D.Phil. (Geography) / The Infrared Atmospheric Sounding Interferometer (lASI), operational in polar-orbit since 2006 on the European MetOp-A satellite, is the most advanced of its kind in space. It has been designed to provide soundings of the troposphere and lower stratosphere at nadir in a spectral interval of 0.25 em" across the range 645-2 760 em". Fine spectral sampling such as this is imperative in the sounding of trace gases. Since its launch, the routine retrievals of greenhouse, species from IASI measurements have made a valuable contribution to atmospheric chemistry studies at a global scale. The main contribution of this thesis is the development of a new trace gas retrieval scheme for IASI measurements. The goal was to improve on the global operational scheme in terms of the algorithm complexity, speed of calculation and spatial resolution achieved in the final solution. This schemedirectly retrieves column integrated trace gas densities at single field-of-view (FOV) from IASI measurements within a 10% accuracy limit. The scheme is built on the Bayesian framework of probability and based on the assumption that the inversion of total column values, as apposed to gas profiles, is a near-linear problem. Performance of the retrieval scheme is demonstrated on simulated noisy measurements for carbon monoxide (CO). Being a linear solution, the scheme is'highly dependent on the accuracy of the a priori. A statistical estimate of the a priori was computed using a principal component regression analysis with 50 eigenvectors. The corresponding root-mean-square (RMS) error of the a priori was calculated to be 9.3%. In general terms, the physical retrieval improved on the a priori, and sensitivity studies were performed to demonstrate the accuracy and stability of the retrieval scheme under a numberof perturbations. A full system characterization and error analysis is additionally preformed to elicidate the nature of this complex problem. The hyperspectral IASI measurements introduce a significant correlation error in the retrieval. The Absorption Line Cluster (ALC) channel selection method was developed in this thesis, to address the correlation error explicitly. When a first neighbour correlation factor of 0.71 is assumed in the measurement error covariance for the clusters of ALC channels, then most of the correlation error is removed in the retrieval. In conclusion, the total column trace gas retrieval scheme developed here is fast, simple, intuitive, transparent and robust. These characteristics together make it highly suitable for implementation in an operational environment intended for air quality monitoring on a regional scale.

The New Zealand alpine zone has many fleshy-fruited plant species, but now has a relatively depauperate animal fauna. The key question is, therefore, are native alpine plants still being dispersed, if so where to and by what? I first measured fruit removal rates among nine common species using animal-exclusion cages to compare natural fruit removal by all animals, and by lizards only. Over two years, mean percent of fruit removed by early winter ranged from 25–60% among species. Speed of fruit removal also varied depending on species. Secondly, I quantified which animals disperse (or predate) seeds of those fruits, into which habitats they deposit the seeds, and the relative importance of each animal species for dispersal, in two ways. A 2-year study using fixed-area transects to monitor faecal deposition showed that introduced mammals (especially possums, rabbits, hares, sheep, pigs and hedgehogs) were abundant and widespread through alpine habitat. Of the 25,537 faeces collected, a sub-sample of 2,338 was dissected. Most mammals dispersed most (> 90%) seeds intact. However, possums (numerically the important disperser) moved most seeds into mountain beech (Nothofagus solandri) forest, while rabbits, hares, and sheep dispersed seeds mainly into open grassland dominated by thick swards of exotic grasses (e.g. Agrostis capillaris and Anthoxanthum odoratum); all are less suitable microsites. Kea (Nestor notabilis), the largest and most mobile of only three remaining native alpine bird species, are potentially useful as a long-distance seed disperser, even though parrots are typically seed predators. I found that kea are numerically more important than all other birds combined, damage very few seeds, and are probably responsible for most dispersal of seeds between mountain ranges. Finally, I investigated the effects of seed deposition microsite (shady/high-light), pulp-removal (whole/cleaned), competition (soil dug/not-dug) and predation (caged/ not) on germination, growth and survival of eight subalpine plant species. There were strong positive effects of shady microsites for seed germination and seedling survival to 3.5 years for six of the eight species. Effects of other treatments were less important and varied among species and stages. Hence, both native birds and introduced mammals are dispersing alpine seeds, but the mammals often deposit seeds in habitats unsuitable for establishment. Any evaluation of the dispersal effectiveness of frugivores must consider their contribution towards the long-term success for plant recruitment through dispersal quantity and quality.

