The chevron skink (Oligosoma homalonotum) is one of the largest, yet least observed skink species in New Zealand. The species was thought to have once been widespread in Northern New Zealand, however currently it is only found on Great Barrier and Little Barrier Islands. Great Barrier Island is the apparent stronghold for the species although it appears to be in decline there, despite a net increase in habitat. Recent studies have increased the understanding of the general ecology of the species, however little is known about the threats to the survival of this species. This study had two main objectives; the first was to establish if rats are a threat to chevron skinks, and the second was to increase current knowledge of the species ecology. The research was undertaken in an area of extensive rodent control (Glenfern Sanctuary) and an adjacent unmanaged reserve in Port Fitzroy, on Great Barrier Island in 2008. The first objective of this study involved confirming that rat densities in the treatment (Glenfern Sanctuary) were sufficiently different to allow meaningful comparisons of chevron skink population characteristics between sites. This was achieved by determining absolute rat densities using Zippin’s removal method at four sites, and correlating these with a relative abundance measure (tracking rates) to give confidence in the observed trends. Rat densities were high (1.94 - 3.00 rats ha-1) in the control, and low (0.00 and 0.06 rats ha-1) in the treatment sites, and these correlated well with tracking rates. In light of these clear differences between the treatment and control, the population structure and condition of chevron skinks were compared between sites. The population structure showed erosion of juvenile and sub-adult size categories, which indicated differences in vulnerabilities between size categories. Physical evidence of failed rat predation was also observed in adult skinks in the unmanaged control, which confirmed that rats were interacting with chevron skinks. Although the adults survived the attacks they suffered injuries including eye damage, punctures, cuts and tail loss. Smaller skinks would be unlikely to survive such attacks due to the severity and scale of the injuries, supporting the assertions of the population structure that smaller skinks may be more vulnerable than adults. The extent of tail loss was converted to a condition index to determine if failed rat predation was more widespread in the population, than was observed by conspicuous injuries. This condition index (body-tail condition index) was stable through all size categories in the treatment, but significantly reduced in adults in the unmanaged sites. That there was no reduction in the condition of smaller skinks in the unmanaged control sites despite high rat densities suggests that interactions between rats and smaller skinks are fatal, and thus not represented in the data. Nine chevron skinks were radio-tracked to determine habitat use, home range and ranging behaviour. Habitat use of chevron skinks was similar to a previous study and demonstrated that trees, crevices and logs were important refuge sites. Chevron skinks were more likely to be found at sites with trees, crevices and debris dams. Chevron skink home ranges indicated that adults moved further away from streams than previously anticipated at this time of year, and skinks demonstrated site fidelity. There was also overlap in home ranges between individuals, and skinks with overlapping home ranges shared common refuges. During flooding events, chevron skinks exhibited an arboreal response that appears to be a behaviour specific to stream associated animals, which allows them to avoid being taken by floodwaters.

The chevron skink (Oligosoma homalonotum) is one of the largest, yet least observed skink species in New Zealand. The species was thought to have once been widespread in Northern New Zealand, however currently it is only found on Great Barrier and Little Barrier Islands. Great Barrier Island is the apparent stronghold for the species although it appears to be in decline there, despite a net increase in habitat. Recent studies have increased the understanding of the general ecology of the species, however little is known about the threats to the survival of this species. This study had two main objectives; the first was to establish if rats are a threat to chevron skinks, and the second was to increase current knowledge of the species ecology. The research was undertaken in an area of extensive rodent control (Glenfern Sanctuary) and an adjacent unmanaged reserve in Port Fitzroy, on Great Barrier Island in 2008. The first objective of this study involved confirming that rat densities in the treatment (Glenfern Sanctuary) were sufficiently different to allow meaningful comparisons of chevron skink population characteristics between sites. This was achieved by determining absolute rat densities using Zippin’s removal method at four sites, and correlating these with a relative abundance measure (tracking rates) to give confidence in the observed trends. Rat densities were high (1.94 - 3.00 rats ha-1) in the control, and low (0.00 and 0.06 rats ha-1) in the treatment sites, and these correlated well with tracking rates. In light of these clear differences between the treatment and control, the population structure and condition of chevron skinks were compared between sites. The population structure showed erosion of juvenile and sub-adult size categories, which indicated differences in vulnerabilities between size categories. Physical evidence of failed rat predation was also observed in adult skinks in the unmanaged control, which confirmed that rats were interacting with chevron skinks. Although the adults survived the attacks they suffered injuries including eye damage, punctures, cuts and tail loss. Smaller skinks would be unlikely to survive such attacks due to the severity and scale of the injuries, supporting the assertions of the population structure that smaller skinks may be more vulnerable than adults. The extent of tail loss was converted to a condition index to determine if failed rat predation was more widespread in the population, than was observed by conspicuous injuries. This condition index (body-tail condition index) was stable through all size categories in the treatment, but significantly reduced in adults in the unmanaged sites. That there was no reduction in the condition of smaller skinks in the unmanaged control sites despite high rat densities suggests that interactions between rats and smaller skinks are fatal, and thus not represented in the data. Nine chevron skinks were radio-tracked to determine habitat use, home range and ranging behaviour. Habitat use of chevron skinks was similar to a previous study and demonstrated that trees, crevices and logs were important refuge sites. Chevron skinks were more likely to be found at sites with trees, crevices and debris dams. Chevron skink home ranges indicated that adults moved further away from streams than previously anticipated at this time of year, and skinks demonstrated site fidelity. There was also overlap in home ranges between individuals, and skinks with overlapping home ranges shared common refuges. During flooding events, chevron skinks exhibited an arboreal response that appears to be a behaviour specific to stream associated animals, which allows them to avoid being taken by floodwaters.

