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.

The ability to understand the complex mechanisms by which species communicate has been the focus of study for many years. The Ad��lie penguin (Pygoscelis adeliae) breeds in vocally challenging Antarctic colonies and has evolved a complex system of intra- and intersexual visual and vocal behaviours. Unique to the Ad��lie penguin, is the presence of two distinct display calls, the Loud Mutual Display (LMD) call and male Ecstatic Display Call (EDC). The EDC is used for both mate choice and territory defence; but apart from general structure and function this call remains basically unstudied. Therefore, the aim of this study is to examine the EDC with regard to its function (during mate choice) and variability over time, with location and with changing conditions. It is predicted that the EDC will be an individual call that is distinct from the LMD call. Additionally, the effects of an inclement breeding season on factors that affect breeding success will be examined using a logistic regression approach. The study took place over two breeding seasons(2000/1 & 2002/3) on Ross Island, Antarctica, with the majority of research being conducted at Cape Bird. Results of the study indicate that the EDC is an individual call that cannot reliably be described as a male display as females also give an EDC that is acoustically comparable. The similarities between the EDC and the LMD call seem to relate only to syllabic organisation (structure), as almost every call parameter was different between call types. Furthermore, several call parameters differed between Ross Island colonies. These parameters varied with both geographical location and colony size. In conjunction with variation in call parameters, the health and breeding success of the colonies was different. The stability of call parameters (from Cape Bird) indicated that parameters that separate colonies not only alter between breeding years, but also vary during a single breeding season. The function of the EDC as an honest signal during mate choice was supported by spectral analyses. These analyses found heavier males had significantly lower Frequency Modulation (FM) in the short repeated syllables of their calls than lighter males. Furthermore, a male���s breeding success could be predicted during the early breeding season by the FM. Logistic regression models showed that early male arrival, weight and good nest quality were most influential in predicting fledging success. The logistic regression method also showed that the parameters measured varied in their predictive ability as the season progressed. This study has not only enhanced the wealth of knowledge regarding Ad��lie breeding behaviour and developed our understanding of the vocal repertoire of this species, but also has implications for honest signalling theory, and the evolution and stability of vocal variation at different spatial and temporal scales.

The ability to understand the complex mechanisms by which species communicate has been the focus of study for many years. The Adélie penguin (Pygoscelis adeliae) breeds in vocally challenging Antarctic colonies and has evolved a complex system of intra- and intersexual visual and vocal behaviours. Unique to the Adélie penguin, is the presence of two distinct display calls, the Loud Mutual Display (LMD) call and male Ecstatic Display Call (EDC). The EDC is used for both mate choice and territory defence; but apart from general structure and function this call remains basically unstudied. Therefore, the aim of this study is to examine the EDC with regard to its function (during mate choice) and variability over time, with location and with changing conditions. It is predicted that the EDC will be an individual call that is distinct from the LMD call. Additionally, the effects of an inclement breeding season on factors that affect breeding success will be examined using a logistic regression approach. The study took place over two breeding seasons(2000/1 & 2002/3) on Ross Island, Antarctica, with the majority of research being conducted at Cape Bird. Results of the study indicate that the EDC is an individual call that cannot reliably be described as a male display as females also give an EDC that is acoustically comparable. The similarities between the EDC and the LMD call seem to relate only to syllabic organisation (structure), as almost every call parameter was different between call types. Furthermore, several call parameters differed between Ross Island colonies. These parameters varied with both geographical location and colony size. In conjunction with variation in call parameters, the health and breeding success of the colonies was different. The stability of call parameters (from Cape Bird) indicated that parameters that separate colonies not only alter between breeding years, but also vary during a single breeding season. The function of the EDC as an honest signal during mate choice was supported by spectral analyses. These analyses found heavier males had significantly lower Frequency Modulation (FM) in the short repeated syllables of their calls than lighter males. Furthermore, a male’s breeding success could be predicted during the early breeding season by the FM. Logistic regression models showed that early male arrival, weight and good nest quality were most influential in predicting fledging success. The logistic regression method also showed that the parameters measured varied in their predictive ability as the season progressed. This study has not only enhanced the wealth of knowledge regarding Adélie breeding behaviour and developed our understanding of the vocal repertoire of this species, but also has implications for honest signalling theory, and the evolution and stability of vocal variation at different spatial and temporal scales.