This thesis presents the results of a series of studies on the epidemiology of TB in brushtail possum and domestic cattle populations in New Zealand. The first set of studies provides an analysis of the results of routine TB testing carried out in the Featherston area from July 1980 to June 2004. The median annual incidence rate of TB reduced from 4.7 cases per 1000 cattle-years at risk for the period 1986 to 1991 to 1.8 cases per 1000 cattle-years at risk for the period 1992 to 2003, coincident with the use of poisoning to control possums in the surrounding forest park (a major possum habitat area). We identified clusters of cattle TB cases adjacent to the forest park and found no evidence of spatio-temporal interaction of TB risk among farms. Our findings support the hypothesis that possums living in the forest park are a source of bovine TB in this area and that farm-to-farm transmission was not an important mechanism of infection spread. A mixed-effects Poisson regression model was developed to investigate the influence of farm-level covariates on the number of cattle confirmed with TB. The model showed that, despite intensification of possum control activities, proximity to forest parks remained a significant predictor of the number of confirmed TB cases per farm per year. Our analyses identified a significant, 3-fold increase in TB risk in dairy cattle relative to beef conditional on the size of local possum habitat, and confirmed the positive influence of cattle population size and the presence of previous infection status as a determinant of the number of confirmed TB cases per farm per year. The second set of studies investigates details of capture events recorded during a longitudinal, capturemark- recapture study of possums in a 22-hectare study site near Castlepoint, from April 1989 to August 1994. Social network analyses were used to identify contact patterns and to estimate the influence of contact on R0 for bovine TB. The average number of contacts per possum ranged from 20 to 26 per year. We estimated that TB would spread if an average of between 1.94 and 1.97 infective contacts occured per year per infected possum. We evaluated the effect of sex, habitat and contact behaviour of 26 postmortem confirmed TB cases in possums with those of 104 matched controls. Unit increases in the number of infected contacts increased the odds of TB infection by 2.61 (95% CI 1.29 – 5.29, P <0.01). Our results show that individual contact behaviour is a determinant of the presence of TB foci within this population and challenge the hypothesis that contact with many individuals increases the probability of infection. A model to predict spatial variation in possum abundance was developed using a Geographic Information System. Details of possum capture events were obtained from 157 10-trap lines distributed within 42 randomly located transects at Molesworth Station. Two GIS-based models were developed to predict the number of possums caught per line using Poisson regression techniques. The first model used remotely sensed environmental data; the second used a combination of remotely sensed and fine-scale data. Both models provided adequate predictive ability with Pearson correlation coefficients greater than 60%. We conclude that the prediction maps produced from this model provide a useful decision support tool for possum control managers. These results have implications for the management of TB in this area of New Zealand, providing the information that will allow effective control activities to be applied at significantly lower cost.

The impacts of possum herbivory were assessed on 713 individual plants of the nationally endangered Pittosporum patulum and 115 individual plants of the threatened ('Gradual Decline') mistletoes (Alepis flavida & Peraxilla tetrapetala) over three years in the Temple and Huxley river valleys in the Ohau catchment, South Island New Zealand. Statistical models were used to test the influence of several explanatory variables on the probability of survival and growth rates of these rare palatable plants. Increasing defoliation levels were the most significant predictors of mortality for both P. patulum and mistletoe, and reduced growth rates in P. patulum. Mortality of P. patulum increased with plant size although smaller plants were also affected by mortality. P. patulum mortality was greater for non-forest habitats, and growth rates were greatest on warm aspects. Mistletoe mortality increased with warm aspect, steeper slopes and at lower altitudes. Plant survival and growth increased in the Temple valley following possum control. Although indicative of a positive treatment effect, other factors may have also influenced this result. Possums are the major herbivore responsible for the widespread decline of P. patulum and beech forest mistletoes throughout New Zealand, although the autecology of P. patulum predisposes it toward extinction more so than mistletoe. Monitoring in conjunction with possum control operations provide good opportunities for understanding the impacts of possums on palatable plants and ecosystems. Assessing defoliation levels on indicator species like P. patulum and mistletoes can serve as a guide for managers to assess ecosystem stress from herbivory.