The chevron skink (Oligosoma homalonotum) is one of the largest, yet least observed skink species in New Zealand. The species was thought to have once been widespread in Northern New Zealand, however currently it is only found on Great Barrier and Little Barrier Islands. Great Barrier Island is the apparent stronghold for the species although it appears to be in decline there, despite a net increase in habitat. Recent studies have increased the understanding of the general ecology of the species, however little is known about the threats to the survival of this species. This study had two main objectives; the first was to establish if rats are a threat to chevron skinks, and the second was to increase current knowledge of the species ecology. The research was undertaken in an area of extensive rodent control (Glenfern Sanctuary) and an adjacent unmanaged reserve in Port Fitzroy, on Great Barrier Island in 2008. The first objective of this study involved confirming that rat densities in the treatment (Glenfern Sanctuary) were sufficiently different to allow meaningful comparisons of chevron skink population characteristics between sites. This was achieved by determining absolute rat densities using Zippin’s removal method at four sites, and correlating these with a relative abundance measure (tracking rates) to give confidence in the observed trends. Rat densities were high (1.94 - 3.00 rats ha-1) in the control, and low (0.00 and 0.06 rats ha-1) in the treatment sites, and these correlated well with tracking rates. In light of these clear differences between the treatment and control, the population structure and condition of chevron skinks were compared between sites. The population structure showed erosion of juvenile and sub-adult size categories, which indicated differences in vulnerabilities between size categories. Physical evidence of failed rat predation was also observed in adult skinks in the unmanaged control, which confirmed that rats were interacting with chevron skinks. Although the adults survived the attacks they suffered injuries including eye damage, punctures, cuts and tail loss. Smaller skinks would be unlikely to survive such attacks due to the severity and scale of the injuries, supporting the assertions of the population structure that smaller skinks may be more vulnerable than adults. The extent of tail loss was converted to a condition index to determine if failed rat predation was more widespread in the population, than was observed by conspicuous injuries. This condition index (body-tail condition index) was stable through all size categories in the treatment, but significantly reduced in adults in the unmanaged sites. That there was no reduction in the condition of smaller skinks in the unmanaged control sites despite high rat densities suggests that interactions between rats and smaller skinks are fatal, and thus not represented in the data. Nine chevron skinks were radio-tracked to determine habitat use, home range and ranging behaviour. Habitat use of chevron skinks was similar to a previous study and demonstrated that trees, crevices and logs were important refuge sites. Chevron skinks were more likely to be found at sites with trees, crevices and debris dams. Chevron skink home ranges indicated that adults moved further away from streams than previously anticipated at this time of year, and skinks demonstrated site fidelity. There was also overlap in home ranges between individuals, and skinks with overlapping home ranges shared common refuges. During flooding events, chevron skinks exhibited an arboreal response that appears to be a behaviour specific to stream associated animals, which allows them to avoid being taken by floodwaters.