The ability to understand the complex mechanisms by which species communicate has been the focus of study for many years. The Adélie penguin (Pygoscelis adeliae) breeds in vocally challenging Antarctic colonies and has evolved a complex system of intra- and intersexual visual and vocal behaviours. Unique to the Adélie penguin, is the presence of two distinct display calls, the Loud Mutual Display (LMD) call and male Ecstatic Display Call (EDC). The EDC is used for both mate choice and territory defence; but apart from general structure and function this call remains basically unstudied. Therefore, the aim of this study is to examine the EDC with regard to its function (during mate choice) and variability over time, with location and with changing conditions. It is predicted that the EDC will be an individual call that is distinct from the LMD call. Additionally, the effects of an inclement breeding season on factors that affect breeding success will be examined using a logistic regression approach. The study took place over two breeding seasons(2000/1 & 2002/3) on Ross Island, Antarctica, with the majority of research being conducted at Cape Bird. Results of the study indicate that the EDC is an individual call that cannot reliably be described as a male display as females also give an EDC that is acoustically comparable. The similarities between the EDC and the LMD call seem to relate only to syllabic organisation (structure), as almost every call parameter was different between call types. Furthermore, several call parameters differed between Ross Island colonies. These parameters varied with both geographical location and colony size. In conjunction with variation in call parameters, the health and breeding success of the colonies was different. The stability of call parameters (from Cape Bird) indicated that parameters that separate colonies not only alter between breeding years, but also vary during a single breeding season. The function of the EDC as an honest signal during mate choice was supported by spectral analyses. These analyses found heavier males had significantly lower Frequency Modulation (FM) in the short repeated syllables of their calls than lighter males. Furthermore, a male’s breeding success could be predicted during the early breeding season by the FM. Logistic regression models showed that early male arrival, weight and good nest quality were most influential in predicting fledging success. The logistic regression method also showed that the parameters measured varied in their predictive ability as the season progressed. This study has not only enhanced the wealth of knowledge regarding Adélie breeding behaviour and developed our understanding of the vocal repertoire of this species, but also has implications for honest signalling theory, and the evolution and stability of vocal variation at different spatial and temporal scales.

The ability to understand the complex mechanisms by which species communicate has been the focus of study for many years. The Adélie penguin (Pygoscelis adeliae) breeds in vocally challenging Antarctic colonies and has evolved a complex system of intra- and intersexual visual and vocal behaviours. Unique to the Adélie penguin, is the presence of two distinct display calls, the Loud Mutual Display (LMD) call and male Ecstatic Display Call (EDC). The EDC is used for both mate choice and territory defence; but apart from general structure and function this call remains basically unstudied. Therefore, the aim of this study is to examine the EDC with regard to its function (during mate choice) and variability over time, with location and with changing conditions. It is predicted that the EDC will be an individual call that is distinct from the LMD call. Additionally, the effects of an inclement breeding season on factors that affect breeding success will be examined using a logistic regression approach. The study took place over two breeding seasons(2000/1 & 2002/3) on Ross Island, Antarctica, with the majority of research being conducted at Cape Bird. Results of the study indicate that the EDC is an individual call that cannot reliably be described as a male display as females also give an EDC that is acoustically comparable. The similarities between the EDC and the LMD call seem to relate only to syllabic organisation (structure), as almost every call parameter was different between call types. Furthermore, several call parameters differed between Ross Island colonies. These parameters varied with both geographical location and colony size. In conjunction with variation in call parameters, the health and breeding success of the colonies was different. The stability of call parameters (from Cape Bird) indicated that parameters that separate colonies not only alter between breeding years, but also vary during a single breeding season. The function of the EDC as an honest signal during mate choice was supported by spectral analyses. These analyses found heavier males had significantly lower Frequency Modulation (FM) in the short repeated syllables of their calls than lighter males. Furthermore, a male’s breeding success could be predicted during the early breeding season by the FM. Logistic regression models showed that early male arrival, weight and good nest quality were most influential in predicting fledging success. The logistic regression method also showed that the parameters measured varied in their predictive ability as the season progressed. This study has not only enhanced the wealth of knowledge regarding Adélie breeding behaviour and developed our understanding of the vocal repertoire of this species, but also has implications for honest signalling theory, and the evolution and stability of vocal variation at different spatial and temporal scales.

