ABSTRACT Contact zones, where related taxa breed sympatrically, provide natural laboratories for studying phylogeography and speciation. In migratory species, these systems offer unique opportunities to disentangle the relative roles of genetic and social factors in migratory behaviour. Cory's ( Calonectris borealis ) and Scopoli's shearwaters ( C. diomedea ) are closely related long‐distance migrants that breed allopatrically across most of their ranges but occur sympatrically in the Alboran Sea. Here, we tested whether the migratory strategies of these shearwaters are determined primarily by their genetic ancestry or by the social environment of their breeding colony. We used light‐level geolocators to track the annual migration of 50 individuals (127 tracks) from six breeding colonies: four sympatric colonies within the Alboran contact zone and one allopatric colony of each species. We also generated whole‐genome sequencing data for 58 individuals (including all 50 tracked birds) to infer species ancestry and identify hybrids. Most Cory's shearwaters wintered in subtropical Atlantic upwelling systems along the African and South American coasts, whereas most Scopoli's shearwaters wintered in tropical waters off West Africa. The two taxa partially overlapped in the Sahelian upwelling and Angolan waters. Individuals breeding in the contact zone exhibited migration strategies that matched their genomic ancestry rather than the colony's predominant pattern. Most importantly, we identified seven recent hybrids between the two taxa, representing 17.5% of the sampled individuals in the contact zone. These hybrids exhibited intermediate migratory strategies, indicating a strong genetic determination of migratory behaviour. The overlap in wintering areas may increase opportunities for interspecific interactions before arrival at the breeding colonies, potentially promoting hybridisation. Our study demonstrates that migratory strategies are strongly influenced by genetic background in long‐distance migratory seabirds and suggests that weak migratory connectivity among populations facilitates hybridisation in contact zones.
ABSTRACT India is a major centre of rice diversity, where long‐term cultivation across contrasting environments has generated substantial genomic and phenotypic variation. We analysed genome‐wide SNP variation in 313 Indian rice accessions to resolve ancestry structure, regional diversity, spatial genetic processes, environmental associations and haplotype variation at key domestication and adaptation genes. Population structure analyses resolved eight ancestry groups corresponding to indica , aus , aromatic and japonica lineages. Ancestry explained substantially more genomic differentiation than biogeographic regionalization, while there is extensive historical connectivity among lineages and regions. Genetic diversity considerably varied across biogeographic zones. After balanced resampling, the Himalayan region showed the highest standardized allelic diversity and private‐allele richness, whereas the North‐East region retained high observed heterozygosity and broad ancestry representation. Isolation‐by‐distance was weak overall but strongly lineage‐ and region‐dependent. Spatial principal component analysis identified significant ancestry‐independent broad‐scale genetic gradients, demonstrating geography‐influenced structure beyond lineage composition. Redundancy analysis detected significant genome–environment associations ( F = 3.07, p = 0.001), with climate explaining more independent genomic variation (2.7%) than soil (0.9%). District‐level tribal population proportion showed only a weak negative association with individual heterozygosity (Spearman ρ = −0.155, p = 0.006), although PTP classes exhibited low‐to‐moderate genetic differentiation. Haplotype analysis revealed strong locus‐specific ancestry and geographic structuring at sd1 , Wx , GS3 and DRO1 . Together, the results show that Indian rice diversity is a reticulate genomic mosaic shaped by ancestry, geography, historical gene flow and environmental heterogeneity. This study provides a landscape‐genomic framework for conservation and targeted germplasm utilization in breeding programmes.