The eco-epidemiology of bovine tuberculosis (Tb) in wild deer (mainly red deer Cervus elaphus) in New Zealand was investigated. Bovine Tb is caused by Mycobacterium bovis. Specific aims were to clarify the likely routes of infection in deer, and to determine the status of deer as hosts of Tb, the likely rates and routes of inter- and intra-species transmission between deer and other wildlife hosts, the role of deer in spreading Tb, and the likely utility of deer as sentinels of Tb presence in wildlife. As the possum (Trichosurus vulpecula) is the main wildlife host of Tb, the research also included some investigation of transmission routes in possums. Patterns of infection were measured in 994 deer killed between 1993 and 2003. Tb prevalence varied between areas (range 8–36%). Few deer had generalised infection, with 21–68% of infected deer having no visible lesions, depending on the area. The retropharyngeal lymph nodes and oropharyngeal tonsils were commonly infected. No dependent fawns less than 0.75 years old were infected, indicating intra-species transmission is rare in wild deer. Where possums were not controlled, the net (cumulative) force of infection in young (1–4 y) deer was 0.10–0.24 per year in males and 0.09–0.12 per year in females, but much lower in older deer (less than 0.05 per year). Possum control reduced the net force of infection quickly, and eventually to zero. However, Tb persisted in possum-controlled areas through immigration of infected deer and, for almost a decade, through the survival of resident deer infected before possum control. Tb was lost from infected deer at an exponential rate of 0.13 per year, mostly as a result of deer recovering from infection rather than dying from it. Wild deer do die of Tb, but there was no discernible effect on age structure. The occurrence of infection in deer was not linked to the local deer or possum density at their kill sites (i.e. in their home range), but the area-wide prevalence of Tb in deer was closely correlated with Tb levels in possums, which were in turn correlated with area-wide measures of possum density. For wild deer in New Zealand, Tb is a persistent but usually inconsequential disease of the lymphatic system. It is acquired mainly by young independent deer, usually orally via the tonsils, and probably as a result of licking infected possums. Many species fed on deer carrion, including possums. Most possums encountering carrion did not feed on it, but a few fed for long periods. Other scavengers such ferrets (Mustela furo), hawks (Circus approximans), and weka (a hen-sized flightless native bird; Gallirallus australis) fed in a way that probably increased the infectivity of carrion to possums. Commercial deer hunting may have facilitated the historical establishment of Tb in possums. Scavenging (including cannibalism) and interactions with dead and dying possums are identified for the first time as potentially important routes for transmission of Tb to possums, and I develop new hypotheses involving peri- and post-mortem transmission in possums that explain many of the epidemiological patterns that are characteristic of the disease in possum. In continuous native forest, deer home range size averaged 250 hectares for six young females, and over twice that for two males. Over 90% of infected deer are likely to die within 2 km (females) or 6 km (males) of where they acquired Tb, but deer could occasionally carry Tb up to 30 km. Deer will be useful as sentinels, but only where other sentinels are rare, because the force of infection for a deer with a single infected possum in its home range is only 0.004 per year, compared to greater than 0.2 per year for deliberately released pigs. Deer are occasionally capable of initiating new cycles of infection in wildlife, but deer control is not essential to eradicate Tb from wildlife.

Aerial control using 1080 (sodium monofluoroacetate) baits is widely used in New Zealand for the control of introduced brushtail possums (Trichosurus vulpecula), with the aim of protecting national conservation and agricultural values from these damaging pests. This thesis integrates research, completed over 25 years, that was motivated by growing recognition in the 1970s of the extent of possum impacts and the need to improve the effectiveness and efficiency of the control operation. Field research assessed the palatability of three types of cereal-based pellet baits and carrot baits in different regions, habitat types and seasons. Palatability was assessed by the consumption of the different bait types presented independently of each other on 15-30 plots, with rotation of bait types at plots on successive nights to provide equal exposure to each bait type. There was regional variation in possums' bait preferences, possibly reflecting genotypic differences, whereas seasonal variation was less evident. Carrot bait was preferred or equally