Appendix 4.4 removed due to copyright restrictions: Suepaul, R.B., Alley, M.R., Jansen van Rensburg, M., 2010, Salt gland adenitis associated with bacteria in blue penguins (Eudyptula minor) from Hauraki Gulf (Auckland, New Zealand). Journal of Wildlife Diseases, 46(1) : 46-54. / According to the New Zealand Threat Classification, little blue penguin (LBP) (Eudyptula minor) populations are under ‘gradual decline’. Although long-term data are available for some mainland populations, the status of LBP on offshore islands remains largely unknown. Most studies have focussed on breeding success and foraging ecology. However, there is a paucity of data pertaining to diseases and parasites, and the potential effects of these factors on LBP health, reproductive success and survival. To date, the LBP population on Tiritiri Matangi Island, Hauraki Gulf, Auckland, New Zealand, has only been monitored periodically, despite the island being an important habitat for LBP throughout their annual cycle. The overall aim of this study was to examine the relative importance of parasites and disease in relation to key aspects of LBP life-history, including: the annual cycle; reproductive success; energetic demands, immunity; and mortality. During 2006 and 2007, the reproductive success of LBP on Tiritiri Matangi Island was investigated with respect to lay date, nest site attributes, parental quality and ectoparasite loads. A nest treatment experiment was conducted to explore flea (Parapsyllus longicornis) and tick (Ixodes eudyptidis) effects on breeding success. Overall reproductive output was low, estimated at 33.3%, with an average of 0.67 chicks fledged per pair. Lay date and body condition (BC) appeared to be the main drivers of reproductive success, with early breeders fledging significantly more chicks than late breeders. Increased BC improved reproductive success. Although late breeders exhibited higher BC scores, increased chick mortality indicated that late nests face a reproductive trade-off. Treatment did not prove effective in reducing ectoparasite loads and there was no correlation between ectoparasite abundance in the nest and reproductive success. Throughout their geographic distribution, penguins are host to a range of ectoparasites. Using Ixodes eudyptidis ticks as indicators, ectoparasite-host dynamics were investigated over the course of one year, in relation to LBP life stages, body condition (BC) and haematological parameters. To investigate the presence of vector-borne diseases, blood parasite prevalence was determined using molecular techniques and microscopy. Tick load exhibited significant seasonal variation, being highest during periods of increased host availability i.e. moult and breeding. However, these increases in abundance were not associated with body condition or decreased reproductive success of adults. Nonetheless, LBP exhibited seasonal fluctuations in haematological parameters, with decreases in white blood cell concentrations during periods of increased energy demands and high tick loads. Blood parasite prevalence was low (<1%), determined to be Plasmodium sp. infection. No other blood parasites were found. These results indicate that the lifecycle of I. eudyptidis is tightly linked with that of its LBP hosts, and that infested individuals exhibit physiological responses to tick load. LBP exhibit annual fluctuations in mortality and experience periodic mass mortalities. To examine factors associated with mortality, post-mortems were conducted on 32 LBP from the Hauraki Gulf. Additionally, 128 LBP necropsy records were obtained from the National Wildlife Database (HUIA) for the period spanning April 1993-January 2009, and the causes of mortality were reviewed. Starvation and disease accounted for the highest mortality levels, with 65% of deaths attributed to either one or both of these factors. Furthermore, there was a strong association between starvation and parasites. Parasitic disease and diseases of uncertain aetiology were the most common disease types. In all age groups, the likelihood of infectious, non-infectious and disease of unknown aetiology was significantly higher in LBP that harboured one or more parasite species. Results from this study suggest that starvation and disease, including parasites, are significant factors associated with mortality of LBP in New Zealand, as has been found in Australian LBP populations. Parasites and disease are increasingly recognised as a challenge to the conservation of wildlife, and information regarding endemism of pathogens and parasites within populations is vital for determining ecosystem health, and identifying aberrant diseases.

