Although humpback whales are among the best-studied of the large whales, population boundaries in the Southern Hemisphere (SH) have remained largely untested. We assess population structure of SH humpback whales using 1,527 samples collected from whales at fourteen sampling sites within the Southwestern and Southeastern Atlantic, the Southwestern Indian Ocean, and Northern Indian Ocean (Breeding Stocks A, B, C and X, respectively). Evaluation of mtDNA population structure and migration rates was carried out under different statistical frameworks. Using all genetic evidence, the results suggest significant degrees of population structure between all ocean basins, with the Southwestern and Northern Indian Ocean most differentiated from each other. Effective migration rates were highest between the Southeastern Atlantic and the Southwestern Indian Ocean, followed by rates within the Southeastern Atlantic, and the lowest between the Southwestern and Northern Indian Ocean. At finer scales, very low gene flow was detected between the two neighbouring sub-regions in the Southeastern Atlantic, compared to high gene flow for whales within the Southwestern Indian Ocean. Our genetic results support the current management designations proposed by the International Whaling Commission of Breeding Stocks A, B, C, and X as four strongly structured populations. The population structure patterns found in this study are likely to have been influenced by a combination of long-term maternally directed fidelity of migratory destinations, along with other ecological and oceanographic features in the region.

Ecosystem function and resilience is determined by the interactions and independent contributions of individual species. Apex predators play a disproportionately determinant role through their influence and dependence on the dynamics of prey species. Their demographic fluctuations are thus likely to reflect changes in their respective ecological communities and habitat. Here, we investigate the historical population dynamics of the killer whale based on draft nuclear genome data for the Northern Hemisphere and mtDNA data worldwide. We infer a relatively stable population size throughout most of the Pleistocene, followed by an order of magnitude decline and bottleneck during the Weichselian glacial period. Global mtDNA data indicate that while most populations declined, at least one population retained diversity in a stable, productive ecosystem off southern Africa. We conclude that environmental changes during the last glacial period promoted the decline of a top ocean predator, that these events contributed to the pattern of diversity among extant populations, and that the relatively high diversity of a population currently in productive, stable habitat off South Africa suggests a role for ocean productivity in the widespread decline.

The migration of Southern Hemisphere humpback whales between their feeding and breeding areas has thus far been considered a highly predictable and seasonal event. However, p revious observations on the humpbacks that pass through the near-shore waters of the west coast of South Africa have revealed deviations from the behaviour and seasonality expected during a typical migration. This "anomaly" is hypothesised to be associated with prey availability in the region. Shore-based observations between July 2001 and February 2003 fro m North Head, Saldanha Bay yielded relative abundances that again did not support a classical migration pattern, with the highest sighting rates from mid-spring through summer. Movement parameters (actual swimming speed, direction and linearity) of humpback groups tracked by theodolite showed mid-spring to be a turning point in their behaviour, after which we observed a significant reduction in actual swimming speed, an increase in 'nondirectional' movement, and a distribution further fro m shore than in other seasons. Additional data on group composition and sex collected between 1993 and 2008, showed a significantly female-biased sex ratio during mid-spring, the first such recorded for any region. Direct observation of feeding on crustacean prey during spring and summer months further supports the notion that humpbacks may have more flexib le forag ing habits than previously appreciated, and that the Southern Benguela upwelling region may function as an important feeding area for these whales.