Biology subjects

Boursot, P.

Publications and source records attributed to Boursot, P..

5 recordsLinked to original sources

bioRxiv2026

Extensive nuclear introgression accompanied ancient mitochondrial capture in the common ancestor of two sister hare species

Pleistocene climatic oscillations promoted contact and hybridization among hare species, leaving lasting genomic signatures. Two sister species, L. castroviejoi (broom hare, endemic to Iberia) and L. corsicanus (Italian hare, endemic to Italy), carry fixed mitogenomes from L. timidus (mountain hare), an Arctic species widespread in southern Europe before deglaciation. Whether such turnover was accompanied by nuclear introgression, and how it affects their genomes today, remains unclear. Here, we date the ancient mitochondrial replacement in the broom-Italian hare ancestor using whole mitogenomes incorporating Iron Age samples. Coalescent modelling of complete genomes infers a substantial mountain hare contribution (24%) to this ancestor ~900 Kya (~5N generations). Accordingly, phylogenetic segmentation identified genomic segments consistent with mountain-to-broom/Italian hare introgression, covering ~17.8% of the autosomes, close to ~18% expected under drift, given admixture's timing and magnitude. Genome polarisation corroborates this estimate, with 25-28% of the mountain hare genome polarising with broom and Italian hares rather than its sister Iberian hare, decreasing to 15-18% at diagnostic sites. The introgression segments concentrate fixed-introgression sites and show sharp transitions of ancestry at their borders. Highly introgressed regions are gene-dense, and regions of reduced introgression are repeat-rich, suggesting that recombination shapes the introgression landscape. They also harbour genes with mitochondrial function that mirror candidates linked to mito-nuclear coadaptation in the Iberian hare, hinting that mitonuclear interactions may influence which variants persist. Our study illustrates how combining demographic, phylogenomic and polarisation-based methods can quantify and localize extensive nuclear introgression, even in the absence of non-introgressed reference populations.

evolutionary biology↗

bioRxiv2024

Influence of gonadal and chromosomal sex on the brain transcriptome in a mouse species with natural sex reversal

Sex chromosomes are expected to play a role in shaping the transcriptional architecture of sexual dimorphism, through the direct expression of sex-linked genes, by regulating autosomal genes, or in interactions with hormones. Yet, their degree of involvement remains elusive partly because chromosomal sex (XX/XY or ZZ/ZW) and gonadal sex (ovaries or testes) are usually inextricably intertwined. They are however dissociated in the African pygmy mouse, Mus minutoides, in which a feminizing X (X*) has evolved resulting in three female genotypes (XX, XX* and X*Y) and one male genotype (XY). Despite hormonal levels similar to the other females, X*Y females show distinctive phenotypes with greater fertility, divergent maternal care strategies and the masculinization of some traits (e.g. enhanced aggressiveness). By comparing the brain transcriptome of the four sexual genotypes, we show, here, that differential gene expression is mainly linked to gonadal sex (male vs. female) but also and significantly, to chromosomal sex, with expression patterns matching the singularity of X*Y female traits. Genes with such patterns are over-represented on sex and sex-linked chromosomes, and some are strong candidates to explain X*Y-specific behavioral and reproductive traits. We also report the preferential inactivation of the X* chromosome in XX* females, which could explain their trait similarities with XX females. Overall, we show that sex chromosomes have profoundly impacted the brain transcriptome in ways that reflect their new transmission modes and new resulting conflicts. This opens exciting prospects on the evolution of sex differences in relation to the dynamic of sex chromosome evolution.

evolutionary biology↗

bioRxiv2024

Genome admixture among four hare species in Iberia: focus on the broom hare (Lepus castroviejoi)

