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    Applying structured decision making for large-scale wildlife management programmes : Project Janszoon as a case study : a thesis presented in partial fulfilment for the degree of Doctor of Philosophy in Conservation Biology at Massey University, Palmerston North, New Zealand
    (Massey University, 2024-11-30) Kenup, Caio
    Managing threatened populations is challenging due to the delicate balance between urgency and uncertainty. While swift action is often needed to prevent further decline or extinction, significant uncertainty frequently surrounds the effectiveness of various management strategies and the future trajectory of populations. This uncertainty complicates the identification of the most effective course of action, especially when resources are limited. Structured decision making (SDM) is an approach that supports informed decision making in the face of uncertainty in conservation projects. The primary aim of this thesis is to develop a decision making framework for Project Janszoon’s bird translocations, guiding management and monitoring decisions to maximise establishment and persistence probabilities for the kākā (Nestor meridionalis) and pāteke (Anas chlorotis). This framework can serve as a blueprint for implementing SDM and adaptive management (AM), promoting their broader use in conservation initiatives within New Zealand and beyond. In Chapter 2, I discuss expert elicitation techniques for generating predictions from expert knowledge while accounting for epistemic uncertainty. Numerical improvements in handling elicited data are proposed, focusing on aggregating and transforming expert-provided values while maintaining their associated uncertainty. Preserving this uncertainty is critical to avoid generating overconfident predictions from expert judgment. In Chapter 3, I explore which uncertainties are worth reducing and to what degree. Value of information (VOI) analysis offers a way to understand how reducing uncertainty affects decision making and conservation outcomes. A key insight from this chapter is that while monitoring is valuable for reducing uncertainty, such reductions do not always improve conservation outcomes. Beyond a certain point, further reductions in uncertainty do not alter decision making. Practitioners must estimate the optimal level of monitoring for each conservation challenge. In Chapter 4, I outline a passive adaptive management framework to reduce uncertainty as management actions are implemented and monitored. The framework’s extendable nature makes it adaptable to other management problems. The tools and concepts presented here are valuable assets for effective decision making for managed populations under uncertainty.
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    Understanding the variations in grazing and rumination behaviours and their associations with production parameters in individual grazing dairy cows : a thesis presented in partial fulfilment of the requirements of the degree of Doctor of Philosophy in Animal Science at Massey University (Manawatū) New Zealand
    (Massey University, 2023) Iqbal, Muhammad Wasim
    This thesis aimed to understand: 1) the accuracy of an accelerometer-based sensor to monitor grazing and rumination behaviours in dairy cows; 2) grazing and rumination behaviour patterns and time budgets over 24 hours; 3) potential factors to influence grazing and rumination behaviours; and 4) effects of grazing and rumination behaviours on production parameters. To do this, data including, but not limited to, grazing time, rumination time, measures of cow performance (e.g., milk production and composition, body weight and body condition score), days in milk, and breeding worth index of 162 grazing dairy cows were collected for three consecutive lactation seasons (2018-2021). The analysis was performed on individual study years and results were reported separately for each year. First, the accuracy of AfiCollar, an accelerometer sensor-based automated device to monitor and record grazing and rumination behaviours in dairy cows was evaluated for a grazing-based system. Spring-calved lactating cows (n = 48) wearing AfiCollar were continuously visually observed for 8 hours (9 am to 5 pm) to quantify minutes per hour spent grazing and rumination. The behaviours being observed were also recorded with the AfiCollar and compared with visual observations using Pearson’s correlation coefficient (r), concordance correlation coefficient (CCC), and linear regression. A strong association was found between the data collected by AfiCollar and the data obtained through visual observation for grazing time (r = 0.91, CCC = 0.71) and rumination time (r = 0.89, CCC = 0.80) with a significant linear relationship between both datasets (p<0.05). Furthermore, variations in the temporal patterns (min/h) and time budgets (% min/day) of grazing and ruminating behaviours recorded using AfiCollar were evaluated in spring calving lactating (n = 162) Holstein-Friesian (HFR), Jersey (JE), and Holstein-Friesian Jersey crossbreed (KiwiCross, KC) cows in their different lactations (1st, 2nd, 3rd, 4th), and with different breeding worth index values (103151). A repeated measure design was performed in SAS using PROC MIXED considering the fixed effects of breed and lactation, the random effect of individual cows, and hours of the day as repeated measure to evaluate their effects on hourly patterns and time budgets of grazing, rumination, and idling behaviours. Regardless of the seasonal variations and feed consumed, cows spent most of their daytime grazing (with peaks around dawn and dusk) and most of their nighttime ruminating. Grazing and ruminating patterns were similar between cows from different breeds and lactations, however, JE cows grazed slightly longer than HFR and KC cows; and first-lactation cows grazed slightly longer than mature cows in their later lactations. The onset and cessation of grazing activity by the cows were adjusted according to varying day lengths by season. In addition, a general linear (PROC GLM) mixed model was fitted to test the effects of days in milk, breeding worth, breed, lactation year, individual cow, season, feed, and their interactions on variations in grazing time, rumination time and their relationship. Results indicated that grazing time varied among breeds in Year-2 and Year-3 and among lactation years in Year-1. Rumination time differed between breeds in only Year-3, and it remained the same within lactation years. Grazing time and rumination time varied among different seasons that were related to varying supplementary feeds. Days in milk, breeding worth (except Year-3), and the individual cow had effects (P<0.05) on grazing and rumination times. Grazing time and rumination time had a negative relationship with each other that varied between different seasons but remained the same among different breeds and lactation years. The variance in grazing and rumination times was mostly explained by individual cows (up to 24%), season (up to 12%), and feed (up to 8%). Moreover, results also showed that grazing and rumination times had positive associations with milk yield, fat, protein, and solids. Grazing time had negative and rumination time had positive associations with liveweight, while both grazing time and rumination time had negative associations with body condition score. Grazing time explained up to 1%, and rumination time explained up to 7% of the variance in milk yield, milk fat, protein, and solids. AfiCollar can reliably monitor grazing and rumination behaviours in dairy cows, however, its accuracy can be improved for a grazing-based system. The animal itself, the season, and the feed are the potential sources of variation in grazing and rumination behaviours and should be considered for management decisions to address the animal’s behavioural requirements. Grazing and rumination behaviours are moderately correlated with performance parameters and explain a small proportion of variance in animal productivity.
