Biology subjects

Milesi, P.

Publications and source records attributed to Milesi, P..

17 recordsLinked to original sources

bioRxiv2026

HOW FIVE DECADES OF LAND-COVER CHANGE RESHAPED SUITABLE HABITAT FOR PUERTO RICAN TREE SPECIES

AimHuman 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. LocationThe Caribbean island of Puerto Rico. Forest cover on the island increased from about 18 to 45% from the late 1940s to the early 2000s. MethodsUsing data on geographic distributions and functional traits for 454 tree species, we evaluated how gain of potential habitat was related to species-specific climatic associations and life-history strategies. We estimated species-specific potential habitat (climatically suitable and forested) with species distribution models and data on forest 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 conditions in reforested areas. ResultsSpecies with relatively more potential habitat in 1951 (climatically suitable and forested) also had relatively larger gains in potential habitat from 1951 to 2000. Species that tend to occupy conditions different from those common in reforested areas (i.e., more marginal habitats) gained relatively less potential habitat and species with broad environmental niches gained more potential habitat. Additionally, species with relatively acquisitive functional traits gained more suitable habitat than those with relatively conservative traits. Main conclusionsOur results show that Puerto Ricos reforestation preferentially increased habitat for species that (1) already had suitable habitat in the landscape, (2) tolerate a wide range of climatic conditions, and (3) exhibit fast, acquisitive functional strategies. These findings illustrate how land-use change in heterogeneous tropical landscapes can generate non-uniform habitat gains across species, potentially favoring generalist over specialist species and reshaping community composition.

ecology↗

bioRxiv2026

A comparative dataset on population genetics, traits, and distributions for nineteen Caribbean tree species

Although genetic diversity is a fundamental component of biodiversity, we lack data for a majority of species, particularly in biodiversity hotspots such as tropical forests. We present a comparative genetic dataset of 19 tropical tree species (including one palm) from the Caribbean island of Puerto Rico and neighboring islands (Hispanola and the US Virgin Islands). Using a reduced-representation sequencing technique (SLAF-seq), we identified species-specific single-nucleotide polymorphism (SNP) datasets with 24,413 to 433,637 high-quality SNPs per species. The focal species represent a range of life-history and climate associations, which may be relevant to their genetic structure. Therefore, we also include complementary information on species functional traits (wood density, leaf thickness, specific leaf area, maximum height, and seed dry mass), as well as geographic distributions and climatic associations from species distribution models.

genetics↗

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

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↗

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

Striking allelic diversity despite structural homogeneity of ace-1 duplications in Anopheles mosquitoes

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.

evolutionary biology↗

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

A new framework for detecting copy number variants from single nucleotide polymorphism data: 'rCNV', a versatile R package for paralogs and CNVs detection

Studies show that copy number variants (CNVs), due to their ubiquitous presence in eukaryotes, contribute to phenotypic variation, environmental adaptation, and fuel species divergence at a previously unknown rate. However, the detection of CNVs in genomes, especially in non-model organisms is challenging due to the need for costly genomic resources and complex computational infrastructure. Therefore, to provide researchers with a low-cost and easily accessible resource, we developed a robust statistical framework and an R software package to detect CNVs using allelic-read depth from SNPs data. The core of the framework exploits i) the allelic-read depth ratio distribution in heterozygotes for individual SNPs and testing it against an expected distribution under a binomial sampling, and ii) SNPs showing an apparent excess of heterozygotes under Hardy-Weinberg equilibrium, to detect alleles in putatively multi-copy regions. The use of multiple statistical tests to find the deviation in allelic-read depth ratio distribution makes our method sensitive to sampling and aware of reference biases thereby minimizing false detection of CNVs. Our framework is well-catered for high throughput short-reads data, hence, most GBS technologies (e.g., RADseq, Exome-capture, WGS). As such, it allows calling CNVs from genomes of varying complexity. The framework is implemented in the R package "rCNV" which effortlessly automates the analysis. We trained our models on simulated data and tested on four datasets obtained from different sequencing technologies (i.e., RADseq: Chinook salmon - Oncorhynchus tshawytscha, American lobster - Homarus americanus, Exome-capture: Norway Spruce - Picea abies, and WGS: Malaria mosquito -Anopheles gambiae).

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↗

bioRxiv2020

Phenotypic plasticity, population structure and adaptation in a young weed species with a worldwide distribution

The colonization success of a species depends on phenotypic plasticity, adaptive potential and population structure. Assessing their relative contributions during a colonization process is challenging, and a large-scale experiment had yet to be done. In this study, we attempted to tease apart their effects on the fitness of one of the most common plant on Earth, the shepherds purse (Capsella bursa-pastoris), a self-fertilizing and allopolyploid weed, with a worldwide distribution. The overarching goal is to eventually understand how the shepherds purse extensive distribution range was established so rapidly. To do so, we carried out three common gardens, located in Europe, Asia and North America, and measured several life-history traits on field-collected accessions belonging to three distinct genetic clusters (Middle East, Europe, and Asia). Our experiment showed that (i) the success of C. bursa-pastoris is mainly due to its high degree of phenotypic plasticity; and (ii), genetic cluster effect reflected a classic pattern observed in core vs marginal populations, with the Middle Eastern cluster (putative core population) outperforming the European and Asian clusters. This study therefore revealed, in a model species, different relative contributions of plasticity and adaptation to fitness, depending on the population and the time since colonization occurred.

evolutionary biology↗

bioRxiv2019

Ecological strategy and genetic load in the shepherd's purse (Capsella bursa-pastoris) from the core and the limit of its natural range.

