Biology subjects

Lascoux, M.

Publications and source records attributed to Lascoux, M..

At least 19 recordsLinked to original sources

bioRxiv2026

Pervasive historical introgression across oak phylogeny shapes gene expression

Oaks were once described as the "worst-case scenario" for the biological species concept because of the presumed pervasive hybridization and introgression among species. However, we still lack a full picture of genome-wide introgression across the eight sections of the Quercus phylogeny. Furthermore, we still do not have a complete characterization of what is introgressed and how it functionally influences the recipient species. Firstly, we used 168 whole genomes from 67 Quercus species belonging to the eight sections of the Quercus phylogeny and a super pan-genome to generate a phylogeny and test for ILS and introgression. Introgression was widespread: ancient introgression occurred between ancestors of the eight sections and more recent introgression took place within sections. Secondly, using genome-wide transcriptome, methylome, and chromatin accessibility data from a subset of 19 species sampled from four sections we demonstrated that introgressed genes are more highly and uniformly expressed than non-introgressed ones. This difference in expression level between introgressed and non-introgressed genes mostly results from cis-regulation, and is most likely due to DNA methylation decay in promoter ACRs. In summary, introgression has been a major evolutionary force during the whole evolutionary history of Quercus and had a significant impact on fundamental processes such as gene regulation and expression.

evolutionary biology↗

bioRxiv2026

The contribution of recent and historical demographic histories to genomic diversity and conservation status in plant species

Demographic factors are intrinsically crucial to evaluate species extinction risk. However, measuring them remains difficult and time-consuming and the use of genomic summary statistics has been advocated to assess the conservation status of a species. In the present study, we estimated (i) the census number (Nc), (ii) effective population size (Ne) over three different time periods, recent, historical and ancient, (iii) neutral genetic diversity ({pi}4), and (iv) a measure of the efficacy of purifying selection ({pi}0/{pi}4) for 101 plant species using population genomic sequencing data. Twenty-one species are from the Plant Species with Extremely Small Populations (PSESP) program of SW China. Threatened species exhibited significantly lower Ne, Nc,{pi} 4, and weaker purifying selection, but had a higher Ne/Nc ratio than non-threatened ones. Nc was the main determinant in identifying conservation status, and contemporary neutral genetic diversity was predominantly influenced by historical Ne. In the absence of demographic information, genetic parameters are a good proxy of conservation status, likely because currently threatened species also had a low historical population size. In summary, our findings suggest that direct estimates of Nc are more useful than{pi} 4, although the latter remains a valuable conservation indicator. Hence, efforts such as the PSESP should be extended. Significance StatementExtinction is essentially a demographic process. However, evaluating the risk of extinction of species based only on demographic parameters remains a difficult task, and today only 18% of plant species are included in the International Union for Conservation of Nature (IUCN) Red List of Threatened Species. Here, we use demographic data and whole genomic data from 101 plant species to show that while census number remains the best predictor of extinction risk, genomic based parameters provide good alternatives. More specifically, current neutral nucleotide diversity and historical effective population size are good predictors of the extinction risk of plant species.

evolutionary biology↗

bioRxiv2026

When South meets North: a joint contact zone coinciding with environmental gradients in three boreal tree species

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 Swedens 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.

evolutionary biology↗

bioRxiv2025

The effect of genome organisation on selection efficiency in two contrasted plant species

