Genomic signatures of migratory preference and historical whaling in eastern South Pacific humpback whales

Abstract Understanding the genetic consequences of migratory behavior and drastic population contractions is essential for the conservation of baleen whales. Here, we investigated population structure and demographic history of eastern South Pacific humpback whales using whole genomes across two feeding and one breeding ground. Nuclear genomic analyses revealed no clear population structure between feeding grounds, suggesting high gene flow and panmixia, despite divergent migratory destinations. However, mitogenomic data showed strong clustering of the different feeding grounds, likely reflecting strong female-driven transgenerational tradition in seasonal migration. Demographic reconstructions identified a population expansion after the Last Glacial Maximum and a pronounced recent population decline consistent with industrial unsustainable whaling in the early 20th century. Despite this bottleneck, current genome-wide diversity remains substantial, possibly reflecting the buffering effect of humpback’s long generation time. Nevertheless, the full genetic consequences of this demographic contraction may not yet be apparent and could become evident in subsequent generations.