Genetic history and stock identity of beluga whales in Kotzebue Sound

We investigate the recent history and stock identity of beluga whales (Delphinapterus leucas) in Kotzebue Sound in the Chukchi Sea, a region long frequented by large numbers of belugas in summer until their near disappearance in the 1980s. Wide variation in numbers since then suggests a complex recent history that hinders recovery efforts. Analysis of teeth sampled during the historical (pre-decline) era using ancient DNA (aDNA) methods found that the original Kotzebue Sound whales were differentiated for mitochondrial DNA (mtDNA) from other summering concentrations across the Pacific Arctic revealing a demographically distinct subpopulation where long-established migratory culture likely facilitated population divergence. Analysis of microsatellite (nDNA) and mtDNA markers in belugas from the contemporary (post-decline) era revealed that whales from other stocks likely visited Kotzebue Sound, including during two low ice years when relatively large numbers of whales were present. Some mtDNA lineages were found only in Kotzebue Sound, with one recorded in both the historical and contemporary eras. Exclusion tests found a number of whales in Kotzebue Sound during the contemporary era that had nDNA genotypes unlikely to arise in other contemporary stocks in the Pacific Arctic. Our findings indicate that the Kotzebue Sound belugas comprised a unique stock of which a few remnants likely still co-occur with belugas from other larger stocks. We recommend that the US government work through the co-management process to greatly reduce or eliminate the taking of belugas, especially adult females, likely to belong to the Kotzebue Sound stock, until they recover.