Genetic connectivity within Eastern Australian humpback whales and their relationship to adjacent South Pacific and Indian Ocean stocks

Humpback whales off the east coast of Australia were heavily exploited by commercial whaling operations. It has been documented in recent years that this population is growing; however, it is considered that still is below preexploitations levels. Here we investigate the genetic diversity of Eastern Australian humpback whales, comparing mitochondrial DNA control region sequence data with that of breeding grounds across the South Pacific (New Caledonia, Tonga, Cook Islands, French Polynesia and Colombia) and eastern Indian (Western Australia) oceans. We compared 156 sequences, representing individual whales sampled off Byron Bay (northbound migration 2002-2003) and Ballina (southbound migration 2003), with 1,112 samples from breeding grounds, comparing a 470 bp fragment of the mtDNA control region consensus sequence. The analysis revealed 42 haplotypes in Eastern Australia, with five unique haplotypes. The Eastern Australian humpback whale haplotype diversity (h) was 0.962 ± 0.005, and the nucleotide diversity (! ) was 2.32 ± 1.18%. These levels were similar to those from the compared breeding grounds, but were significantly different only at haplotype level with New Caledonia, Cook Island, French Polynesia and Colombia breeding grounds. We found significant differences at haplotype and nucleotide levels with all the breeding grounds when a pair-wise AMOVA was performed, except with Tonga at nucleotide level. The genetic differentiation observed here and our previous analyses presented to the SC/IWC support the proposed stock sub-division of the breeding stock E into three sub-stocks, E1 (Eastern Australia), E2 (New Caledonia) and E3 (Tonga). INTRODUCTION The humpback whale (Megaptera novaeangliae Borowski, 1781) is distributed worldwide, with populations in all the major oceans (Kellogg, 1929; Clapham and Mead, 1999). During the last two centuries humpback whales were hunted intensively, especially in the Southern Hemisphere, where it was estimated that the population was reduced perhaps only to a few percent of its pre-exploitation abundance (Chapman, 1974). Based on catch records corrected for illegal Soviet whaling, a total of more than 200,000 humpback whales were killed from 1904 to 2000 (Baker and Clapham, 2002; Clapham and Baker, 2002). The Eastern Australian humpback whale stock, as a result of commercial whaling, declined to levels estimated to be a few hundred individuals by 1962 (Paterson et al., 1994). However, this stock has shown signs of recovery after more than 40 years since the end of commercial exploitation (Paterson and Paterson, 1984;1989; Paterson et al., 1994), with a current estimated abundance of about 7,000 individuals (Noad et al., 2006; Paton et al., 2006). Historically, humpback whales migrating through and/or wintering at Eastern Australia, New Zealand and the western South Pacific islands were considered to form the Group V stock (Mackintosh, 1965). It seemed that these whales spent the summer feeding in Antarctic waters east and west of the Balleny Islands (Mackintosh, 1965), but for management purposes they were considered to form the Antarctic Area V stock, which was limited by 130°E and 170°W, in the Southern Ocean (Donovan, 1991). Recently, under the Comprehensive Assessment of Southern Hemisphere humpback whales, the stock structure of this whale species has been reviewed and this breeding stock (BS) has been re-named E (IWC, 1998). Sub-divisions within this stock have been proposed, but they have not been completely