preferred to cereal bait in 14 out of 20 field trials. The proportion of possums eating baits was then investigated by, firstly, developing a technique for tracing bait acceptance using rhodamine B, a UV-fluorescent dye. In four field trials, more than 95% of possums accepted three types of dye-marked bait, eliminating bait refusal as a major reason for low kills in winter control operations. In a fifth trial, conducted in summer, only 68% of possums accepted bait suggesting that seasonal availability of favoured foods may influence bait acceptance. Since possums must encounter baits before deciding whether to eat them, field studies were undertaken to assess the coverage achieved in normal aerial baiting operations. Large gaps, up to 400 m in width, were often found between baiting swaths; these could allow some possums to survive. A controlled field experiment, using acceptance of rhodamine-dyed bait as a measure of effectiveness, showed that bait distribution was least accurate where flight paths were not marked. Where gaps of 100 m between flight paths were deliberately created, bait acceptance was slower and less than where coverage was complete. Sowing baits at 3 kg/ha was as effective as at 10 kg/ha, indicating the potential for substantially reducing operational costs by using machinery capable of faultlessly distributing baits at low rates. Navigational guidance systems were evaluated and found to improve the accuracy of bait distribution. During 1993-1997, when a lower sowing rate of 5 kg/ha was adopted operationally by regional managers, control effectiveness was unchanged but annual savings of around $9 million accrued. Because of the lack of suitable sowing machinery, a bucket was developed to permit faultless distribution of baits at lower rates, demonstrating the possibility of yet further cost-savings. The possibility of seasonal food availability affecting bait acceptance was investigated in three different forest habitats. Dyed baits were aerially distributed on 100 ha at each site in each season over two years. In each trial, fat-based condition indices of possums were calculated and the abundance of possum-preferred plant foods described. Bait acceptance was consistently high (85-100%) in the 24 trials, and was not influenced by either condition or availability of preferred foods. It seems likely that seasonal variation in operational effectiveness is caused by either the availability of sharply seasonal, scarce foods that possums may feed on intensively for brief periods, or by warmer temperatures that render 1080 less effective. The influence of 1080 on acceptance of (rhodamine-dyed) baits was investigated in a field trial. Examination of possums for dye-marking showed that 25% of possums refused to eat either a lethal quantity of bait or any bait at all, compared with 98% of possums eating non-toxic bait. This indicated that 1080 is aversive to possums, which is a potential major reason for their surviving control operations. Pen trials were therefore conducted to further examine the problem and to seek solutions. Toxic carrot baits were rejected by 27.5% of possums, equally by smell and taste aversion, whereas toxic cereal pellets were rejected by 34%, mainly by taste aversion. Orange and cinnamon were shown to be among the most preferred of 42 flavours tested and, when applied to toxic baits, 1080 was effectively masked. Bait refusal was reduced to ≤7%, the same as that recorded for possums presented with flavoured non-toxic baits. For long-term control of possum populations, aerial 1080 baiting can be used sequentially with other poisoning methods. However, the compatibility of these methods is dependent on the likelihood of possums developing bait shyness if sublethally dosed. Studies were therefore conducted to characterise and compare the four main toxicants used (1080, cyanide, cholecalciferol and brodifacoum) for induction and mitigation of bait shyness. Shyness was induced in approximately 80% of possums sublethally dosed with cyanide, 60% with 1080, 20% with cholecalciferol, and 0% with brodifacoum. Cyanide and 1080 shyness were found to persist in many possums for at least 12 and 24 months, respectively. Use of alternative bait types, and of baits containing an alternative slow-acting toxin (brodifacoum) were shown to be effective ways of overcoming shyness. This, and other related research, is reviewed to provide operational specifications that maximise the likelihood that all targeted possums will (i) encounter bait, (ii) eat it, and (iii) die. The likely future use of aerial 1080 baiting is described and the technological, economic, environmental and social constraints on its sustainability are discussed. Finally, the uptake of the research by possum managers is considered, and areas identified in the thesis where information is incomplete are summarised as prioritised topics for further research.