The management of wildlife tourism has been dominated by ideologies informed by western colonialism and its values of nature. These ideologies, made transparent through communicative and interpretative discourses, influence the way management policies and practices are devised and enacted. The inherent scientific and utilitarian views are supported by a doctrine of separation. This is apparent in the dualism posed, and enacted, between nature and culture that sees humans as being the sole carriers of culture that separates them from the uncultured and uncivilised world of nature into which all other animals, and certainly untamed wildlife, belong. It justifies the use of non-humans for human purposes and continues to allow us to treat non-human animals and other forms of nature in often abominable ways. This thesis investigates two situations in which wildlife tourism occurs in Australia. Fraser Island and Penguin Island are two wildlife tourism destinations on opposite sides of the continent with very different wildlife but some very similar issues. From these two contexts data was collected through interviews, focus groups, participant observation, and from literary and documentary sources. Understanding the empirical data collected from these case studies is facilitated through a social constructionist view of discourse analysis that allows an unpacking of the messages and a stance from which to challenge the dominant ideologies that frame management and interaction. In the thesis I demonstrate that anthropology, in its incarnation as environmental anthropology and as a team player in a necessarily interdisciplinary approach to understanding and resolving environmental issues, has much to offer. This engagement has the potential to enhance not only the sustainable future of naturebased activities like wildlife tourism but also the relevance of anthropology in the postcolonial contemporary world. The need for a holistic framework encompassing all the stakeholders in any wildlife tourism venture is proposed. This approach to wildlife tourism is best serviced by examining perspectives, values and concerns of all members of the wildlife tourism community at any given destination. It is only through this type of holistic and situated focus that we can hope to effectively understand, and then manage, in the best interests of all parties. More specifically, and finally, I argue for a rethinking of the way wildlife tourism interactions are managed in some settings. The ideology of separation, enacted both conceptually and physically to create maintain boundaries, is demonstrated through the two case studies and the ways in which interactions between humans and wildlife are currently managed. An alternative is posed, that by reconstructing management in settings where wildlife tourists may be more accepting of their own responsibility towards nature, a model can be developed that allows people and wildlife to co-exist without ‘killing’ the natural instincts of either.

Animal behaviour is especially sensitive to environmental variability and prey availability during the breeding season, and this is particularly true for non-volant, central place foragers such as the endangered African Penguin (Spheniscus demersus). Individual sex and morphology, as well as the level of assortment within mated pairs can influence both the behaviour and the reproductive success of species exhibiting biparental care. This study made use of a large biometric database and nest attendance video footage to determine the influence of intrinsic (assortative mating, brood size and chick age) and extrinsic (environmental conditions, anthropic disturbance) factors on breeding behaviour and performance of African Penguins on Bird Island, Algoa Bay, during peak breeding (March - July) in 2013. While sexual dimorphism in African Penguins is subtle, the colony-specific discriminant functions presented here provide an accurate sexing tool when only bill and flipper length are available. Despite the premise that selection of a large, high-quality mate in this longlived, monogamous seabird governs lifetime fitness, only low levels of assortative mating were found, and this only for earlier breeders, when larger females (but not males) bred. The 2013 season was a particularly successful one, coinciding with above-average sardine and anchovy abundance, and almost 80 percent of monitored nests were double-brooded, with very low levels of mortality. A- and B-chicks of double broods and singleton chicks grew at similar rates and exhibited similar body condition indices. In these conditions, chick developmental rates were independent of parental size, assortment or provisioning behaviour. Females raising a double brood were significantly lighter and in poorer body condition than those raising a single chick, although the same trend was not evident in males. Offspring sex ratio in 2013 (2.27:1) favoured male chicks, suggesting that there is potential to over-produce the larger sex when resources are plentiful. Peak nest arrival and departure times of parents did not change over the course of monitored breeding attempts (March-June), nor were they different for disturbed and undisturbed nests or for a single or double brood. The increase in CCTV-observed provisioning rate as chicks grew larger was best explained by brood size, at-sea chlorophyll a concentration, and maximum air temperature, but was unrelated to parental morphology or assortative index. Importantly, parental absenteeism commenced earlier and was markedly greater in nests frequently handled by researchers than in undisturbed nests. Both the time spent together by parents, and absenteeism were measurably affected by maximum afternoon air temperatures, the effects of which are expected to be exacerbated by poorer foraging conditions and climate change. A third of manually-monitored nests shared chick-guarding duties unequally, although this phenomenon was independent of parental sex or morphology. The adaptive benefits of mating patterns and division of labour during chick-rearing may only become apparent in a year of below-average food availability and it is highly recommended that this study be repeated in a year of scarce food resources. These findings augment past foraging ecology studies and demonstrate that investigator disturbance and environmental conditions can affect the nesting behaviour of this highly threatened seabird.

