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    Ecology, epidemiology and evolution of enteric microbes in fragmented populations of the endangered takahe (Porphyrio hochstetteri) : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Veterinary Science at Massey University, Manawatū, New Zealand
    (Massey University, 2015) Grange, Zoe Lorraine
    Pathogenic diseases are increasingly recognised as a challenge to the conservation of wildlife. Complex host-pathogen relationships and transmission dynamics in wild populations can limit our understanding of how pathogens contribute to the decline and endangerment of wildlife. Endangered wildlife populations maintained in reserves present a unique opportunity to investigate wildlife host-microbe relationships in a controlled semi-natural environment where diversity, abundance and the movement of species are restricted. The aim of this study was to investigate the prevalence and molecular differentiation of enteric bacteria carried by endangered takahe (Porphyrio hochstetteri). Through the use of network analysis and molecular epidemiology, the study explored the effects of geographic isolation and translocation on the prevalence, transmission and evolution of Campylobacter and Salmonella spp. within fragmented populations of takahe. Translocation and conservation management has created a dynamic network of takahe populations which vary in their likelihood to maintain and transmit pathogens. My study suggests that range expansion following a significant bottleneck and intensive conservation management of takahe has had unforeseen consequences on microbial diversity. The management of takahe in different environmental settings has influenced the carriage of Campylobacter jejuni and Campylobacter coli. A newly discovered rail-associated Campylobacter sp. nova 1 was prevalent in all populations. However, more discriminatory whole genome analysis of isolates detected a significant biogeographic variation in C. sp. nova 1 genotypes. Possible explanations for the observed pattern include the spatial expansion and isolation of hosts resulting in reduced gene flow of Campylobacter spp. and allopatric speciation, and the presence of heterogeneous environmental attributes or cross-species transmission of Campylobacter spp. from sympatric reservoir hosts. An assessment of vertebrate reservoirs in an island ecosystem indicated cross-species transmission of Campylobacter spp. was not likely to be a factor contributing to the maintenance and phylogeographical distribution of Campylobacter spp. in takahe. This study was the first of its kind to explore microbial dynamics in a large proportion of a well-described but fragmented population of a wild bird. Results suggest historic and current management practices may be having unforeseen influences on enteric microbes, the consequences of which are unknown but could be detrimental to the health of translocated populations of takahe.
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    Diet overlap between coexisting populations of native blue ducks (Hymenolaimus malacorhynchos) and introduced trout (family: Salmonidae) : assessing the potential for competition : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy at Massey University
    (Massey University, 1996) Towers, Dale Jeffery; Towers, Dale Jeffery
    I investigated diet overlap between blue ducks and trout, to assess the possibility that introduced trout (Family: Salmonidae) may be acting as an agent-of-decline on New Zealand's endemic blue ducks (Hymenolaimus malacorhynchos). Blue ducks inhabit fast-flowing rivers and streams. Both rainbow (Oncorhynchus mykiss) and brown trout (Salmo trutta) were liberated into New Zealand's rivers and streams in the 1870s. Stream macroinvertebrates are consumed by both blue ducks and trout raising the possibility that the two animals may compete for food resources. The importance of different prey in the diets of trout and blue ducks was assessed both in terms of numbers of prey consumed and prey dry weight. To analyse each predator's diet in terms of prey dry weight, I developed regression equations for commonly eaten macroinvertebrates. These allowed for the estimation of dry weight from prey head width and body length measurements. A power equation, y = ax b is used to express the relationship. The precision of dry weight estimation varied between taxa ranging between ± 10% and ± 40%. For the majority of taxa, dry weight could be estimated with greatest precision from body length. The relative abundance of macroinvertebrate prey was measured in trout stomachs and faeces of adult blue ducks collected from Tongariro, Manganuiateao, Ikawetea and Makaroro Rivers in 1991/92. Trichoptera and Ephemeroptera larvae were the most abundant macroinvertebrate prey in the diet of blue ducks inhabiting all rivers. Diptera were also consumed in large numbers by blue ducks on Tongariro and Manganuiateao Rivers but were less important than Trichoptera and Ephemeroptera in terms of dry weight. Prey consumed by blue ducks were also of high importance in the diets of trout in all four rivers. A