Seabirds have become adapted for foraging in an oceanic environment that can be highly dynamic. Oceanographic processes determine the spatial distribution of seabird prey, while seasonality often has a temporal influence on prey availability. In penguins, these factors are reflected in the different species� foraging strategies. Penguins can broadly be categorized as inshore foragers that live in subtropical to temperate regions and profit from a stable food supply throughout the year close to their breeding sites, and offshore foragers that breed in a pelagic environment at higher latitudes where oceanographic processes and seasonality create much more dynamic, temporally limited prey situations. In this light, offshore foragers can be expected to be much more flexible in their foraging behaviour so as to quickly respond to changes in a dynamic marine environment, while inshore foragers are more likely to exhibit predictable foraging patterns. I examined the foraging ecology of two New Zealand penguin species - the offshore foraging Snares penguin Eudyptes robustus and the inshore foraging Yellow-eyed penguin Megadyptes antipodes and how their foraging strategies reflect an adaptation to the marine environment they exploit. Diet composition of breeding Snares penguins (incubation and early chick-guard) was determined using the water-offloading method. Before the chicks hatched, the penguins generally brought little food back from their long foraging trips. During chick-guard, the stomach contents comprised mainly of crustaceans (~55%), fish (~24%) and cephalopods (~21%). However, the presence at times of many fish otoliths and squid beaks suggests that the latter two prey classes may play an even more important role in the adults� diet than the simple percentages based on mass suggest. The penguins� nesting routines were strongly synchronised between the years and correlated with the onset of the spring planktonic bloom. Using GPS data loggers and dive recorders I found that during the incubation phase, male penguins that performed long (ca. 2 week) foraging trips exhibited a strong affinity to forage in the Subtropical Front some 200 km east of the Snares. At that stage (late mid-October) the front featured elevated chlorophyll a concentrations, a pattern that can be observed every year. Thus, it seems that the front represents a reliable and predictable source of food for the male penguins. After the males returned, the female penguins also performed long foraging trips (<1 week) but never reached the front, primarily because they had to time their return to the hatching of their chicks. After the chicks had hatched, the female Snares penguins were the sole providers of food. At this stage, the penguins performed short foraging trips (1-3 days) and foraged halfway between the Snares and Stewart Island (ca. 70-90 km north of the Snares), where nutrient-rich coastal waters flow eastwards to form the Southland Current. The penguins concentrated their diving effort in these waters, underlining the importance of the warm coastal waters as a food source for breeding Snares penguins. However, diving behaviour between 2003 and 2004 differed with penguins searching for prey at greater depths in the latter year. This underlines the Snares penguins� behavioural flexibility in response to a changing marine environment. The Yellow-eyed penguins as typical inshore foragers showed very consistent foraging patterns at all stages. GPS logger deployments on penguins at Oamaru revealed that the birds foraged almost exclusively at the seafloor and targeted specific areas that featured reefs or epibenthic communities. As a result, the penguins� at-sea movements appeared conservative and at times almost stereotypic. Nevertheless, a comparison of Yellow-eyed penguins breeding on the adjacent Codfish and Stewart islands revealed a degree of plasticity in the species� foraging behaviour. Birds from Codfish Island extended their foraging ranges considerably and switched from primarily bottom to mid-water foraging during the post-guard stage of breeding. It seems likely that this switch is a result of enhanced feeding conditions (e.g. increased prey abundance/quality) in an area further away from the island, but the time required to get there renders this strategy not viable when chicks are small and need to be guarded and fed on a daily basis. As such, the change of behaviour represents a traditional pattern rather than a dynamic response to a sudden change in the marine environment. In comparison, penguins from Stewart Island showed consistent foraging patterns during all stages of breeding. Given the high levels of chick starvation on Stewart Island, the lack of plasticity in foraging behaviour is surprising and might indicate that Yellow-eyed penguins find it difficult to react quickly to a sub-optimal food situation. Overall, it seems that Yellow-eyed penguins show a specialisation for a consistent benthic environment and, thus, lack the behavioural flexibility apparent in Snares penguins, which find their food in a changing pelagic marine environment.