Species range expansion is a complex process whose outcome depends on the interplay of demographic, environmental and genetic factors. In plants, self-fertilizing species that do not require a mate to reproduce usually show higher invasive ability. However, this comes at a cost as both selfing and bottlenecks occurring during colonization lead to an increase in deleterious mutations accumulation (genetic load). Although they are theoretically clearly spelled out, the relationships between genomic and phenotypic characteristics of expanding populations have hitherto rarely been characterized. In the present study we analyzed how different accessions of the shepherds purse, C. bursa-pastoris, coming from the front of colonization or from the core of the natural range performed under increasing density of competitors. We first showed that, as expected, accessions from the front of colonization performed the worst for most life history traits compared with accessions from core populations. Second, competitor density had a negative impact on both vegetative growth and reproductive output in term of fruits production for all accessions. However, somewhat unexpectedly given their higher genetic load and their lower absolute performance, accessions from the front of colonization were less affected by competition than accessions from the core of the species range. This could be due to phenotypic tradeoffs and a shift in phenology that allow the accessions from the front of colonization to avoid competition. These results are discussed in terms of ecological strategies of expanding populations.

evolutionary biology↗

bioRxiv2018

Assessing the potential for assisted gene flow using past introduction of Norway spruce in Southern Sweden: Local adaptation and genetic basis of quantitative traits in trees.

Norway spruce (Picea abies) is a dominant conifer species of major economic importance in Northern Europe. Extensive breeding programs were established to improve phenotypic traits of interest. In southern Sweden seeds used to create progeny tests were collected on about 3000 trees of outstanding phenotype (\"plus\" trees) across the region. Some were of local origin but many were recent introductions from the rest of the natural range. The mixed origin of the trees together with partial sequencing of the exome of >1,500 of these trees and phenotypic data retrieved from the Swedish breeding program offered us a unique opportunity to dissect the genetic basis of local adaptation of three quantitative traits (height, diameter and budburst). Through a combination of multivariate analyses and genome-wide association studies, we showed that there was a very strong effect of geographical origin on growth (height and diameter) and phenology (budburst) with trees from southern origins outperforming local provenances. Association studies also indicated that growth traits were highly polygenic and budburst somewhat less. Hence, our results suggest that assisted gene flow and genomic selection approaches could help alleviating the effect of climate change on P. abies breeding programs in Sweden.

evolutionary biology↗

bioRxiv2018

Towards the new normal: Transcriptomic and genomic changes in the two subgenomes of a 100,000 years old allopolyploid, Capsella bursa-pastoris

Allopolyploidy has played a major role in plant evolution but its impact on genome diversity and expression patterns remains to be understood. Some studies found important genomic and transcriptomic changes in allopolyploids, whereas others detected a strong parental legacy and more subtle changes. The allotetraploid C. bursa-pastoris originated around 100,000 years ago and one could expect the genetic polymorphism of the two subgenomes to become more similar and their transcriptomes to start functioning together. To test this hypothesis, we sequenced the genomes and the transcriptomes (three tissues) of allote-traploid C. bursa-pastoris and its parental species, the outcrossing C. grandiflora and the self-fertilizing C. orientalis. Comparison of the divergence in expression between subgenomes, on the one hand, and divergence in expression between the parental species, on the other hand, indicated a strong parental legacy with a majority of genes exhibiting a conserved pattern and cis-regulation. However, a large proportion of the genes that were differentially expressed between the two subgenomes, were also under trans-regulation reflecting the establishment of a new regulatory pattern. Parental dominance varied among tissues: expression in flowers was closer to that of C. orientalis and expression in root and leaf to that of C. grandiflora. Since deleterious mutations accumulated preferentially on the C. orientalis subgenome, the bias in expression towards C. orientalis observed in flowers suggests that expression changes could be adaptive and related to the selfing syndrome, while biases in the roots and leaves towards the C. grandiflora subgenome may be reflective of the differential genetic load.

evolutionary biology↗

bioRxiv2018

Genomic data provides new insights on the demographic history and the extent of recent material transfers in Norway spruce

Primeval forests are today exceedingly rare in Europe and transfer of forest reproductive material for afforestation and improvement have been very common, especially over the last two centuries. This can be a serious impediment when inferring past population movements in response to past climate changes such as the last glacial maximum (LGM), some 18,000 years ago. In the present study, we genotyped 1,672 individuals from three Picea species (P. abies, P. obovata, and P. omorika) at 400K SNPs using exome capture to infer the past demographic history of Norway spruce and estimate the amount of recent introduction used to establish the Norway spruce breeding program in Southern Sweden. Most of these trees belong to P. abies and originate from the base population of the Swedish breeding program. Others originate from populations across the natural ranges of the three species. Of the 1,499 individuals stemming from the breeding program, a large proportion corresponds to recent introductions. The split of P. omorika occurred 23 million years ago (mya), while the divergence between P. obovata and P. abies began 17.6 mya. Demographic inferences retrieved the same main clusters within P. abies than previous studies, i.e. a vast northern domain ranging from Norway to central Russia, where the species is progressively replaced by Siberian spruce (P. obovata) and two smaller domains, an Alpine domain, and a Carpathian one, but also revealed further subdivision and gene flow among clusters. The three main domains divergence was ancient (15 mya) and all three went through a bottleneck corresponding to the LGM. Approximately 17% of P. abies Nordic domain migrated from P. obovata ~103K years ago, when both species had much larger effective population sizes. Our analysis of genome-wide polymorphism data thus revealed the complex demographic history of Picea genus in Western Europe and highlighted the importance of material transfer in Swedish breeding program.

evolutionary biology↗