Biology subjects

Farelo, L.

Publications and source records attributed to Farelo, L..

7 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↗

bioRxiv2025

Museum genomics links MC1R alleles to adaptive winter coat color polymorphism in the long-tailed weasel

Understanding the architecture of biological adaptations is a major endeavor of evolutionary biology. Using Natural History collections, we study the genetic basis and evolution of white/brown winter coat color variation in the long-tailed weasel (Neogale frenata), a crucial phenological adaptation for camouflage in habitats with seasonal snow. We produced whole-genome sequencing data for museum specimens, along two winter color morph transition areas in North America, at the West and East coasts. Genome-wide association scans identified a single genomic region linked to color variation polymorphism with approximately 300kb and 200kb in the West and East regions, respectively, which included the pigmentation gene MC1R. We identified three MC1R alleles, two of which with deletions of nine or eight amino acids, alternatively associated with the winter brown morphs in the West and East, respectively. These deletions affect the second transmembrane domain, and in one case also the first extracellular loop, which in silico analyses predicted to impact the proteins function. Our findings show alternative intraspecific evolutionary solutions for environmental adaptation in long-tailed weasels, building on the evidence that major genes of the melanin production pathway are hotspots for recurrent and independent evolution of winter camouflage adaptation.

evolutionary biology↗

bioRxiv2025

Ancient balanced polymorphism underlies long-standing adaptation for seasonal camouflage in the least weasel

Unraveling how adaptive traits originate and evolve is key to understanding the mechanisms shaping species diversity and their adaptive potential. Seasonal color molts, from summer-brown to winter-white, evolved in at least 21 mammals and birds to maintain camouflage in environments with seasonal snow, but the occurrence of winter-brown morphs reflects seemingly convergent local adaptation to distinct snow conditions. In the least weasel (Mustela nivalis), alternative winter morphs map to the pigmentation gene MC1R, but the evolutionary history and functional basis of this variation remain unknown. Using in vitro cellular assays, we show that winter-brown coats are caused by a derived protein-coding amino acid substitution that reduces MC1R affinity to its ligands, ASIP and -MSH. Using targeted enrichment and sequencing, we find that this mutation arose de novo within the species, around one million years ago, and was maintained across the geographically structured populations generated during its evolution in Europe. Using simulations, we show that genetic drift cannot explain the long-term maintenance of this variant, which is likely driven by spatially varying selection acting on the phenotypic polymorphism, anchoring local adaptive responses. Our results underscore how long-standing adaptive variation can fuel recurrent adaptation to heterogeneous environments through time.

evolutionary biology↗

bioRxiv2025

Comparative genomics and phylogenomics of the Mustelinae lineage (Mustelidae, Carnivora)

Mustelinae are among the most diverse and taxonomically complex subfamilies within the Mustelidae, yet their evolutionary history and genetic diversity remain largely unexplored at the whole-genome level. Here, we present the first comprehensive comparative and phylogenomic study of this lineage, integrating nuclear and mitochondrial genomes from ten species across the Holarctic and Indomalayan realms. Our dataset includes two novel genome assemblies (Mustela strigidorsa, M. sibirica) and an improved genome for M. nivalis, enabling robust cross-species analyses of genome size, chromosomal evolution, genetic diversity, and demographic history. We uncover striking inter-and intraspecific variation in genome-wide heterozygosity and genome size, with evidence of marked homozygosity in some Asian lineages (M. eversmanii, M. sibirica, M. strigidorsa) and remarkable genetic diversity in widespread species such as M. nivalis and M. erminea. Phylogenomic results support the previously suggested split of M. richardsonii from M. erminea, but we found no evidence for speciation within M. nivalis. Ancestral reconstruction of chromosomal rearrangements revealed key chromosomal fissions that shaped the Mustelinae radiation, including early events predating the divergence of modern Mustela species. The results confirmed the ancestral karyotype of Mustela (2n=44) and the Mustelinae (2n=42). Finally, demographic reconstructions exposed species-specific responses to Quaternary climatic cycles, ranging from long-term resilience in M. nivalis to repeated population bottlenecks in M. putorius and M. sibirica. Collectively, our findings establish a genomic foundation for future evolutionary and conservation genomic research on this emblematic Mustelidae lineage.

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↗