatedly drive adaptation in species as distantly-related as lodgepole pine and Arabidopsis (~ 300 My). Using gene co-expression networks to quantify each gene’s pleiotropy, we find enrichment for greater network centrality/interaction strength and broader expression across tissues (i.e. higher pleiotropy), contrary to the ”cost of complexity” theory. These genes may be particularly important in helping both wild and crop species cope with future climate change, representing a set of important candidates for future study.

Delivering material selected for breeding purposes into the wild in the context of sustainable forest management might reduce the levels of genetic diversity of future forests in comparison to that of natural populations. Another consequence might be a reduction of their resilience under uncertain future climatic and socio-economic conditions if these new populations lack adaptability. Despite the long tradition of breeding activities in Europe, there is still a need to assess the impact of genetically enriched material on forests’ resilience. In this study, we address (1) the genetic diversity of selected material compared to its wild ancestors, and (2) how to enrich breeding material to support forests’ resilience under changing socio-environmental conditions. We analysed 16 study cases of selected material delivered from breeding activities in four European forest tree species (Pinus halepensis Mill., Pinus nigra J.F. Arnold, Pinus pinaster Ait. and Populus nigra L.) with different levels of breeding. To answer these two questions, we first assessed and compared the genetic diversity of selected material versus natural populations using both putatively neutral and adaptive (based on diverging selection) Single Nucleotide Polymorphisms (SNPs). We then suggest how to enrich these populations for resilience under future climatic conditions by defining a core collection for each species including material from populations that will likely disappear under future conditions. Thanks to the large SNP datasets available for our focal species, we were able to detect some trends in our data. Expected and observed heterozygosity values for selected populations were almost always identical. The selected material showed small but significant genetic differentiation from their original population and their inbreeding coefficient was generally lower. However, the level of genetic improvement (i.e. low vs high) was not correlated with the observed genetic differences between selected material and natural populations.The genetic characterization of natural populations distributed across the species range, and the future projection of their range stability, made it possible to identify core-collections that would significantly enrich breeding populations under uncertain future environmental conditions.

Recent studies have highlighted the significant role of copy number variants (CNVs) in phenotypic diversity, environmental adaptation and species divergence across eukaryotes. The presence of CNVs also has the potential to introduce genotyping biases, which can pose challenges to accurate population and quantitative genetic analyses. However, detecting CNVs in genomes, particularly in non-model organisms, presents a formidable challenge. To address this issue, we have developed a statistical framework and an accompanying r software package that leverage allelic-read depth from single nucleotide polymorphism (SNP) data for accurate CNV detection. Our framework capitalises on two key principles. First, it exploits the distribution of allelic-read depth ratios in heterozygotes for individual SNPs by comparing it against an expected distribution based on binomial sampling. Second, it identifies SNPs exhibiting an apparent excess of heterozygotes under Hardy-Weinberg equilibrium. By employing multiple statistical tests, our method not only enhances sensitivity to sampling effects but also effectively addresses reference biases, resulting in optimised SNP classification. Our framework is compatible with various NGS technologies (e.g. RADseq, Exome-capture). This versatility enables CNV calling from genomes of diverse complexities. To streamline the analysis process, we have implemented our framework in the user-friendly r package 'rCNV', which automates the entire workflow seamlessly. We trained our models using simulated data and validated their performance on four datasets derived from different sequencing technologies, including RADseq (Chinook salmon-Oncorhynchus tshawytscha), Rapture (American lobster-Homarus americanus), Exome-capture (Norway spruce-Picea abies) and WGS (Malaria mosquito-Anopheles gambiae).