Seabirds have become adapted for foraging in an oceanic environment that can be highly dynamic. Oceanographic processes determine the spatial distribution of seabird prey, while seasonality often has a temporal influence on prey availability. In penguins, these factors are reflected in the different species� foraging strategies. Penguins can broadly be categorized as inshore foragers that live in subtropical to temperate regions and profit from a stable food supply throughout the year close to their breeding sites, and offshore foragers that breed in a pelagic environment at higher latitudes where oceanographic processes and seasonality create much more dynamic, temporally limited prey situations. In this light, offshore foragers can be expected to be much more flexible in their foraging behaviour so as to quickly respond to changes in a dynamic marine environment, while inshore foragers are more likely to exhibit predictable foraging patterns. I examined the foraging ecology of two New Zealand penguin species - the offshore foraging Snares penguin Eudyptes robustus and the inshore foraging Yellow-eyed penguin Megadyptes antipodes and how their foraging strategies reflect an adaptation to the marine environment they exploit. Diet composition of breeding Snares penguins (incubation and early chick-guard) was determined using the water-offloading method. Before the chicks hatched, the penguins generally brought little food back from their long foraging trips. During chick-guard, the stomach contents comprised mainly of crustaceans (~55%), fish (~24%) and cephalopods (~21%). However, the presence at times of many fish otoliths and squid beaks suggests that the latter two prey classes may play an even more important role in the adults� diet than the simple percentages based on mass suggest. The penguins� nesting routines were strongly synchronised between the years and correlated with the onset of the spring planktonic bloom. Using GPS data loggers and dive recorders I found that during the incubation phase, male penguins that performed long (ca. 2 week) foraging trips exhibited a strong affinity to forage in the Subtropical Front some 200 km east of the Snares. At that stage (late mid-October) the front featured elevated chlorophyll a concentrations, a pattern that can be observed every year. Thus, it seems that the front represents a reliable and predictable source of food for the male penguins. After the males returned, the female penguins also performed long foraging trips (<1 week) but never reached the front, primarily because they had to time their return to the hatching of their chicks. After the chicks had hatched, the female Snares penguins were the sole providers of food. At this stage, the penguins performed short foraging trips (1-3 days) and foraged halfway between the Snares and Stewart Island (ca. 70-90 km north of the Snares), where nutrient-rich coastal waters flow eastwards to form the Southland Current. The penguins concentrated their diving effort in these waters, underlining the importance of the warm coastal waters as a food source for breeding Snares penguins. However, diving behaviour between 2003 and 2004 differed with penguins searching for prey at greater depths in the latter year. This underlines the Snares penguins� behavioural flexibility in response to a changing marine environment. The Yellow-eyed penguins as typical inshore foragers showed very consistent foraging patterns at all stages. GPS logger deployments on penguins at Oamaru revealed that the birds foraged almost exclusively at the seafloor and targeted specific areas that featured reefs or epibenthic communities. As a result, the penguins� at-sea movements appeared conservative and at times almost stereotypic. Nevertheless, a comparison of Yellow-eyed penguins breeding on the adjacent Codfish and Stewart islands revealed a degree of plasticity in the species� foraging behaviour. Birds from Codfish Island extended their foraging ranges considerably and switched from primarily bottom to mid-water foraging during the post-guard stage of breeding. It seems likely that this switch is a result of enhanced feeding conditions (e.g. increased prey abundance/quality) in an area further away from the island, but the time required to get there renders this strategy not viable when chicks are small and need to be guarded and fed on a daily basis. As such, the change of behaviour represents a traditional pattern rather than a dynamic response to a sudden change in the marine environment. In comparison, penguins from Stewart Island showed consistent foraging patterns during all stages of breeding. Given the high levels of chick starvation on Stewart Island, the lack of plasticity in foraging behaviour is surprising and might indicate that Yellow-eyed penguins find it difficult to react quickly to a sub-optimal food situation. Overall, it seems that Yellow-eyed penguins show a specialisation for a consistent benthic environment and, thus, lack the behavioural flexibility apparent in Snares penguins, which find their food in a changing pelagic marine environment.

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 (<200). These findings suggest that the South Island population was founded by only a small number of individuals, and that subsequent levels of gene flow have remained low. Finally, we present a novel approach to detect errors in historic museum specimen data in cases where a priori suspicion is absent. Museum specimens provide an invaluable resource for biological research, but the scientific value of specimens is compromised by the presence of errors in collection data. Using individual-based genetic analysis of contemporary and historic microsatellite data we detected eight yellow-eyed penguin specimens with what appear to be fraudulently labelled collection locations. This finding suggests errors in locality data may be more common than previously suspected, and serves as a warning to all who use archive specimens to invest time in the verification of specimen data. Overall, yellow-eyed penguins have a remarkable dynamic history of recent expansion, which has resulted in two demographically independent populations. These results reveal that anthropogenic impacts may be far more complex than previously appreciated.