Spatial and temporal genetic structuring in yellow-eyed penguins

Improving our understanding of the forces driving population decline and the processes that affect the dynamics of threatened populations is central to the success of conservation management. The application of genetic tools, including our ability to examine ancient DNA, has now revolutionised our ability to investigate these processes. The recent human settlement of the Pacific, particularly in New Zealand, provides a unique, accessible system for revealing anthropogenic impacts on native biota. In this thesis I use genetic analyses from modern, historic and subfossil DNA to investigate temporal and spatial genetic structuring of the endangered yellow-eyed penguin (Megadyptes antipodes), and use these analyses to answer questions related to the conservation of this species. The yellow-eyed penguin is endemic to the New Zealand region and currently breeds on the subantarctic Auckland and Campbell Islands and the southeast coast of the South Island. The current total population size is estimated around 6000-7000 individuals, of which more than 60% inhabit the subantarctic. Despite intensive conservation measures by governmental and local community agencies, population sizes have remained highly unstable with strong fluctuations in numbers on the South Island. The species was believed to be more widespread and abundant before human colonisation of New Zealand, thus current management assumed the mainland population to be a declining remnant of a larger prehistoric population. Genetic and morphological analyses of subfossil, historic and modern penguin samples revealed an unexpected pattern of penguin extinction and expansion. Only in the last few hundred years did M. antipodes expand its range from the subantarctic to the New Zealand mainland. This range expansion was apparently facilitated by the extinction of M. antipodes' previously unrecognised sister species, M. waitaha, following Polynesian settlement in New Zealand. The demise of M. waitaha is the only known human-mediated extinction of a penguin species. Despite M. antipodes' recent range expansion, genetic analyses of microsatellite markers reveal two genetically and geographically distinct assemblages: South Island versus subantarctic populations. We detected only two first generation migrants that had dispersed from the subantarctic to the South Island, suggesting a migration rate of less than 2%. Moreover, the South Island population has low genetic variability compared to the subantarctic population. Temporal genetic analyses of historic and modern penguin specimens further revealed that the harmonic mean effective population size of the M. antipodes South Island population is low (