Does the distribution of fitness effects of new mutations vary across the genome? Under the classical Fisher Geometric Model (FGM) we might not expect it to. In FGM, phenotypic traits are envisioned as dimensions of a landscape, with fitness determined by position in the landscape, i.e., the particular combination of traits of an individual. New mutations are represented by vectors that move from an ancestral to a new phenotype. In classical FGM these vectors affect all trait dimensions simultaneously (universal pleiotropy). However, introducing partial and modular pleiotropy into an FGM framework leads to an expectation that parameters of the DFE will vary with mutational pleiotropy-the number of traits affected by individual mutations. Here we address this prediction by investigating whether traits related to mutational pleiotropy, expression level and network connectivity, affect the parameters of the DFE using whole genome data from A. thaliana and C. grandiflora, two closely related Brassica species that vary significantly in their demography and mating system, and therefore, in effective population size and the effects of linked selection. Results were similar across both species. We found that expression level and network connectivity were predictive of the parameters of the deleterious DFE, even once co-correlations among genome biology traits were accounted for. Our results suggest that, across the genome, molecular evolutio(high mutational pleiotropy). nary patterns agree with the predictions of FGM, albeit relaxing the assumption of universal pleiotropy, and that variation in mutational pleiotropy among genes is sufficient to have detectible effects on the DFE. Significance statementHow do the effects of new mutations vary across the genome? If mutations in some genes affect many traits (high mutational pleiotropy), we hypothesise they will be more strongly deleterious, with lower variance in their selective effects. We test this by investigating the distribution of effects of new mutations across genes that vary in features that are related to mutational pleiotropy: expression level, gene network connectivity, and number of associated GO terms. The mean strength and coefficient of variation of selection of new mutations varied across genes with different features in the manner expected by our hypothesis. This demonstrates that important parameters of molecular evolution can vary across the genome with genome architecture.

evolutionary biology↗

bioRxiv2025

Gene copy number variation (gCNV) contributes to adaptation along environmental gradient

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.

evolutionary biology↗

bioRxiv2025

Estimating the reduction in genetic diversity from background selection under non-equilibrium demography and partial selfing

The effect of natural selection on linked sites has been suggested to be a major determinant of genetic diversity. While it is in principle possible to estimate this effect from genome sequence data, interactions between selection, demography and inbreeding are expected to make inference less reliable. Here we investigate whether the genome-wide reduction in diversity due to background selection ([B]) can be accurately estimated when populations are at demographic non-equilibrium and/or reproduce by partial self-fertilisation. We show that the classic-BGS model is surprisingly robust to both demographic non-equilibrium and low rates of selfing, although both processes do lead to biased estimation of the distribution of fitness effects (DFE) of deleterious mutations. A high rate of selfing leads to poor estimation of both[B] and DFE parameters. We propose an alternative inference approach where background selection, demography and partial selfing are jointly estimated from windowed site frequency spectra. This approach, while approximate in nature, resolves most of the bias observed under the classic-BGS model and can also generate estimates of past demography that account for the effect of background selection and partial selfing. We apply the approach to genome sequence data from Capsella grandiflora and C. orientalis, which have contrasting mating systems and display a forty-fold difference in nucleotide diversity. Our results suggest that background selection has a weak effect on levels of genetic diversity in the outcrosser C. grandiflora ([B] = 0.89) and a more substantial effect in the predominantly selfing species C. orientalis ([B] = 0.44), but that background selection alone cannot explain their disparity in genetic diversity.

evolutionary biology↗

bioRxiv2024

Amino acid properties, substitution rates, and the nearly neutral theory

Do the properties of amino acids affect their rates of substitution? The nearly neutral theory predicts that greater selective constraint leads to slower rates of evolution; similarly, we expect amino acids that are more different from each other to have lower rates of exchange because such changes are most likely to affect protein structure and function. Here we test these predictions, using substitution rates estimated from empirical amino acid exchangeability matrices. To measure degree of amino acid difference, we focussed on two physicochemical properties, hydrophobicity and molecular weight, uncorrelated metrics that are known to have important implications for protein structure and function. We find that for both hydrophobicity and molecular weight, amino acid pairs with large differences had lower rates of substitution. We also found that amino acids that differed in both properties had the lowest rates of substitution, suggesting that both physicochemical properties are under selective constraint. Mutation properties, such as the number of mutations or the number of transitions as opposed to transversions separating amino acid pairs, were also important predictors of substitution rates. The relationship between amino acid substitution rates and differences in their physiochemical properties holds across several taxonomically restricted datasets. This finding suggests that purifying selection affects amino acid substitution rates in a similar manner across taxonomic groups with different effective population sizes.

evolutionary biology↗

bioRxiv2024

Conserved Evolutionary Response to Whole Genome Duplication in Angiosperms Revealed Using High Resolution Gene Expression Profiling

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.

evolutionary biology↗

bioRxiv2023

Recurrent hybridization and gene flow shaped Norway and Siberian spruce evolutionary history over multiple glacial cycles

