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.

Certain populations of killer whales Orcinus orca feed primarily or exclusively on marine mammals. However, whether or not baleen whales represent an important prey source for killer whales is debatable. A hypothesis by Springer et al. (2003) suggested that overexploitation of large whales by industrial whaling forced killer whales to prey-switch from baleen whales to pinnipeds and sea otters, resulting in population declines for these smaller marine mammals in the North Pacific and southern Bering Sea. This prey-switching hypothesis is in part contingent upon the idea that killer whales commonly attack mysticetes while they are in these high-latitude areas. In this study, we used photographic and sighting data from long-term studies of baleen whales in 24 regions worldwide to determine the proportion of whales that bear scars (rake marks) from killer whale attacks, and to examine the timing of scar acquisition. The results of this study show that there is considerable geographic variation in the proportion of whales with rake marks, ranging from 0% to > 40% in different regions. In every region, the great majority of the scars seen were present on the whales' bodies when the animals were first sighted. Less than 7% (9 of 132) of scarred humpback whales with multi-year sighting histories acquired new scars after the first sighting. This suggests that most killer whale attacks on baleen whales target young animals, probably calves on their first migration from low-latitude breeding and calving areas to high-latitude feeding grounds. Overall, our results imply that adult baleen whales are not an important prey source for killer whales in high latitudes, and therefore that one of the primary assumptions underlying the Springer et al. (2003) prey-switching hypothesis (and its purported link to industrial whaling) is invalid.

A clear understanding of population structure is essential for assessing conservation status and implementing management strategies. A small, non-migratory population of humpback whales in the Arabian Sea is classified as “Endangered” on the IUCN Red List of Threatened Species, an assessment constrained by a lack of data, including limited understanding of its relationship to other populations. We analysed 11 microsatellite markers and mitochondrial DNA sequences extracted from 67 Arabian Sea humpback whale tissue samples and compared them to equivalent datasets from the Southern Hemisphere and North Pacific. Results show that the Arabian Sea population is highly distinct; estimates of gene flow and divergence times suggest a Southern Indian Ocean origin but indicate that it has been isolated for approximately 70,000 years, remarkable for a species that is typically highly migratory. Genetic diversity values are significantly lower than those obtained for Southern Hemisphere populations and signatures of ancient and recent genetic bottlenecks were identified. Our findings suggest this is the world's most isolated humpback whale population, which, when combined with low population abundance estimates and anthropogenic threats, raises concern for its survival. We recommend an amendment of the status of the population to “Critically Endangered” on the IUCN Red List.

Accurate identification of units for conservation is particularly challenging for marine species as obvious barriers to gene flow are generally lacking. Bryde's whales (Balaenoptera spp.) are subject to multiple human-mediated stressors, including fisheries bycatch, ship strikes, and scientific whaling by Japan. For effective management, a clear understanding of how populations of each Bryde's whale species/subspecies are genetically structured across their range is required. We conducted a population-level analysis of mtDNA control region sequences with 56 new samples from Oman, Maldives, and Bangladesh, plus published sequences from off Java and the Northwest Pacific. Nine diagnostic characters in the mitochondrial control region and a maximum parsimony phylogenetic analysis identified 2 genetically recognized subspecies of Bryde's whale: the larger, offshore form, Balaenoptera edeni brydei, and the smaller, coastal form, Balaenoptera edeni edeni. Genetic diversity and differentiation indices, combined with a reconstructed maximum parsimony haplotype network, indicate strong differences in the genetic diversity and population structure within each subspecies. Discrete population units are identified for B. e. brydei in the Maldives, Java, and the Northwest Pacific and for B. e. edeni between the Northern Indian Ocean (Oman and Bangladesh) and the coastal waters of Japan.