King penguins have successfully colonized cold ecosystems of the southern hemisphere by developing physiological mechanisms that are not well understood. The aim of this study was to investigate, at different integrative levels from the gene to the whole animal, the functional responses developed by penguins to overcome polar constrains. We focused on acclimatization mechanisms enabling the first departure to sea of king penguin immatures and the rapid growth of Adélie penguin chicks.To explore differentially expressed genes in pectoralis muscle during penguin’s first sea acclimatization, we used Affymetrix microarrays design for chicken. We first set up and validated a new method to analyze heterologous hybridization transcriptomic profiles. We highlighted a selective shift in metabolic pathways favoring the use of lipids as fuel to sustain highly energetic needs imposed by marine life-style. Our results revealed a development of a global antioxidant response, potential consequences of penguin marine life-style that imposes repeated dives under apnea.Secondly, our integrative study on Adélie penguin’s chick revealed the development of molecular and cellular mechanisms which sustain an original strategy by first allocating most of the energy to growth and then promoting thermogenic processes.Our results showed that both king and Adélie penguins develop complex and coordinated physiological responses to energetic constraints highlighting their high phenotypic plasticity. / King penguins have successfully colonized cold ecosystems of the southern hemisphere by developing physiological mechanisms that are not well understood. The aim of this study was to investigate, at different integrative levels from the gene to the whole animal, the functional responses developed by penguins to overcome polar constrains. We focused on acclimatization mechanisms enabling the first departure to sea of king penguin immatures and the rapid growth of Adélie penguin chicks.To explore differentially expressed genes in pectoralis muscle during penguin’s first sea acclimatization, we used Affymetrix microarrays design for chicken. We first set up and validated a new method to analyze heterologous hybridization transcriptomic profiles. We highlighted a selective shift in metabolic pathways favoring the use of lipids as fuel to sustain highly energetic needs imposed by marine life-style. Our results revealed a development of a global antioxidant response, potential consequences of penguin marine life-style that imposes repeated dives under apnea.Secondly, our integrative study on Adélie penguin’s chick revealed the development of molecular and cellular mechanisms which sustain an original strategy by first allocating most of the energy to growth and then promoting thermogenic processes.Our results showed that both king and Adélie penguins develop complex and coordinated physiological responses to energetic constraints highlighting their high phenotypic plasticity.

The Blue Penguin (Eudyptula minor) is assumed to be declining over much of its range, largely due to introduced predators. Anecdotal evidence suggests that one of the areas of declining population is the West Coast of the South Island. The purpose of this study was to determine the reasons for the assumed decline of blue penguins in South Westland. This was done by studying breeding ecology at several blue penguin colonies to assess the importance of breeding success and adult mortality on the penguin population. Three blue penguin colonies in South Westland, at Five Mile and Three Mile beaches south of Okarito, and at the Wanganui River mouth near Harihari, were monitored throughout the 2008/09 breeding season. During each burrow visit the number of eggs and chicks were recorded as well as the date of laying, hatching or fledging. Five colonies of blue penguin were also monitored in Buller over the same breeding season in a study conducted by the West Coast Blue Penguin Trust, a community trust based on the West Coast. The results of both studies were compared to determine the effect of predator control on breeding parameters, such as breeding success. Of 137 eggs laid in South Westland, 108 chicks survived until fledging, giving an overall breeding success of 78.8%. In Buller, 64 chicks survived to fledging from 101 eggs laid, resulting in an overall breeding success of 63.4%. Breeding success was significantly higher at penguin colonies in South Westland, compared to the Buller colonies. There was no evidence that predator control had an effect on breeding success in South Westland or Buller. The mean number of chicks fledged per pair that produced eggs was 1.55 in South Westland and 1.16 in Buller. The overall proportion of occupied breeding burrows compared to the total number of suitable burrows at the South Westland sites was 73.8% (n = 103). At the Buller sites, only 60.3 % (n = 151) of the total number of burrows was occupied. Road kills are a major threat to blue penguins in Buller due to the proximity of colonies to the state highway. Fortunately, incidences of road death in South Westland are rare and due to the distance from roads, do not pose a significant threat to South Westland blue penguins. Further study of blue penguin colonies in South Westland is needed to learn more about annual variation in breeding productivity and to determine if breeding success is consistently high over an extended time period. If this is the case, then the cause of blue penguin decline on the West Coast is unlikely to be due to problems with breeding as the breeding success during this study is one of the highest recorded for blue penguins. Although there was no apparent effect of predator control on breeding productivity during this study there is evidence from other locations that predators, in particular stoats, have contributed to the decline of blue penguin populations. More research into the impact of predators on penguins over a longer period of time is needed on the West Coast before a change is made to how predators are managed.