maximum diet overlap value of 0.69 (Schoener's index) was found using numeric data while a maximum value of 0.89 was found when dry weight data were examined. The highest overlap occurred between blue ducks and trout on Manganuiateao River. Blue ducks on all four rivers were found to take macroinvertebrates having a smaller mean body length than that occurring on average in the benthos. Trout were found to consume prey having a larger mean body length than that occurring in the benthos. The body length of prey consumed by trout was positively correlated with trout fork-lengths (rs = 0.49 p < 0.05). However, the mean body length of prey consumed by small trout (FL < 250mm) was significantly larger than that taken by blue ducks (T199 = -2.74 p = 0.007). To test the hypothesis that foraging by rainbow trout alters the composition of the aquatic macroinvertebrate community, data were compared from reaches of river above and below waterfalls on Ikawetea and Makaroro Rivers. Discriminant analysis indicated that the macroinvertebrate communities occurring in sections of river free of trout were not consistently dissimilar from those in sections inhabited by trout. However, an enclosure / exclosure experiment conducted in Tongariro River in April, 1993 found that in the absence of rainbow trout the density of Trichoptera, Ephemeroptera and Plecoptera in the benthos significantly (F2, 33 = 3.615 p = 0.038) increased. In addition, in those enclosures containing trout the density of large macroinvertebrates (body length > 7.1 mm) was less than in enclosures free of trout after 6 days. To examine the response of blue ducks to trout-induced changes in the benthos I conducted an experiment to assess the foraging behaviour of blue ducks in artificial stream channels varying in prey availability. Blue ducks showed a graded response in respect to relative food availability, with a significant correlation between prey density and number of foraging visits to channels (rs = 0.738, p < 0.05). In addition a significant correlation was found between the proportion of total foraging time spent in a channel and the proportion of total insect numbers in that channel (rs = 0.833, p < 0.05). For those endeavouring to develop a strategy to ensure the long term survival of this unique waterfowl my research indicates that where trout and blue ducks coexist resource partitioning may result in little interspecific competition occurring and hence competition appears unlikely to be a principal agent-of-decline of blue ducks.
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    Characteristics of green rimu fruit that might trigger breeding in kakapo : a thesis presented in partial fulfilment of the requirements for the degree of Masters in Zoology at Massey University, Turitea Campus, Palmerston North, New Zealand
    (Massey University, 2010) Cottam, Yvette
    Species living in unpredictable habitats cannot prepare for a regular reproductive year, and must reproduce when conditions are favourable. The timing of reproduction of the seed predators involves anticipating an abundant food supply by tracking cues or triggers which initiate reproduction. These cues are poorly understood. The most supported theory is that a cue or cues is the size or abundance of the developing fruit crop, and possibly involves nutritional compounds in the crop. The rimu (Dacrydium cupressinum) is a masting podocarp tree strongly linked to reproduction in kakapo (Strigops habroptilus). On Codfish Island kakapo only breed in rimu mast years and nesting is timed so chicks hatch when the rimu fruit crop (the sole food source for chicks) is due to ripen. This thesis investigates the theory that some component in unripe rimu fruit is involved in timing of nesting in kakapo. I characterised seasonal changes (over one year) in nutritional components (gross nutrients), polyphenolic compounds and other potential target polyphenolic substances with possible hormonal activity, including isoflavones and antioxidants, during rimu fruit development.A number of the compounds found in rimu fruit are known to affect reproduction in other species and could be potential triggers for reproduction in kakapo. In non-mast years insufficient fruit is available to trigger reproduction and there is no breeding, supporting the idea that the abundance of the fruit crop is also involved in the timing of reproduction. The trigger for breeding in these birds could be ingestion of a threshold level of a trigger substance or substances, or, as in the antbird, it could be entirely visual. The most likely contenders for the trigger in green rimu fruit include increasing levels of crude protein, crude fat, individual fatty acids, dietary fibre (changing the digestibility of other nutrients), calcium, phosphorus, calcium, total polyphenolic content and antioxidant levels, some flavenoids or a combination of these. It is possible that the physiological changes necessary for reproduction are triggered by the abundance of the unripe fruit crop but that nesting itself is triggered by changes in the green, undeveloped fruit associated with ripening.
