Complete Mitochondrial Genomes Provide Evidence of a Killer Whale Refugium Off the Coast of Japan During the Last Glacial Maximum

ABSTRACT Aim During glacial periods, highly mobile species often shifted to warmer, ice‐free regions known as refugia, which frequently maintained higher genetic diversity than newly colonised areas after glacial retreat. We analyse complete mitogenome sequences from 11 killer whale samples in Nemuro Strait to test the hypothesis that waters around Japan may have preserved a refugial population of killer whales that retained historical genetic diversity. Location Western North Pacific. Taxon Orcinus orca ater , Cetacea. Methods Sequencing of complete mitochondrial genomes (16,387 bp) from 11 killer whale samples collected in the Nemuro Strait, southern Okhotsk Sea. Distribution of haplotypes in the social network was visualised using the data on social associations. The probability of individuals belonging to one or more possible reproductive groups was estimated based on 17 microsatellite loci. Results Seven samples shared a haplotype common in the western North Pacific, one had a haplotype previously found only in the eastern North Pacific, and three exhibited novel haplotypes. Killer whales with different haplotypes were connected into a single social network, but some degree of social segregation is evident within the network. No significant genetic clustering based on microsatellite markers was detected between Nemuro Strait and areas near the Kamchatka Peninsula. Main Conclusions With five distinct mitogenomes, Nemuro Strait now ranks second in mitogenomic diversity after the central Aleutian Islands. These findings support the hypothesis of a glacial refugium off Japan preserving a portion of pre‐glacial genetic diversity. The lack of genetic clustering between Nemuro Strait and areas near the Kamchatka Peninsula indicates that all R‐type killer whales in the western North Pacific belong to a single population. The low mitogenomic diversity north of Nemuro Strait likely reflects a founder effect, where a few groups colonised the region after the LGM, while most of the population with higher genetic diversity remained near Japan.