This project was formulated with the purpose of advancing knowledge of the invasion dynamics of rats within archipelagos in New Zealand. The concentration on islands reflected the conservation focus of this project - islands are the last refuges for many native New Zealand species that cannot survive in the wild on the mainland. This project can be divided into four areas: 1. Data collection: There was no intent for innovation here, but a deeper understanding of the environments in which rats are born, breed, migrate, and die was developed. 2. Development of tools for data exploration: • A user-friendly point-and-click graphical interface for the R program was designed to allow any user to easily explore simple genetic characteristics of the data. • A novel method for exploring the genetic similarity between individuals was developed and showcased with real data, proving successful in cases of both high and low genetic differentiation, and in detecting likely individual migrants. 3. Improvement of a method for estimating migration: • An attempt was made to improve the Markov chain Monte Carlo procedure underlying this method. • The migration model used by the method was significantly improved, so that it could cope with any level of migration. Previously, results from situations where migration rates were high were invalid. 4. Investigated topics of ecological interest: • Field measurements of rats were used to show that Norway rats tend to have larger masses than ship rats, southern rats are generally larger than northern rats, but the effect on mass of living on an island as opposed to the mainland depends on the latitude. It was also shown that relative tail length is a good species discriminator. • Multiple paternity was confirmed for both Norway and ship rats. This breeding characteristic might form part of the explanation for why rats are such successful invaders. During the project, case studies involving rats on Big South Cape Island, Great Barrier Island and in the Bay of Islands were used to highlight the methods developed, and provided some unexpected and fascinating results.

Beaked whales (family Ziphiidae) are one of the least known of all mammalian groups. The majority of species have been described from only a handful of specimens. Found in deep ocean waters, these species are widespread and often sexually dimorphic. Little is known of intra-specific variation in morphology, and many species are very similar in external appearance. A reference database of mitochondrial DNA sequences was compiled for all 20 recognised ziphiid species to aid in species identification. All reference sequences were derived from validated specimens, which were often represented only by bone or teeth. DNA was obtained from this ‘historic’ material using ‘ancient’ DNA methods. For three species, holotypes were sampled. Phylogenetic analyses using this database led to the discovery of a new, previously unrecognised species of beaked whale (Mesoplodon perrini), new specimens of Longman's beaked whale (Indopacetus pacificus), a species known previously from only two partial skulls and the synonymy of a third (M. traversii = M. bahamondi). Phylogenetic reconstructions based on sequence data from three mitochondrial and two nuclear loci (total, 2815 bp) using neighbour joining, parsimony, and maximum likelihood methods, resolved many of the sister-species relationships in this group. Inferred relationships among Mesoplodon beaked whales indicated that cranial and tooth morphology may be far more variable between closely related species than previously assumed. No support was found for a linear-progression of tooth form as suggested by Moore (1968) in his phenetic evaluation of relationships among the Ziphiidae. The geographic distribution of Mesoplodon species with similar or divergent tooth morphology is likely due to a combination of sexual selection and selection for species recognition. Both hypotheses predict similar patterns, such as dissimilar tooth morphology among species with sympatric or parapatric distributions. However, only sexual selection appears to offer an explanation for why there are so many Mesoplodon beaked whales. Investigation of mtDNA diversity among a number of beaked whale species indicated that nucleotide diversity was generally lower in this group than in other wide-ranging oceanic cetaceans. The cause of this low diversity was not clear but may be indicative of overall low abundance. Particularly low levels of diversity were found in Baird's beaked whale Berardius bairdii , Arnoux's beaked whale B. arnuxii and the northern bottlenose whale Hyperoodon ampullatus. Strong geographic structure in haplotype frequencies was observed among a worldwide sample of Cuvier's beaked whales Ziphius cavirostris. / Subscription resource available via Digital Dissertations only.

This project was formulated with the purpose of advancing knowledge of the invasion dynamics of rats within archipelagos in New Zealand. The concentration on islands reflected the conservation focus of this project - islands are the last refuges for many native New Zealand species that cannot survive in the wild on the mainland. This project can be divided into four areas: 1. Data collection: There was no intent for innovation here, but a deeper understanding of the environments in which rats are born, breed, migrate, and die was developed. 2. Development of tools for data exploration: • A user-friendly point-and-click graphical interface for the R program was designed to allow any user to easily explore simple genetic characteristics of the data. • A novel method for exploring the genetic similarity between individuals was developed and showcased with real data, proving successful in cases of both high and low genetic differentiation, and in detecting likely individual migrants. 3. Improvement of a method for estimating migration: • An attempt was made to improve the Markov chain Monte Carlo procedure underlying this method. • The migration model used by the method was significantly improved, so that it could cope with any level of migration. Previously, results from situations where migration rates were high were invalid. 4. Investigated topics of ecological interest: • Field measurements of rats were used to show that Norway rats tend to have larger masses than ship rats, southern rats are generally larger than northern rats, but the effect on mass of living on an island as opposed to the mainland depends on the latitude. It was also shown that relative tail length is a good species discriminator. • Multiple paternity was confirmed for both Norway and ship rats. This breeding characteristic might form part of the explanation for why rats are such successful invaders. During the project, case studies involving rats on Big South Cape Island, Great Barrier Island and in the Bay of Islands were used to highlight the methods developed, and provided some unexpected and fascinating results.