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    Black-fronted terns and banded dotterels : causes of mortality and comparisons of survival : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Ecology at Massey University, Palmerston North, New Zealand
    (Massey University, 2002) Keedwell, Rachel Jane
    1. The braided rivers of the South Island, New Zealand, provide feeding and breeding habitat for a range of endemic bird species. Many of these species are entirely reliant on braided river habitat for breeding, but because of a reduction in habitat quantity and quality due to weed infestation, hydroelectric power development and water abstraction, and high predation rates by introduced mammals, the survival of many of these bird species is under threat. 2. Predation is the primary cause of mortality for most braided river bird species, but most studies have only measured the effects of predation at the egg stage. In this study. I monitored breeding success of banded dotterels (Charadrius bicinctus) and black-fronted terns (Sterna albostriata) on the Ohau River, South Island, from 1998-2000, and examined the effects of predation on both species. The black-fronted tern is an endangered species about which very little is known, so I also investigated aspects of its breeding biology. 3. I used time-lapse video cameras at 39 nests of banded dotterels and determined that nest monitoring did not affect nest survival rates, nor do predators use human scent trails to locate nests. I attached radio transmitters to 49 banded dotterel chicks to assess rates and causes of mortality, but although a minimum of 18% of chicks were killed by predators, the transmitters did not provide information on the relative importance of the different predator species. Hatching success at 338 banded dotterel nests was 68%, and 48% of hatched nests fledged at least one chick. 4. Hatching success for 1022 black-fronted tern nests was 50.2%, and a minimum of 27.6% of 897 chicks survived through to fledging. Cause of mortality was assessed for 148 chick, juvenile and adult terns, and I found that predators were responsible for 47% of deaths. Feral cats (Felis catus) and Norway rats (Rattus norvegicus) were probably responsible for 19% and 51% of predator related deaths, respectively. Mortality rates remained high immediately after fledging because of predation. Annual adult mortality was estimated at 88-92% but the associated confidence intervals were wide (57-99%). I document aspects of black-fronted tern ecology such as incubation period, fledging period, egg and chick weights, and develop a preliminary method for sexing adult black-fronted terns based on body measurements. I measured black-fronted tern chick growth and survival and found that hatching asynchrony results in lower growth and survival in second hatched chicks. I collated all existing data black-fronted tern populations and from these data estimate that the population size is less than 10 000 but conclude that better data on population size and trends are required. 5. Using population viability analysis models, I compare the survival of banded dotterels and black-fronted terns on the braided rivers. Higher productivity and shorter generation times, rather than any behavioural differences, are probably the key factors that result in stronger population growth for banded dotterels, despite both species being subject to similar levels of predation. Simulations indicate that predator control could be the most effective way to increase black-fronted tern survival. 6. This study provides the first comprehensive record of black-fronted tern breeding biology. I provide evidence that the black-fronted tern population is almost certainly in decline and the species urgently needs further research. In addition, the interrelationships between rabbit (Oryctolagus cunniculus) abundance, predator abundance and nest predation rates are poorly understood and urgently need attention in order to better manage braided river communities and ensure the survival of black-fronted terns and other vulnerable bird species.
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    Hormonal stimulation of ovarian development, ovulation and oviposition in Japanese quail : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Physiology at Massey University, Palmerston North, New Zealand
    (Massey University, 2002) Bennett, Ellen Joan
    Stimulation of ovarian development and ovulation leading to production of fertile offspring using exogenous hormones has been successful in mammals, but until recently this was not the case for avian species. These techniques would be useful for increasing the reproductive output of endangered birds such as the kakapo. Pregnant mare serum gonadotropin (PMSG) was used to stimulate ovarian development in Japanese quail as it is readily available, easy to use, and equally effective as avian gonadotropins. The research examined the best method for administering PMSG, and the doses, duration and frequency of treatment required to stimulate follicular growth. Treatment with PMSG can stimulate ovarian development, ovulation and oviposition in Japanese quail held under a short day photoperiod. However, there was considerable variation in ovarian response to PMSG between birds receiving the same treatment. In birds in which large yellow follicles developed, many follicles were similar in size and were not arranged in a hierarchy. Doses of 20-80 IU PMSG were the most appropriate for stimulating ovarian development in Japanese quail. Doses lower than 20 IU PMSG stimulated little or no ovarian development in most birds, and doses higher than 80 IU PMSG led to overstimulation of follicular development in most birds. Continuous delivery of PMSG by osmotic pumps and daily treatment using injections were equally effective in stimulating ovarian development in Japanese quail. The use of daily injections is a more practical method of delivering PMSG to birds, as it does not involve surgery and allows more control over dosage and timing of treatment. Treating birds with injections of PMSG every two days rather than daily led to a rate of ovarian growth similar to that of long day birds. Treatment every four days was not sufficient to stimulate ovarian development in quail. Restricting the feed intake of quail did not have any affect on the ovarian response to PMSG treatment. Although PMSG can stimulate ovarian development and ovulation in Japanese quail, further work is required to increase the number of birds that respond to treatment, increase the number of eggs produced by an individual, and improve egg quality.
