Population structure of Southern Hemisphere humpback whales
The humpback whale was almost driven to extinction by commercial whaling in the Southern Ocean. Little is known about the degree of interchange among the remaining Southern Hemisphere populations. This thesis aimed to assess the connectivity among breeding grounds, feeding areas and migratory corridors of humpback whales using mitochondrial and nuclear DNA markers. The population structure of humpback whale populations in breeding grounds across the South Pacific and eastern Indian oceans was investigated, with an interest in the origins of whales in eastern Polynesia, using an extensive collection of mitochondrial DNA (mtDNA) sequences (n = 1,112; 470 base pairs in length). Samples were obtained from living whales at six breeding grounds: New Caledonia, Tonga, Cook Islands, French Polynesia (Society Islands), Colombia and western Australia. We found significant differentiation, at both the haplotype and nucleotide level, among the six breeding grounds (FST = 0.033; ?ST = 0.022) and for most pair-wise comparisons. The differentiation of the eastern Polynesia
humpback whales is consistent with the hypothesis of a relic subpopulation, rather
than vagrancy or colonization from known neighbouring breeding grounds. Regardless of their origin, it seems probable that islands of eastern Polynesia are now the primary breeding grounds for humpback whales feeding in the management Area VI (170°W – 120°W) of the Antarctic, as defined by the International Whaling Commission.
A population of humpback whales migrates along the western South American coast, with breeding grounds mainly off Colombia and Ecuador and feeding areas off the western coast of the Antarctic Peninsula and in the channels and fjords ofsouthern Chile. We analysed the genetic relationship between humpback whales from these two summer feeding areas of the eastern South Pacific population to assess the potential heterogeneity in the migratory pattern of the population. We compared mitochondrial DNA control region sequences from 132 whales from the Antarctic Peninsula and 52 whales from the Magellan Strait areas. An AMOVA
showed significant differences between the two feeding areas (FST = 0.180; ?ST =
0.169). A phylogenetic analysis showed both areas are represented in the AE clade that is only found in the Southern Hemisphere in the Colombian breeding ground. Genetic and previous demographic data (based on photo-identification) strongly suggest that both feeding areas are related to the same breeding ground but that heterogeneity exists among the feeding areas of this population, similar to that observed in the North Pacific and North Atlantic populations of humpback whales.Humpback whales migrating through eastern Australia and New Zealand have been linked with those breeding off northeastern Australia, New Caledonia, Fiji
and Tonga, forming a single stock (Breeding Stock E). We investigated the relationship between the New Caledonian and Tongan breeding grounds, based on interchange of individual whales (genetically identified) and population genetic differentiation (mitochondrial DNA control region sequences and nuclear DNA microsatellites). We found significantly higher recapture probabilities within each breeding ground compared to the recapture probability between them using
genetic identification, and significant differences at the population level in the FST and ?ST for mitochondrial and nuclear markers. These analyses suggest differentiation among the Breeding Stock E, supporting a proposed sub-stock division for New Caledonia (E2) and Tonga (E3). Historically, humpback whales off New Zealand coasts were caught during their migratory journeys between Antarctic feeding areas and tropical breeding grounds in the South Pacific. Here we investigated the genetic diversity of New Zealand humpback whales, comparing mitochondrial DNA control region sequence data with that from breeding grounds across the South Pacific (New Caledonia, Tonga, Cook Islands, French Polynesia and Colombia) and eastern Indian (western Australia) Oceans. We analyzed 30 samples collected around New Zealand, revealing 20 haplotypes. All haplotypes were found in New Caledonia and some were also found in other breeding grounds. New Zealand humpback whale haplotype diversity and nucleotide diversity were similar to those from the compared breeding grounds, but were significantly different at haplotype level
from the Cook Islands, French Polynesia and Colombia breeding grounds. We found significant differences at haplotype level with the same three locations when a pair-wise AMOVA was performed. Three breeding grounds (western Australia, New Caledonia and Tonga) did not show significant differences at either nucleotide or haplotype levels. This genetic evidence and the available demographic data suggest a closer relationship of the New Zealand stock with New Caledonia and to a lesser extent with Tongan whales, supporting New Zealand as a primary migratory corridor for the humpback whales breeding in these western Pacific Islands.