Over the last decades, extensive genome-wide resequencing studies have highlighted the extent of hybridization and introgression between closely related species. Animal and plant species went through cycles of contractions and expansions as a result of glacial cycles. These repeated sequences of reproductive isolation and admixture at continental scales have led to the accumulation over time of an ancient, deep-seated and complex genetic structure. This structure was blurred by extensive gene flow, or reinforced by strong local adaptation. This already multi-layered structure has often been further enhanced by hybridization. We investigated this complexity in Norway spruce (Picea abies) and Siberian spruce (P. obovata), two closely related species dominating Eurasian boreal forests and forming a vast hybrid zone. Here, we genotyped 542 individuals of both species and their hybrids at 480K SNPs. Individuals came from 55 populations, extending from western Europe to Siberia with a focus on the main hybrid zone. Despite extensive gene flow and a clear Isolation-by-Distance pattern at the continental scale, distinct genetic clusters emerged, indicating barriers and corridors to migration. Coalescent-based demographic inferences revealed that Norway and Siberian spruce repeatedly hybridized during the Pleistocene with introgression pattern varying depending on the latitude. In northern ranges, P. obovata expanded into P. abies while P. abies expanded into P. obovata in the southern parts. Two cryptic refugia located in the large hybrid zone played a critical role in shaping the current distribution of the two species. Our study highlights the importance of considering the whole species complex instead of separate entities to shed light on their complex demographic histories.

evolutionary biology↗

bioRxiv2023

Complex Polyploids: Origins, Genomic Composition, and Role of Introgressed Alleles

AbstractIntrogression 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 polyploids ancestral species, profoundly reshaping the polyploids 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 of polyploidization and introgression events under the multispecies coalescent and then using an approximate Bayesian computation (ABC) 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.

genomics↗

bioRxiv2023

Global and local adaptation to aridity in a desert plant Gymnocarpos przewalskii

In order to thrive and survive plant species need to combine stability in the long term and rapid response to environmental challenges in the short term. The former would be reflected by global adaptation across species and the latter by pronounced local adaptation among populations of the same species. It remains unclear how much overlap is to be expected between the parts of the genome associated to these two contrasted adaptation processes. In the present study, we generated a high-quality genome and re-sequenced 177 individuals for Gymnocarpos przewalskii, an important desert plant species from North-West China, to detect local adaptation. To test for global adaptation to aridity at the molecular level we compared genomic data of 15 species that vary in their ability to withstand drought. A total of 118 genes were involved in global adaptation to aridity. Sixty-five G. przewalskii genes were shared across all xerophytic species, of which sixty-three were under stabilizing selection and two under directional selection. While 20% of G. przewalskii genome showed signatures of local adaptation to aridity during population divergence, only 13 of those genes were also under global adaptation. Hence, our results suggest that long-term stability is crucial for adaptation to extreme environmental stress but is only maintained in a small group of highly pleiotropic genes while a rapid response to recent changes elicits a genome-wide response, including gene family expansion. The overlap between the two evolutionary mechanisms appears limited.

evolutionary biology↗

bioRxiv2023

Past family selection in Populus nigra leads to an amplification of rust damages when neighbors are related

The competitive ability of domesticated plants, which may have conferred a fitness advantage in the wild, may result in a reduction of yield in agricultural and forestry contexts, as what matters is the group rather than the individual performance. Traits related to competitive ability can be affected by the presence or absence of related individuals in their neighborhood. Consequently, local relatedness might reveal plant-to-plant interaction that can enhance the predictive abilities of genomic models when accounted for, though it remains difficult to measure. To overcome this difficulty, we analyzed data from the French breeding program of Populus nigra L., where 1,452 genotypes were replicated six to eight times, each time encountering a different neighborhood. We assessed local relatedness and investigated genomic estimated breeding values on tree height and vulnerability to rust with a single-step GBLUP incorporating local relatedness as a covariate. The results indicate that incorporating local relatedness as an additional factor in GBLUP models has a significantly greater influence on resistance to rust than on tree height, though its overall effect on genomic predictions themselves was limited. The influence of local relatedness is small but likely trait-specific, and the genetic architecture of the trait under selection could attenuate or improve the efficacy of breeding for group performance.