Pleistocene climatic fluctuations have often driven range shifts and hybridization among related species, leaving present-day genomic footprints. In the Iberian Peninsula, Lepus timidus, after its post-deglaciation retreat, has left extensive mitochondrial DNA traces in three other hare species, but the genomic correlates and underlying biogeographic scenarios are still incompletely understood. This study focuses on Lepus castroviejoi, endemic to the Cantabrian region, using its non-Iberian sister species, L. corsicanus, for comparison. By analyzing coalescent patterns from 10 genomes, we estimate that these species remained isolated since their divergence, around 50,000 years ago, consistent with their current allopatry. Further analyses with 25 additional genomes indicate that small fractions of the L. castroviejoi genome originate from L. granatensis, L. timidus, and L. europaeus (0.72%, 0.08%, and 0.04%, respectively). Introgression dating based on tract lengths suggests L. granatensis was already admixed with L. timidus when it hybridized with L. castroviejoi, which could explain the granatensis-timidus ancestry tract junctions detected in L. castroviejoi. Genomic segments with such junctions contain genes enriched for cell signaling and olfactory receptor activity, possibly facilitating genetic exchange. This research demonstrates how genomic ancestry inferences can reveal complex multiway admixture histories and illuminate past biogeographic events.

evolutionary biology↗

bioRxiv2021

The evolutionary pathways for local adaptation in mountain hares

Understanding the evolution of local adaptations is a central aim of evolutionary biology and key for the identification of unique populations and lineages of conservation relevance. By combining RAD sequencing and whole-genome sequencing, we identify genetic signatures of local adaptation in mountain hares (Lepus timidus) from isolated and distinctive habitats of its wide distribution: Ireland, the Alps and Fennoscandia. Demographic modelling suggested that the split of these mountain hares occurred around 20 thousand years ago, providing the opportunity to study adaptive evolution over a short timescale. Using genome-wide scans, we identified signatures of extreme differentiation among hares from distinct geographic areas that overlap with area-specific selective sweeps, suggesting targets for local adaptation. Several identified candidate genes are associated with traits related to the uniqueness of the different environments inhabited by the three groups of mountain hares, including coat colour, ability to live at high altitudes and variation in body size. In Irish mountain hares, a variant of ASIP, a gene previously implicated in introgression-driven winter coat colour variation in mountain and snowshoe hares (L. americanus), may underlie brown winter coats, reinforcing the repeated nature of evolution at ASIP moulding adaptive seasonal colouration. Comparative genomic analyses across several hare species suggested that mountain hares adaptive variants appear predominantly species-specific. However, using coalescent simulations we also show instances where the candidate adaptive variants have been introduced via introgressive hybridization. Our work shows that standing adaptive variation, including that introgressed from other species, was a crucial component of the post-glacial dynamics of species.

evolutionary biology↗

bioRxiv2020

The legacy of recurrent introgression during the radiation of hares

AO_SCPLOWBSTRACTC_SCPLOWHybridization may often be an important source of adaptive variation, but the extent and long-term impacts of introgression have seldom been evaluated in the phylogenetic context of a radiation. Hares (Lepus) represent a widespread mammalian radiation of 32 extant species characterized by striking ecological adaptations and recurrent admixture. To understand the relevance of introgressive hybridization during the diversification of Lepus, we analyzed whole exome sequences (61.7 Mb) from 15 species of hares (1- 4 individuals per species), spanning the global distribution of the genus, and two outgroups. We used a coalescent framework to infer species relationships and divergence times, despite extensive genealogical discordance. We found high levels of allele sharing among species and show that this reflects extensive incomplete lineage sorting and temporally layered hybridization. Our results revealed recurrent introgression at all stages along the Lepus radiation, including recent gene flow between extant species since the last glacial maximum, but also pervasive ancient introgression occurring since near the origin of the hare lineages. We show that ancient hybridization between northern hemisphere species has resulted in shared variation of potential adaptive relevance to highly seasonal environments, including genes involved in circadian rhythm regulation, pigmentation, and thermoregulation. Our results illustrate how the genetic legacy of ancestral hybridization may persist across a radiation, leaving a long-lasting signature of shared genetic variation that may contribute to adaptation within and among species.

evolutionary biology↗