| Summary: | Humpback whales undertake long-distance seasonal migrations between low latitude winter breeding grounds and high latitude summer feeding grounds. Although arguably one of the best studied of all baleen whales, there remain some critical gaps in our understanding of their population structure, migratory movement and the mixing of putative populations on the feeding grounds. Addressing these uncertainties is important in the development of demographic models that reconstruct the historical trajectory of population decline and recovery following the cessation of commercial whaling. Utilising both mitochondrial and nuclear genetic markers, this thesis examines the population structure and distribution of humpback whales that migrate to separate winter breeding grounds along the north-western and north-eastern coasts of Australia, and their interaction with the endangered populations of the South Pacific. The project investigated three important gaps in knowledge: population structure among putative breeding populations, the mixing of breeding populations on high latitude Antarctic feeding grounds and evidence for sex-specific migration along the eastern Australian migratory corridor. The thesis also reports the discovery and utility of novel nuclear genetic markers (single nucleotide polymorphisms, SNPs). These markers hold promise for facilitating more effective multi-laboratory collaboration. Among the Australian putative populations, weak but significant differentiation was detected across ten microsatellite loci and mitochondrial control region sequences. This pattern of low level differentiation is emerging as a characteristic of Southern Hemisphere humpback whale populations indicating extensive movement at least historically, if not presently. As the first step towards assessing the mixing of Australian and endangered South Pacific humpback whale breeding populations on the Antarctic feeding grounds, a series of simulations were conducted to estimate the statistical power of both mitochondrial and nuclear microsatellite data from these populations for a mixed-stock analysis (MSA). The results of these simulations confirmed that we can draw robust conclusions from our MSA of Antarctic feeding ground samples collected south of eastern Australia and New Zealand in 2010. Using combined mtDNA and microsatellite datasets revealed substantial contributions from both eastern Australia and New Caledonia, but not western Australia; strengthening emerging evidence that these Antarctic waters are utilized by humpback whales from both eastern Australia and the more vulnerable breeding population of New Caledonia, representing Oceania. There was no compelling evidence for sex-specific migration within the eastern Australian breeding population as indicated by the lack of significant differences detected in the patterns of haplotype sharing, haplotype frequency or haplotype differentiation between males and females. Instead, the significant differentiation revealed between the sexes at the nucleotide level for one sampling location and between sampling locations at the haplotype level suggests that humpback whale migration along eastern Australia may be more complex than previously thought. Increasing the statistical power of our genetic datasets through the addition of new informative markers, including the SNPs discovered in this project, and incorporating non-genetic data, will assist in future studies of the population genetic structure and dynamics of Southern Hemisphere humpback whales.
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