geneSPLASH: An initial, ocean-wide survey of mitochondrial (mt) DNA diversity and population structure among humpback whales in the North Pacific

We report on initial results of a comprehensive, ocean-wide survey of mitochondrial (mt) DNA diversity and population structure among humpback whales in the North Pacific. Using n = 2,188 samples collected from 10 feeding and 8 breeding regions by the program Structure of Populations, Levels of Abundance and Status of Humpbacks (SPLASH) primarily in the winter and summer of 2004, we first used microsatellite genotyping (average, 9.5 loci) to identify replicate samples within regions and matches between regions. After review for quality control and removal of replicate samples, we identified n = 1,856 regional individuals, 33 of which demonstrated migratory movement between feeding and breeding regions based on genotype matching. Feeding regions showed no overall sex bias in sampled individuals (1.06:1, n = 1031), although a significant departure from unity was found for two regions, the Bering Sea (female bias) and Eastern Aleutians (male bias). Breeding grounds showed a strong overall male bias (2.19:1, n = 825), with the greatest bias found in Mexico-Baja (3.08:1, n = 118). From 500 bp of the mtDNA control region sequence representing each of the n = 1,856 regional individuals, we identified 28 unique haplotypes representing two divergent lineages or clades, one of which is thought to have originated from an historical connection with the Southern Hemisphere. Haplotype frequencies differed markedly among feeding regions (overall FST = 0.179, p < 0.001, n = 1031) and among breeding grounds (overall FST = 0.106, p < 0.001, n = 825), supporting previous characterization of strong maternal fidelity to migratory destinations. Among feeding regions, Russia, southeastern Alaska and California/Oregon, were notable for particularly high levels of differentiation from each other (up to FST = 0.478, p < 0.001). Among breeding regions, Okinawa and the Central American were notable for particularly high level of differentiation from each other (FST = 0.454, p < 0.001) and from most other breeding grounds. However, a comparison between feeding and breeding regions also showed a large number of significant differences, even for those regions known to be strongly connected by patterns of individual migration (e.g., by photo-identification, Calambokidis et al. 2008). Thus the influence of maternal fidelity seems to operate somewhat independently on feeding and breeding grounds over an evolutionary time scale, confounding a simple longitudinal division of the oceanic population into ‘stocks’. The potential to define multiple Genetic Management Units or Units to Conserve, on both feeding grounds and breeding grounds presents the most complex pattern of population structure yet described for large whales.


Baker, C.S., D. Steel, J. Calambokidis, J. Barlow, A.M. Burdin, P.J. Clapham, E.A. Falcone, J.K.B. Ford, C.M. Gabriele, U. Gozález-Peral, R. LeDuc, D. Mattila, T.J. Quinn, L. Rojas-Bracho, J.M. Straley, B.L. Taylor, J. Urbán-R., M. Vant, P. Wade, D. Weller, B.H. Witteveen, K. Wynne and M. Yamaguchi. 2008. geneSPLASH: An initial, ocean-wide survey of mitochondrial (mt) DNA diversity and population structure among humpback whales in the North Pacific. Final report for Contract 2006-0093-008 to the National Fish and Wildlife Foundation. (See also SPLASH summary at Cetacean Conservation Genetics Lab of the Marine Mammal Institute at OSU)

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