ABSTRACT Photopigments, formed by an opsin protein bound to a light‐sensitive chromophore, underlie vertebrate vision. Long‐wavelength–sensitive (LWS) opsins mediate red‐light detection, and most teleosts retain a single functional LWS1. A shorter‐shifted green‐sensitive paralog (LWS2) is found only in a few lineages. By mining teleost genomes and sequencing retinal transcriptomes, we identify elopomorphs as an additional lineage retaining LWS2 (alongside characins and osteoglossomorphs). Surprisingly, we reveal a previously overlooked, shorter‐shifted paralog, LWS3, restricted to gobies (Percomorpha) and arising from an ancestral duplication either in the teleost or in the percomorph ancestor. Structural modelling of twelve LWS opsins reveals convergent evolution at four key amino acid sites (214, 259, 261, 269) in the retinal‐binding pocket, indicating convergent substitutions in human MWS (an old‐world primate‐specific duplicate of the vertebrate LWS1), teleost LWS2, and goby LWS3 relative to red‐sensitive counterparts, consistent with repeated spectral shifts towards greener wavelengths. In several lineages, including characins, mormyrids, gobies, and primates, these shorter‐shifted LWS opsins have at least partially replaced the canonical green‐sensitive RH2‐based visual pigment. Retinal transcriptomes revealed variable lws3 expression across adult gobies, either complementing lws1 in most species, or dominating the visual opsin expression profile as in the sicydiines. In situ hybridisation in the whitebarred goby ( Amblygobius phalaena ; Valenciennes, 1837) showed that lws1 and lws3 are expressed in separate double‐cone members, analogous to rh2 expression in other fish species. Together, these results show that repeated convergence towards shorter LWS sensitivity in vertebrate evolution involves coordinated changes at the molecular, regulatory, and functional levels, providing a striking example of multilevel sensory adaptation.
ABSTRACT As climate change drives rapid environmental shifts, crops face significant challenges due to their limited adaptive genetic diversity, threatening food security. Crop wild relatives and potentially feral populations can serve as valuable reservoirs of adaptive diversity for breeding. Exploring and conserving this diversity is therefore essential, as it may encompass a wide range of adaptations. In this study, we investigate the genetic basis of local climate adaptation and the risk of maladaptation under future conditions in spontaneous populations—naturally occurring in the wild—of Brassica rapa (field mustard). A total of 62 populations were sampled, revealing strong differentiation between feral (France, Slovenia) and wild (Algeria, Sicily) populations. A genome–environment association analysis identified genomic regions associated with climatic variables, with broader patterns suggesting a polygenic architecture. Feral populations broadened the climatic range explored, but their reduced genetic diversity limited our ability to capture the full spectrum of adaptive variation in wild populations, indicating that the genetic architecture of climate adaptation is only partly shared between the two groups. We also used genomic offset (GO) analyses to assess mismatches between current and predicted‐optimal genetic composition under 2050 climate projections. A common garden experiment indicated that GO captures some component of fitness variation, with feral populations providing additional predictive information beyond the environmental space occupied by wild populations. These findings highlight the complex genetic architecture of climate adaptation in B. rapa , as well as the potential and limitations of genomic tools for guiding conservation and crop improvement under climate change.
ABSTRACT The extraordinarily polymorphic Major Histocompatibility Complex (MHC) is an iconic genomic region that has been associated with, for example, disease susceptibility, mate choice, and fitness. Both the MHC class I and II gene families have expanded considerably in songbirds (Passeriformes) compared to other bird orders, but our understanding of the functional relevance of the large number of gene copies in songbirds is hampered by lack of data on gene expression. We therefore took advantage of longitudinal data from our wild long‐term monitored population of great reed warblers Acrocephalus arundinaceus as well as a long‐term experiment to study patterns of MHC class I (MHC‐I) gene expression during individuals' lifetimes and across generations, and between tissues. As could be expected within a species, the expressed diversity increased linearly with genomic MHC‐I diversity. However, most MHC‐I alleles were expressed at low levels, with only a handful of alleles showing moderate to high expression in each individual. The MHC‐I expression patterns in blood were highly consistent (i) over an individual's lifetime, (ii) between parents and offspring, and (iii) among siblings, and (iv) were strongly correlated with expression in other tissues. The moderately to highly expressed MHC‐I genes likely play a key role in antigen presentation in adaptive immunity and thus comprise primary targets for studies of host‐pathogen coevolution.
