Abstract
We develop a general framework for analysing and testing genetic structure within a migratory assemblage that is based on measures of genetic differences between individuals. We demonstrate this method using microsatellite DNA data from the Bering‐Chukchi‐Beaufort stock of bowhead whales ( Balaena mysticetu s), sampled via Inuit hunting during the spring and autumn migration off Barrow, Alaska. This study includes a number of covariates such as whale ages and the time separation between captures. Applying the method to a sample of 117 bowhead whales, we use permutation methods to test for temporal trends in genetic differences that can be ascribed to age‐related effects or to timing of catches during the seasons. The results reveal a pattern with elevated genetic differences among whales caught about a week apart, and are statistically significant for the autumn migration. In contrast, we find no effects of time of birth or age‐difference on genetic differences. We discuss possible explanations for the results, including population substructuring, demographic consequences of historical overexploitation, and social structuring during migration.