The doctoral studies described in this thesis involve the phenotypic characterization of the tremor rat, an animal model of Canavan disease, and a proof of principle gene transfer study in this model. The phenotype of the tremor rat is examined at the genetic, molecular, cellular, neurochemical, physical and behavioural levels, and tremor mutants are described within the context of Canavan disease. Tremor mutants appear to share many phenotypes with both human patients and to the knock-out mouse model. The deletion of aspartoacylase results in a total loss of the capacity to metabolize N-acetyl-aspartate to acetate and aspartate in brain, leading to elevations in brain N-acetyl-aspartate levels, changes in cell and tissue morphology, and physical and behavioural deficits including mild akinesia and loss of normal motor coordination and balance. Parallel to this work was the development of a gene transfer approach to treat Canavan disease, involving Adeno-associated virus mediated delivery of aspartoacylase to the mammalian central nervous system. Gene transfer was undertaken in tremor rat mutants, and analysis was made of gene expression and function as well as the effect of aspartoacylase expression on improving the phenotypic deficits observed in mutant animals. Gene expression was observed at the RNA and protein level, with recombinant protein observed in cell soma and processes. Although not significant the data suggested a trend of decreased NAA levels after aspartoacylase transfer in comparison to animals injected with a vector encoding green fluorescent protein. Improvement was noted in the rotorod phenotype with mutant animals receiving aspartoacylase gene transfer performing better at tests of balance and coordinated locomotion than animals receiving a control vector. The study provided evidence that Adeno-associated virus mediated aspartoacylase gene transfer to the brain improves some of the deficits in tremor mutants, and supports the rationale of human gene transfer for Canavan disease. / Subscription resource available via Digital Dissertations only.

Light microscopy, low ionic strength solution culture and image analysis methods were used to make detailed measurements on root hair populations of different genotypes of white clover (Trifolium repens L.) and ryegrass (Lolium perenne L.). A model of root hair population structure was developed and validated that will facilitate research on root hairs of these species. Diagrams were drawn of the root hair length and frequency on entire root systems. The distributions of root hairs on these diagrams often differed from textbook diagrams of root hairs because root hair length and frequency varied considerably along the root axis. The key issue examined was the response at species, population and genotype levels of root hair populations perturbed by aluminium and phosphate, and the implications of these responses for our understanding of the strategies adopted by plants growing in stressful environments. Demographic growth analysis gave the best understanding of the mechanisms of root hair population response to genetic variability, resource depletion and environmental perturbation. Root hair length seemed to be controlled by the individual root hair. However the number of root hairs appeared to be controlled by the root. Therefore it is the root that controls the distribution of the hairs on the root, and how this distribution is modified by perturbation. Root hair populations were shown to have strategies that were similar to their shoot system growth strategies-guerrilla for clover, phalangeal for ryegrass. The root and root hair systems, and shoot systems also demonstrated similar characteristics when the r and K strategy model was applied. At an ecosystem level, clover and ryegrass occupied the same orthogonal in the CSR (competitive-stress-ruderal) model. Therefore at a larger scale, these plants are able to coexist, but they do this by having different strategies at a species level. / Subscription resource available via Digital Dissertations only.