genetics↗

bioRxiv2023

Dominance between self-incompatibility alleles determines the mating system of Capsella allopolyploids

The shift from outcrossing to self-fertilization is one of the main evolutionary transitions in plants, and has broad effects on evolutionary trajectories. In Brassicaceae, the ability to impede self-fertilization is controlled by two genes, SCR and SRK, tightly linked within the S-locus. A series of small non-coding RNAs also encoded within the S-locus regulates the transcriptional activity of SCR alleles, resulting in a linear dominance hierarchy between them. Brassicaceae allopolyploid species are often self-compatible (SC) even when one of their parents is self-incompatible, but the causes of the loss of self-incompatibility (SI) in polyploid lineages have generally remained elusive. We used a series of synthetic hybrids obtained between self-fertilizing Capsella orientalis and outcrossing C. grandiflora to test whether the breakdown of SI in allopolyploid species, such as C. bursa-pastoris, could be explained by the dominance interactions between S-haplotypes inherited from the parental lineages. After establishing a database of reference S-allele sequences, we used RNA-sequencing data from young inflorescences to measure allele-specific expression of the SCR and SRK genes in diploid and tetraploid synthetic hybrids. We then compared the observed expression of SCR alleles with the predicted dominance relationship between S-haplotypes in pollen and with the seed set from autonomous self-fertilization in the synthetic hybrids. Our results formally establish that upon hybridization, the immediate effect on the mating system depends on the relative dominance between S-alleles inherited from the parental species. They illustrate that a detailed understanding of the genetic architecture of the control of SI is essential to predict the patterns of association between the mating system and changes in ploidy. Lay summaryPolyploidy is the inheritable condition of carrying more than two sets of chromosomes. It can result from within-species genome duplication (auto-polyploidy), or from the merging of sets of chromosomes from different species following hybridization (allo-polyploidy). Because sexual reproduction between individuals of different levels of ploidy is generally not successful, self-fertilization has been considered a key component of the establishment success of polyploid lineages. However, the reasons why the mating system of polyploids may differ from that of their parental species remains mysterious. In plants of the Brassicaceae family, several allopolyploid species arose from hybridization between an outcrossing and a self-fertilizing species, and in most cases the resulting lineages are self-fertilizing. It has been proposed that the mating system of these allopolyploids depends on the dominance relationships between the functional and non-functional self-incompatibility alleles inherited from the parental species. Here, we tested this prediction by characterizing at the transcriptional (RNA-seq) and phenotypic levels (estimation of autonomous seed production) a series of synthetic Capsella diploid and tetraploid hybrids. We found that the predicted dominance relationships matched the observed expression of self-incompatibility alleles, as well as the mating system phenotypes. Hence, the mating system of newly formed Capsella allotetraploids depends on the dominance relationship between self-incompatibility alleles inherited from the parents. Overall, our results improve our understanding of the mechanisms by which changes in ploidy can alter the system of mating over the course of evolution.

evolutionary biology↗

bioRxiv2023

Separating phases of allopolyploid evolution with resynthesized and natural Capsella bursa-pastoris

Allopolyploidization is a frequent evolutionary transition in plants that combines whole-genome duplication (WGD) and interspecific hybridization. The genome of an allopolyploid species results from initial interactions between parental genomes and long-term evolution. Telling apart the contributions of these two phases is essential to understanding the evolutionary trajectory of allopolyploid species. Here, we compared phenotypic and transcriptomic changes in natural and resynthesized Capsella allotetraploids with their diploid parental species. We focused on phenotypic traits associated with the selfing syndrome and on transcription-level phenomena such as expression level dominance, transgressive expression, and homoeolog expression bias. We found that selfing syndrome, high pollen and seed quality in natural allotetraploids likely resulted from long-term evolution. Similarly, transgressive expression and most down-regulated expression-level dominance were only found in natural allopolyploids. Natural allotetraploids also had more expression-level dominance toward the self-fertilizing parental species than resynthesized allotetraploids, mirroring the establishment of the selfing syndrome. However, short-term changes mattered, and 40% of the cases of expression-level dominance in natural allotetraploids were already observed in resynthesized allotetraploids. Resynthesized allotetraploids showed striking variation of homoeolog expression bias among chromosomes and individuals. Homoeologous synapsis was its primary source and may still be a source of genetic variation in natural allotetraploids. In conclusion, both short- and long-term mechanisms contributed to transcriptomic and phenotypic changes in natural allotetraploids. However, the initial gene expression changes were largely reshaped during long-term evolution leading to further morphological changes.

