Dempson, J. B. | Search bioRxiv

bioRxiv2025

Large haplotypes linked to climate and life history variation in divergent lineages of Atlantic salmon (Salmo salar)

Advances in sequencing are revealing that linked genomic architectures, enabling the evolution of co-adapted alleles at multiple loci, often shape complex phenotypes. Several recent studies have identified such architectures (e.g., chromosomal rearrangements and supergenes) contributing to adaptation or divergence across diverse species, from plants to mammals. Specifically, within Atlantic salmon (Salmo salar), genomic studies are revealing large haplotypes and structural variants that may underpin local adaptation in the species. Using data from >4000 individuals from 134 locations spanning the North Atlantic Ocean, we identify a large ([~]3-Mbp) genomic region on Ssa18 showing patterns of differentiation and linkage disequilibrium indicative of a large haplotype block containing three divergent haplotypes (herein A, B, and C haplotypes). In Europe, haplotypes A and B were common, whereas A and C were more common within North America, suggesting a shared ancestral A haplotype, with different continent-specific alternative haplotypes. Data support independent origins of divergent haplotypes in each continent, as well as signals of trans-oceanic introgression of haplotypes. Haplotype frequency is strongly associated with latitude, climate, and life history (smolt age); however, the strength and direction of these relationships vary across continents. Overall analyses were consistent with other studies that identify chromosomal rearrangements; however, long read sequence data could not confirm evidence of a structural variant, although an ancestral fusion polymorphism may explain the formation and maintenance of the observed haplotypes. Our study contributes to ongoing efforts to understand the evolutionary role of linked genomic architecture in Atlantic salmon and its significance in salmonid diversification.

genomics↗

bioRxiv2022

Parallel genomic basis of age at maturity across spatial scales in Atlantic Salmon

Complex traits often exhibit complex underlying genetic architectures resulting from a combination of evolution from standing variation, hard and soft sweeps, and alleles of varying effect size. Increasingly, studies implicate both large-effect loci and polygenic patterns underpinning adaptation, but the extent that common genetic architectures are utilized during repeated adaptation is not well understood. Sea age or age at maturation represents a significant life history trait in Atlantic Salmon (Salmo salar), the genetic basis of which has been studied extensively in European Atlantic populations, with repeated identification of large-effect loci. However, the genetic basis of sea age within North American Atlantic Salmon populations remains unclear, as does the potential for a parallel trans-Atlantic genomic basis to sea age. Here, we used a large SNP array and low coverage whole genome re-sequencing to explore the genomic basis of sea age variation in North American Atlantic Salmon. We found significant associations at the gene and SNP level with large-effect loci (vgll3, six6) previously identified in European populations, indicating genetic parallelism, but found that this pattern varied based on both sex and geographic region. We also identified largely non-repeated sweep signatures and sets of highly predictive loci associated with sea age among populations and sexes within North America, indicating polygenicity and low rates of repeated genomic parallelism. Despite low genome-wide parallelism, we uncovered a set of conserved molecular pathways associated with sea age that were consistently enriched among comparisons. Together, our results indicate parallelism of the molecular basis of sea age in North American Atlantic Salmon across large-effect genes and molecular pathways despite population-specific patterns of polygenicity. These findings reveal roles for both contingency and repeated adaptation at the molecular level in the evolution of life history variation.

evolutionary biology↗