Cooperative breeding, widely reported in birds, is found in <1–5% of territories in some populations of the Brown skua, Catharacta lonnbergi. In the New Zealand region, up to 30-50% of skua territories may be occupied by trios or larger groups. This study examines its occurrence at the Chatham Islands, east of New Zealand. Here 16% of territories are occupied by trios and 2% by groups. All members of skua trios and groups participate in sexual and other breeding activity, and the associations arc thus communal. Sexual discrimination of breeding birds by morphometric measurements shows that all communal groups known since 1978-79 have been polyandrous. These groups are long-lived associations, some of which are known to have persisted for at least 14 years. Trios are as long-lived and stable as pairs, and birds on communal territories do not move from them even when an appropriate-sex space becomes available on an adjacent pair territory. The members of trios are not close kin. All members of communal associations participate in territorial defence and chick rearing. In trios, the males appear to be equals, although in any one year the actual paternity of offspring may reside with only one of them. Overall reproductive success for Chatham Island skuas is high, for both pairs and communal groups, compared with other populations. However, communal trios and groups have lower reproductive success than pairs even over a l0 year period, particularly when considered on a per adult basis. Furthermore, no improvement in chick ‘quality’ is discernible. Unusually for skuas, the breeding population at the Chatham Islands is non-migratory. Skuas are present on their breeding territories during the winter, and exhibit characteristic territorial and agonistic behaviours, albeit at lower intensity than during the breeding season. It is suggested that communal breeding in this skua population is not adaptive per se, but a secondary consequence of year-round residence. This is a departure from the conventional resolution of communal breeding. Residence is facilitated by benign climatic conditions and year-round prey availability. When territory space becomes available outside the breeding season, in a small number of cases more than a pair of skuas are able to establish themselves. Thereafter, trios and larger groups persist and behave in the same manner as pairs. The flux between trios and pairs when birds are lost is determined, in part, by the sex of that bird. Thus a trio which loses its one female will ‘acquire’ a replacement female and persist as a trio, whereas a trio which loses one of its two males will thereafter continue as a pair. Keywords: Cooperative breeding, communal breeding, polyandry, Stercorariidae, skuas, skua trios, skua behaviour, skua breeding, Chatham Islands / Chapter 1 previously published as: Cooperative breeding in the Skuas (Stercorariidae): History, distribution and incidence. Journal of the Royal Society of New Zealand 24: 245-260 (1994). Publisher version available at http://www.royalsociety.org.nz/Site/publish/Journals/jrsnz/1994/default.aspx / Chapter 2 previously published as: Winter territory occupation and behaviour of Skuas at the Chatham Islands, New Zealand. Emu 90: 108-113 (1990). Publisher version available at http://www.publish.csiro.au/nid/96.htm / Chapter 3 previously published as: Communually breeding Skuas: Breeding success of pairs, trios and groups of Catharacta lonnbergi on the Chatham Islands, New Zealand. Journal of Zoology, London 218: 393-405 (1989). The definitive version is available at www.blackwell-synergy.com

The population dynamics of juvenile snapper, Pagrus auratus, were investigated in the Hauraki Gulf, north-eastern New Zealand, between 1982 and 1990. Attention focused on age and growth, temporal and spatial variation in abundance, and recruitment. Daily increment formation was validated in the sagittae of snapper up to about 160 days old. Increment width varied with time of year, and snapper age, and increments were not resolvable with a light microscope during winter. Increment counts inside a prominent metamorphic mark showed that larval duration was 18-32 days, and was inversely related to water temperature. Spawning dates were back-calculated from increment counts in settled juveniles, and ranged from September to March with a peak in November-January. The onset of spawning was temperature dependent. Fast-growing snapper had smaller sagittae than slow-growing snapper, indicating an uncoupling of otolith and somatic growth. Snapper gonads differentiated first as ovaries during the second year of life, and then some juveniles changed sex to become males during their third year. Sex change occurred before maturity, so snapper are functionally gonochoristic. Growth was slow during the larval phase, but increased rapidly after metamorphosis to about 0.6-0.9 mm.day-1. From the first winter, growth followed a well-defined annual cycle, with little or no growth during winter, and linear growth of 0.16-0.43 mm.day-1 during spring-autumn for 0+/1+ and 1+/2+ snapper. Snapper grew faster at higher temperatures. Trawl catch rates were affected by numerous gear and environmental factors, but probably provided reasonable estimates of snapper relative abundance. Recommendations are made for improving snapper trawl survey procedures. There was a strong annual abundance cycle in the Kawau region, peaking in spring, and declining to a minimum in winter. Snapper were patchily distributed at a spatial scale of 1-2 km, probably because of preference for specific micro-habitats. Year class strength of 1+ snapper varied 17-fold over seven years, and was strongly positively correlated with autumn sea surface temperature during the 0+ year. The strengths of the 1991 and 1992 year classes are predicted to be below average, and extremely weak, respectively.