genetics↗

bioRxiv2023

Hybridization mediated range expansion and climate change resilience in two conifers

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 genetically isolated populations that are at risk under current climate change.

evolutionary biology↗

bioRxiv2023

Synchronous effective population size changes and genetic stability of forest trees through glacial cycles

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 performed comparative population genomic analyses and demographic inferences for seven widely distributed and ecologically contrasted 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. Hence, 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 were able to retain their evolutionary potential over very long periods of time despite strong environmental changes. One-Sentence SummaryPopulation genomic analyses reveal that forest trees retained their evolutionary potential over the Quaternary.

evolutionary biology↗

bioRxiv2022

Teasing apart the joint effect of demography and natural selection in the birth of a contact zone

Vast population movements induced by recurrent climatic cycles have shaped the genetic structure of plant species. This is especially true in Scandinavia that was repeatedly glaciated. During glacial periods trees were confined to refugia, south and east of the ice sheet, from which they recolonized Scandinavia as the ice melted away. This multi-pronged recolonization led to large contact zones in most species. We leverage large genomic data from 5000 trees to reconstruct the demographic history of Norway spruce (Picea abies) and test for the presence of natural selection during the recolonization process and the establishment of the contact zone. Sweden is today made up of two large genetic clusters, a southern one originating from the Baltics and a Northern one originating from Northern Russia. The contact zone delineating these two clusters closely matches the limit between two major climatic regions. This suggests that natural selection contributed to the establishment and the maintenance of the contact zone. To test this hypothesis we first used Approximate Bayesian Computation; an Isolation-with migration model with genome-wide linked selection fits the data better than a purely neutral one. Secondly, we identified loci characterized by both extreme allele frequency differences between geographic regions and association to the variables defining the climatic zones. These loci, many of which are related to phenology, form clusters present on all linkage groups. Altogether, the current genetic structure reflects the joint effect of climatic cycles, recolonization and selection on the establishment of strong local adaptation and contact zones. Significance StatementUnderstanding how past climatic events, human actions and evolutionary forces contributed to the present distribution of genetic diversity is crucial to predict their reaction to the current climate crisis. Vast distribution shifts induced by past environmental changes, local ecological processes, natural selection and human transfers contributed to the current distribution of Norway spruce across Northern Europe. Genome-wide polymorphisms from thousands of individuals show that Scandinavia was recolonized after the Last Glacial from both south and north. This two-pronged recolonization established a contact zone between two genetic clusters that matches the limit between two major climate zones. The contact zone is shaped and maintained by natural selection on a large number of loci that form blocks of co-adapted loci spread genome-wide.

evolutionary biology↗

bioRxiv2021

Genome-wide evolutionary response of European oakssince the Little Ice Age

The pace of tree microevolution during Anthropocene warming is largely unknown. We used a retrospective approach to monitor genomic changes in oak trees since the Little Ice Age (LIA). Allelic frequency changes were assessed from whole-genome pooled sequences for four age-structured cohorts of sessile oak (Quercus petraea) dating back to 1680, in each of three different oak forests in France. The genetic covariances of allelic frequency changes increased between successive time periods, highlighting genome-wide effects of linked selection. We found imprints of convergent linked selection in the three forests during the late LIA, and a shift of selection during more recent time periods. The changes in allelic covariances within and between forests mirrored the documented changes in the occurrence of extreme events (droughts and frosts) over the last three hundred years. The genomic regions with the highest covariances were enriched in genes involved in plant responses to pathogens and abiotic stresses (temperature and drought). These responses are consistent with the reported sequence of frost (or drought) and disease damage ultimately leading to the oak dieback after extreme events. Our results therefore provide evidence of selection operating on long-lived species during recent climatic changes.

evolutionary biology↗