Global conservation genomics of blue whales calls into question subspecies taxonomy and refines knowledge of population structure

Blue whales (Balaenoptera musculus) are the largest living animal and, like other baleen whales, became endangered due to whaling. Here, we used population genomics to infer the number, distribution and other characteristics of subspecies and populations. We used the largest DNA dataset in blue whales, both in terms of genomic markers (16,661 SNPs and mtDNA) and geographic coverage (n = 276 for SNPs; n = 531 for mtDNA). We found greatest divergence among the eastern Pacific, Indo-western Pacific and Antarctic blue whales. There were indications that natural selection in different environments promoted divergence among these groupings. Within these regions, there was divergence between the eastern North and eastern South Pacific, and among the eastern Indian Ocean, the western South Pacific and the northern Indian Ocean. There was no divergence within the Antarctic. These findings are consistent with the current classification of Antarctic and Indo-western Pacific blue whales in the Southern Hemisphere as different subspecies but call into question the subspecies taxonomy of eastern Pacific blue whales. The study shows that opposite breeding seasons on either side of the equator do not necessarily inhibit connectivity across the equator, and reinforces that population structure needs to be well understood to conserve the diversity within species.