Origins of adaptive genomic variation in a wild rodent

Population history is a key yet underexplored determinant of local adaptation. Here, we assess its role by inferring the geographic origin of alleles at climate-associated loci. Using whole-genome data from 151 bank voles (Clethrionomys glareolus) sampled in Britain and four mainland European source populations with ancestry representing the Carpathian and Western refugia, we evaluate the origins of SNPs linked to climate adaptation at 1074 candidate loci. Most SNPs at adaptive loci represent widespread polymorphisms, shared across both European refugia and Britain. However, the larger and older Carpathian refugium contributed more unique SNPs associated with climate adaptation, which are more positively correlated with high temperatures, compared to the smaller contribution of uniquely Western alleles. Together, these results demonstrate that local adaptation is shaped not only by shared ancestral variation but also the distinct evolutionary legacies of individual refugia.