Genome-wide SNPs analysis unveils population structure of North Pacific blue whales (Balaenoptera musculus)

Blue whales ( Balaenoptera musculus ) experienced substantial population declines in the 19th and 20th centuries due to commercial whaling and are currently listed as endangered species. As a result, they have attracted considerable scientific interest, not least the species' population structure. While the population structure of blue whales has been intensively studied in the Antarctic and South Pacific, the population structure within the North Pacific remains poorly understood. Acoustic and movement data suggest the presence of at least two distinct populations, but genetic evidence has been lacking due to limited sample availability. This study provides the first comprehensive genetic analysis of blue whales across the North Pacific (NP), using the eastern South Pacific (ESP) as an outgroup. We analysed 12,951 SNPs in 50 specimens (NP: n = 35, ESP: n = 15) and a population-informative subset of 96 SNPs in 60 specimens across the North Pacific (ENP: n = 23, WNP: n = 37), along with 480bp of the mitochondrial control region, to investigate population structure. ADMIXTURE analyses, supported by PCA and DAPC, identified three distinct genetic clusters: one separating the eastern South from the North Pacific and two additional dominant clusters within the North Pacific. These North Pacific clusters exhibited trends of site fidelity, with one primarily associated with the eastern North Pacific and the other with the western North Pacific. Our findings provide strong genetic support for the presence of at least two distinct populations in the North Pacific, highlighting the need for a shift in management perspectives - from a single to a two-stock framework.