Population genetic structure among feeding aggregations of humpback whales in the Southern Ocean

Humpback whales (Megaptera novaeangliae) undertake seasonal migrations between low-latitude breeding grounds in winter and high-latitude feeding grounds in summer. In the Southern Hemisphere, seven primary breeding stocks have been identified based on tropical distribution between which there is limited gene flow. In the summer, these stocks are distributed among six Management Areas (Areas I–VI) defined by the International Whaling Commission in the Southern Ocean feeding grounds. The extent to which different breeding stocks mix on these feeding grounds, and the genetic structure and relationships between them, remains unclear. This uncertainty has led to the review and development of hypotheses to refine stock boundaries in the Antarctic. This study is the first to analyse the circumpolar genetic structure of humpback whales in their feeding aggregations. Sequences of the mitochondrial control region and microsatellite DNA variation were obtained for 399 humpback whale samples, obtained within the six Antarctic Management Areas. Results from both sets of markers were consistent in showing a complex pattern of differentiation between feeding aggregations across the feeding range. Management Area I surrounding the Antarctic Peninsula, associated with Breeding Stock G in the south-eastern Pacific Ocean, was highly differentiated from all other feeding aggregations, suggesting strong fidelity towards the Peninsula. In contrast, adjacent feeding grounds showed much lower levels or no significant differentiation, suggesting interchange of individuals and overlap of breeding stocks on their summer feeding grounds. These results have important implications from the perspective of conservation and management, as failure to recognize overlapping distributions may result in misleading estimates of abundance and growth trends of particular recovering humpback whale populations.We thank K.P. Findlay and P.B. Best for helping to develop the original request to access the IDCR SOWER samples. We also thank INACH for providing funding and support in the AP surveys. We thank A. Larrea, L. Medrano, E. Pérez and P. Acuña for field assistance. We thank M. Leslie, C. Pomilla, J. Murrell, D. Steel, A. Hickey and S. Lavery for assistance in the laboratory. We also thank F. Kershaw for the map presented in Fig. 1. Laboratory analysis was supported by a Marsden Fund grant to C.S. Baker for INAC and GLOBEC samples; all other laboratory analyses were supported by grants to HCR. C. Olavarría was supported by a University of Auckland International Doctoral Scholarship and a scholarship from Fundación CEQUA. A.R. Amaral is supported by a Grant (SFRH/BPD/79002/2011) from the Portuguese Science Foundation