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    Evolutionary genetics and the major histocompatibility complex of New Zealand robins (Petricidae) : a thesis submitted for the degree of Doctor of Philosophy in Molecular BioSciences at Massey University, New Zealand
    (Massey University, 2003) Miller, Hilary C.
    The genes of the major histocompatibility complex (MHC) are highly polymorphic and play a direct role in disease resistance. Loss of variation at MHC loci may increase extinction risk in endangered species, due to an inability to combat a range of pathogens. In this thesis, the evolution of class II B MHC genes is investigated, and levels of variation at these loci are measured in two species of New Zealand robin, the endangered Chatham Island black robin (Petroica traversi), and the non-endangered South Island robin (Petroica australis australis). Transcribed class II B MHC loci from both black robin and South Island robin were characterised prior to analysis of MHC variation. To this end, a non-lethal protocol for isolation of transcribed sequences from blood using 3'RACE and RT-PCR was developed. Four class II B cDNA sequences were isolated from black robin, and eight sequences were isolated from the South Island robin, indicating there are at least four class II B loci. RFLP analysis indicated that all class II MHC loci were contained in a single linkage group. Analysis of 3'untranslated region sequences enabled orthologous loci to be identified in the two species, and indicated that multiple rounds of gene duplication have occurred. A partial genomic DNA sequence of a putative pseudogene was also isolated from the black robin. Evolution of MHC genes in New Zealand robins appears to be influenced by gene conversion and balancing selection, resulting in loss of orthologous relationships in the coding region, and a highly diverse peptide-binding region. In order to assess the effect of population bottlenecks on MHC variation, levels of variation in the extant black robin population, which is descended from a single breeding pair, were compared with artificially bottlenecked populations of South Island robin and their respective source populations. Both RFLP and sequence analysis indicated that the black robin is monomorphic at class II B loci, while both source and bottlenecked populations of South Island robin have retained moderate to high levels of variation. Comparison of MHC variation with minisatellite DNA variation in each population indicated that genetic drift was the predominant force determining MHC diversity in bottlenecked populations in the short-term. Despite its lack of MHC variation, the black robin population appears to be viable under existing conditions. The evolutionary history of New Zealand's Petroica species, investigated by phylogenetic analysis of mitochondrial DNA sequences, is also discussed.
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    Conservation genetics of the world's most endangered seabird, the Chatham Island tāiko (Pterodroma magentae) : a thesis presented in fulfillment of the requirements for the degree of Doctor of Philosophy in Molecular Biosciences at Massey University, Auckland, New Zealand
    (Massey University, 2008) Lawrence, Hayley Ann
    The research field of genetics provides useful tools to investigate the biology of species that are difficult to observe and study and are especially valuable in guiding the conservation of endangered species. The Chatham Island Tāiko (Tchāik, Pterodroma magentae) is the world’s most endangered seabird with an estimated population size of just 120-150 birds, including only 8-15 breeding pairs. This thesis used genetic techniques to investigate aspects of Tāiko biology and relationships in order to aid Tāiko conservation. The mitochondrial cytochrome b gene and duplicated regions of domain I of the mitochondrial control region were DNA sequenced in almost the entire known Tāiko population. The level of genetic variation revealed in Tāiko was unexpectedly high considering endangered species typically exhibit low genetic diversity. Sequencing of ancient DNA from subfossil Tāiko bones allowed an investigation of the past level of genetic variation and the species’ previous geographic distribution. A large proportion of the genetic diversity of the extinct Tāiko populations was retained in the remnant population. However, genetic variation in Tāiko chicks was low, thus genetic diversity in the population could be lost in just a few generations. There are many nonbreeding Tāiko so DNA sexing was used to examine sex ratios in the population. Almost all unpaired birds were male, which signified a potential Allee effect (i.e. that a reduced density of potential mates is decreasing population productivity). Further understanding of the Tāiko mating system and behaviour was obtained by parentage, sibship and pairwise relatedness analyses of genotypes at eight microsatellite DNA loci. It is important that Tāiko are found so they can be protected from introduced predators. The results of mitochondrial DNA sequencing and microsatellite DNA genotyping indicated that there are likely to be more Tāiko breeding in undiscovered areas. Analysis of philopatry using both mitochondrial and nuclear markers can assist conservation by the identification of areas to search for these undiscovered individuals. Tāiko may have once and could still be found on islands near South America since DNA sequencing showed the Magenta Petrel type specimen (collected in 1867 in the South Pacific Ocean) is a Tāiko.