Population differentiation of humpback whales from far Polynesia (Group F breeding grounds) based on mitochondrial DNA sequences

It has been proposed that South Pacific humpback whales (Megaplera novaeangliae) are divided into three main stocks (E, F and G) based on the distribution of breeding grounds. Recently photo-identification data have shown a limited degree of demographic interchange between adjacent breeding grounds of the western stocks and important segregation with the G stock (Colombia, Eastern Pacific). Here we investigate maternal gene flow among six regional breeding grounds: Western Australia (D stock), New Caledonia (Eiil sub-stock), Tonga (Eii2 sub-stock). Cook Islands (F stock), French Polynesia (F stock) and the Pacific coast of Colombia (G stock). Mitochondrial DNA control region sequences (n = 1069, 447 bp) identified 138 haplotypes defined by 85 polymorphic sites. An analysis of molecular variance (AMOVA, FsT and ^r) showed significant differentiation at both the haplotype and nucleotide level between all the breeding grounds considered in this study, (with the exception of Tonga and the Cook Islands at the nucleotide level, st). This suggests that the Cook Islands and French Polynesia should be considered two stocks, not the single F stock proposed previously. These analyses also indicate that New Caledonia and Tonga should be considered two stocks (Eiil and Eii2), as suggests by recent photo-identification analysis of these two regions. The data were also analysed using Boundary Rank (BR), a geographically constrained clustering method. The results of the BR analysis agreed with the AMOVA results in suggesting that both the stocks E and F may not reflect fully the population structure in the western South Pacific. The extensive data set presented here could be used for an improved allocation of feeding grounds to breeding grounds. A proposal to use genetic assignment test to allocate humpback whales samples from the IDCR/SOWER cruises to South Pacific breeding grounds was submitted and approved two years ago at SC53. To date, these samples have not been received for analysis.