Genomic signatures of selection and putative adaptive introgression during the African expansion of the house mouse

Ancient whole genomes reveal regional selection during adaptation to Neolithic lifestyle in Western Eurasia

The introduction of agriculture in Western Eurasia during the Mesolithic-Neolithic transition reshaped human lifestyle, demography and pathogen exposure. Yet, the associated selective pressures remain incompletely resolved because previous ancient DNA studies relied on targeted SNP panels and yielded non-overlapping results. Here, using high-coverage whole-genome data from 152 ancient individuals, including 12 newly sequenced genomes from the Iron Gates, we show that adaptation during this transition was geographically structured and involved selection of both Early Farmer and Hunter-Gatherer alleles. By combining scans of population differentiation, extended haplotype homozygosity, and adaptive admixture, we identify candidate loci under selection in ancestral and admixed populations. Extending the analysis beyond SNPs, we also detect differential copy-number variants, ancestry-associated shifts in transposable-element abundance, and an early Neolithic hepatitis B infection. Functional analyses including effects on gene expression suggested selection on immune, metabolic, reproductive, sensory, and behavioural processes. Taken together, our results reveal a broader and more regionally variable adaptive landscape than previously appreciated.

The epigenomic landscape of deep lineage divergence: The case of the European sea bass

Background Understanding the role of non-coding genomic variation in speciation remains a major challenge in evolutionary biology. Here, we investigated whether regulatory elements contribute to this process between Atlantic and Mediterranean lineages of European sea bass (Dicentrarchus labrax), a well-characterized case-study near speciation where barriers to introgression exist in the presence of connectivity between diverging populations. Results We generated a novel, highly contiguous genome assembly, which was annotated at the epigenomic level using ATAC-seq and ChIP-seq with six embryonic developmental stages and five tissue types in adult fish, identifying thousands of promoters, enhancers, and open chromatin regions. Integrating this annotation with whole-genome sequence data from 65 individuals across three geographically distinct populations, we identified 57,505 outlier SNPs and 332 structural variants (SVs) showing elevated differentiation between Atlantic and East Mediterranean lineages. Outlier SVs affected key regulatory elements and coding genes, while outlier SNPs were enriched in regulatory elements, particularly enhancers active in adult tissues. Local genomic divergence correlated positively with regulatory element density, especially on chromosomes 1, 9, and 18, which are enriched in genes related to osmoregulation, immune response, and oxidative stress — processes relevant to adaptation across contrasting marine environments. Conclusions These findings support a major role for regulatory variation in driving deep lineage divergence through local adaptation.

Multiple Eurasian Origins and Admixture Shaped the Genomic Legacy of the House Mouse Invasion in Africa

Commensal mammals offer unique opportunities to study how human‐mediated dispersal, admixture, and secondary contact shape genomic variation during range expansion, yet for one of the most successful invasive commensals globally, the western house mouse Mus musculus domesticus, invasion dynamics across Africa remain largely unexplored. Here, we present a large‐scale population genomic analysis of 380 whole‐genome sequences, including 303 newly sequenced low‐coverage genomes, of which 216 are from 13 distinct African populations, enabling us to investigate how human‐mediated dispersal and secondary contact with native species shape the genomic legacy of a commensal mammal invasion. Ancestry analyses reveal contributions from at least three major Eurasian source lineages contributing to African populations: an Iberian–West Asian lineage present in Morocco, Algeria, and Niger; a Mediterranean lineage represented in Tunisia; and a Northern European lineage dominant in West and Central Africa. Demographic inferences indicate both recent and ancient episodes of divergence and population contraction. In West and Central Africa, divergence times broadly overlap with European maritime expansion and colonial trade. In contrast, North African populations exhibit older coalescent signals, consistent with early participation in the western Mediterranean radiation. We also detect substantial introgression from the native Mus spretus into North African populations in regions of sympatry. Collectively, our results reveal that the African invasion of the house mouse was not a single demographic process but a mosaic of population‐specific histories shaped by multiple introductions, shifting connectivity through time, admixture, and interspecific gene flow. These findings reinforce the importance of population‐level perspectives in invasion genomics, especially for commensal mammals whose dispersal is closely tied to human movement, and establish the most extensive open genomic resource for wild African house mice.

An introgressed haplotype decouples phenotype from genome-wide ancestry

Chromosomal inversions accelerate genetic evolution and drive ecological speciation across an island gradient.

Chromosomal rearrangements are hypothesized to facilitate speciation by suppressing recombination in locally adapted genomic regions, yet how they shape evolutionary rates during rapid divergence remains poorly understood. Here, we investigate the genomic architecture of two sister Carex (Cyperaceae) species on Réunion Island, which rapidly diverged (∼0.5 Mya) to occupy contrasting tropical-montane and dry-subalpine habitats. Using chromosome-level assemblies and population genomics, we show that genomic divergence is not uniform across the genome but is concentrated within specific large-scale inversions. Crucially, genes within these structural variants exhibit significantly accelerated rates of protein evolution, as evidenced by elevated ω, compared to the collinear genome. This is consistent with recombination suppression and subsequent relaxation of purifying selection driving these patterns, which may complement or even outweigh the signal of positive selection. Functional analysis and environmental associations reveal that these "genomic accelerators" include key adaptive loci: Inversions on chromosomes 14 and 28 are enriched for mechanosensitive ion channels and auxin transport, which is consistent with facilitating the interspecific physiological shift to aridity. Partial redundancy analyses reveal that ongoing intraspecific ecological adaptation is highly polygenic across the collinear genome. Our results demonstrate that genomic architecture actively dictates evolutionary speed, suggesting that certain lineages boosted by structural variants may bypass the typical constraints of purifying selection to rapidly exploit vacant ecological opportunities.

A pangenome framework uncovers the role of deletions in repeated evolution of cave-derived traits.

Structural variants (SVs) are increasingly recognized as key contributors to adaptive evolution, yet they remain underexplored compared with single-nucleotide variation. To understand how large-scale genomic changes shape repeated evolution, we leveraged multiple levels of sequence data across the powerful evolutionary model system of the Mexican tetra fish (Astyanax mexicanus). We constructed one of the first pangenome graphs from a naturally evolving vertebrate, enabling comprehensive discovery of SVs among 120 fish from 11 populations. We discover substantial amounts of structural variation and explore the roles of genomic biases and selection in shaping the distribution of these variants. More than 2400 high-confidence cave-specific deletions are enriched in biological pathways involved in vision, metabolism, and behavior and cluster nonrandomly in quantitative trait loci linked to cavefish traits. Additionally, 67 genes harbor unique deletions between independent cavefish lineages. These reused genes show evidence of population-specific selection (99% contain selective sweeps compared with 8%-15% in genes lacking SVs), indicating that deletions likely rose in frequency through repeated positive selection rather than drift. Together, these results reveal that recurrent deletion events have repeatedly contributed to the evolution of cave-adapted phenotypes and highlight deletions as underexplored contributors of adaptive evolution in extreme environments.