The eco-epidemiology of bovine tuberculosis (Tb) in wild deer (mainly red deer Cervus elaphus) in New Zealand was investigated. Bovine Tb is caused by Mycobacterium bovis. Specific aims were to clarify the likely routes of infection in deer, and to determine the status of deer as hosts of Tb, the likely rates and routes of inter- and intra-species transmission between deer and other wildlife hosts, the role of deer in spreading Tb, and the likely utility of deer as sentinels of Tb presence in wildlife. As the possum (Trichosurus vulpecula) is the main wildlife host of Tb, the research also included some investigation of transmission routes in possums. Patterns of infection were measured in 994 deer killed between 1993 and 2003. Tb prevalence varied between areas (range 8–36%). Few deer had generalised infection, with 21–68% of infected deer having no visible lesions, depending on the area. The retropharyngeal lymph nodes and oropharyngeal tonsils were commonly infected. No dependent fawns less than 0.75 years old were infected, indicating intra-species transmission is rare in wild deer. Where possums were not controlled, the net (cumulative) force of infection in young (1–4 y) deer was 0.10–0.24 per year in males and 0.09–0.12 per year in females, but much lower in older deer (less than 0.05 per year). Possum control reduced the net force of infection quickly, and eventually to zero. However, Tb persisted in possum-controlled areas through immigration of infected deer and, for almost a decade, through the survival of resident deer infected before possum control. Tb was lost from infected deer at an exponential rate of 0.13 per year, mostly as a result of deer recovering from infection rather than dying from it. Wild deer do die of Tb, but there was no discernible effect on age structure. The occurrence of infection in deer was not linked to the local deer or possum density at their kill sites (i.e. in their home range), but the area-wide prevalence of Tb in deer was closely correlated with Tb levels in possums, which were in turn correlated with area-wide measures of possum density. For wild deer in New Zealand, Tb is a persistent but usually inconsequential disease of the lymphatic system. It is acquired mainly by young independent deer, usually orally via the tonsils, and probably as a result of licking infected possums. Many species fed on deer carrion, including possums. Most possums encountering carrion did not feed on it, but a few fed for long periods. Other scavengers such ferrets (Mustela furo), hawks (Circus approximans), and weka (a hen-sized flightless native bird; Gallirallus australis) fed in a way that probably increased the infectivity of carrion to possums. Commercial deer hunting may have facilitated the historical establishment of Tb in possums. Scavenging (including cannibalism) and interactions with dead and dying possums are identified for the first time as potentially important routes for transmission of Tb to possums, and I develop new hypotheses involving peri- and post-mortem transmission in possums that explain many of the epidemiological patterns that are characteristic of the disease in possum. In continuous native forest, deer home range size averaged 250 hectares for six young females, and over twice that for two males. Over 90% of infected deer are likely to die within 2 km (females) or 6 km (males) of where they acquired Tb, but deer could occasionally carry Tb up to 30 km. Deer will be useful as sentinels, but only where other sentinels are rare, because the force of infection for a deer with a single infected possum in its home range is only 0.004 per year, compared to greater than 0.2 per year for deliberately released pigs. Deer are occasionally capable of initiating new cycles of infection in wildlife, but deer control is not essential to eradicate Tb from wildlife.

Thesis by publication -- 8 co-authored articles. / Thesis (PhD)--Macquarie University, Division of Environmental and Life Sciences, Department of Biological Sciences. / Includes bibliographical references. / Preface -- Management issues of urban common brushtail possums (Trichosurus vulpecula): a loved or hated neighbour -- Effects of deslorelin implants on reproduction in the common brushtail possum (Trichosurus vulpecula) -- Brushtail possums (Trichosurus vulpecula) in metropolotan Sydney: population biology and response to contraceptive implants -- Strategic survey for Toxoplasma gondii and Neospora caninum in the common brushtail possum (Trichosurus vulpecula) from urban Sydney, Australia -- Leptospirosis serology in the common brushtail possum (Trichosurus vulpecula) from urban Sydney, Australia -- Conclusions. / The common brushtail possum (Trichosurus vulpecula) is indeed a common inhabitant of many Australian citites, and one of the few marsupials that has adapted well to the urban environment. Their close proximity to people provides a great opportunity to experience native wildlife in the backyard, however, their utilization of house roofs, bold behaviour and appetite for garden plants often leads to conflict with householders. Population numbers are sufficiently high to require ongoing management to minimise negative impacts for humans and brushtail possums alike in a socially acceptable manner. The aim of this thesis was to identify current management issues and address the need for improved and novel management strategies. The potential of slow-release implants, containing the GnRH agonist deslorelin, as a contraceptive agent for brushtail possums was tested on a captive population. Males appeared resistant to treatment, but deslorelin was found to inhibit reproduction in female brushtail possums for at least one breeding season, making it a promising tool to control fertility in some wild populations. A further aim was to trial deslorelin implants on a wild urban population, to collect more information about the urban biology of this species and to point out issues which have previously not been addressed. Close proximity and interaction of urban brushtail possums with humans and their domestic animals can increase the risk of disease exposure and transmission and influence the health of wild populations. Serosurveys showed that animals were readily exposed to Leptospira spp. and Toxoplasma gondii. This thesis also provides the first data on brushtail possum dispersal in urban areas, knowledge which is highly relevant to the development of management strategies such as fertility control. The findings from this research broaden our knowledge about urban brushtail possums and should assist wildlife authorities in developing alternative or improved management procedures. / Mode of access: World Wide Web. / xxv, 287 p. ill., maps