Contrasting whole-genome diversity patterns and adaptation in honeybees from two southern European glacial refugia

Human-driven environmental change makes understanding genetic variation essential for protecting keystone species such as the honeybee, <i>Apis mellifera</i>. We compared whole-genome mitonuclear variation in subspecies inhabiting the Iberian and Italian Peninsulas, which have been shaped by distinct glacial histories and modern beekeeping pressures. Italian honeybees showed a stronger anthropogenic imprint, driven largely by recent human-mediated gene flow. Both subspecies showed mitonuclear asymmetry, an approximate south-to-northeast clinal pattern, evidence of ancient or recent admixture with other subspecies and lineages, and genomic signatures of a 20th-century bottleneck. African ancestry was present in both, though ancient and predominantly mitochondrial in Iberia, but recent and predominantly nuclear in Italy. Italian honeybees also had persistently lower historical effective population sizes, lower nucleotide diversity, and higher kinship. Shared and subspecies-specific enriched genes suggest both convergent and unique adaptive responses. These results highlight complex evolutionary dynamics and the significant genetic impact of modern beekeeping.