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    Mangrove-avifauna relationships in Aotearoa New Zealand : conservation insights from banded rail (Gallirallus philippensis) ecology : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Conservation Biology at Massey University, Auckland, New Zealand
    (Massey University, 2023) de Satgé, Jacques
    Among terrestrial vertebrates, birds are the most ubiquitous taxa in mangroves globally, using these habitats to breed, roost, and forage. However, within the past half century, the large-scale loss and fragmentation of mangrove forests throughout much of their distribution has corresponded with declines in populations of mangrove-using avifauna. Despite these declines, remarkably little is known about the avifauna that inhabit mangrove forests, nor the ecological relationships that exist between birds and mangrove habitats. The absence of this understanding presents a significant barrier to effective avifauna conservation in mangrove environments. The ecological relationships between the banded rail (Gallirallus philippensis assimilis) and mangroves (Avicennia marina var. australasica) in Aotearoa New Zealand are poorly understood, reflecting a lack of scientific research addressing mangrove avifauna globally. The study of banded rails has been hindered by their cryptic behaviours and exacerbated by mangroves being logistically challenging habitats to work in because of their intertidal nature, dense vegetation, and muddy substrates. The paucity of research in this field is a concern given that New Zealand’s population of banded rails – largely restricted to mangroves in the coastal and estuarine regions lining the northern shores of the North Island – is declining and categorised as ‘at-risk’ of extinction. Mangroves in New Zealand are globally anomalous, having expanded rapidly in recent decades and having been subject to intensive management predicated on vegetation removal. In this context, understanding the importance of mangrove habitats for banded rails is of ecological interest and conservation concern. This thesis elucidates the ecological relationships between banded rails and mangroves in the context of recent mangrove expansion and contemporary management practices (especially in terms of removals) in New Zealand by (1) reviewing mangrove management practices and their effects on avifauna, (2) determining the relative habitat quality of mangroves for banded rails, (3) establishing and implementing a reliable survey method for banded rails, and (4) quantifying banded rail habitat selection and use in saltmarsh-mangrove complexes of northern New Zealand. First, to understand the extent, configuration, and repercussions of mangrove removal in New Zealand, I reviewed all legal mangrove removals until 2020, using resource consent documents from relevant regional authorities. I determined that the area of mangrove removed is small relative to mangroves’ contemporary area and expansion. Decisions regarding mangrove removal largely prioritised human-centric desires for recreational spaces rather than principles of ecological restoration. In addition, I showed that an ecological understanding of the repercussions of removal on avifauna is limited by insufficient monitoring. Drawing on limited data, I suggested that mangrove removal creates a conservation trade-off, benefitting species that use open habitats, such as waders and shorebirds, at the expense of mangrove-using avifauna. I then emphasised the importance of addressing the drivers of mangrove expansion rather than its symptoms, situating New Zealand’s management response in the theory of invasion biology. Second, I assessed the habitat quality of New Zealand’s mangroves for banded rails, using a resource-based approach. I quantified the abundance and diversity of macrofauna – key food resources to banded rails – collected from a stratified sampling regime across four habitat zones in four saltmarsh-mangrove complexes, determining that old-growth mangroves held the highest abundance and biomass of banded rail food resources. Additionally, I assessed the availability of these resources to banded rails using existing literature and field-based observations, theorising that mangroves provided the highest availability of food resources within saltmarsh-mangrove complexes. Third, I established and implemented a survey method novel to the study of banded rails (and cryptic marsh birds more broadly). I determined that a combination of camera traps and drift fences (CDF) provides an effective method for surveying banded rails in intertidal habitats, capable of providing both presence-absence data and inferences into banded rail movement patterns. I observed banded rail movements between saltmarsh and mangrove habitats to be correlated with temporal and tidal cycles, the first time banded rail habitat use has been assessed in relation to environmental cues. I explored the applicability and value of the CDF method as a monitoring tool, suggesting the method could support new research avenues for cryptic species and complement monitoring methods used for banded rails in New Zealand. Fourth, I quantified the habitat selection and habitat use patterns of banded rails at a home-range scale in saltmarsh-mangrove complexes, assessing data from GPS biotelemetry via resource selection ratios and a generalised linear mixed effects model. I determined that banded rail home ranges are largely restricted to saltmarsh and mangrove habitats finding that individuals select for mangrove habitats to support foraging efforts, select for saltmarsh habitats as roosting grounds, and generally avoid open habitats such as mudflats and residential gardens. I showed that habitat use may vary among individuals, noting two individuals that chose to roost in mangrove habitats overnight – a novel observation for this species. Additionally, biotelemetry findings confirmed movement patterns observed by camera traps in that banded rail habitat use was mediated by temporal and tidal cycles. Banded rails were significantly more likely to use mangroves during the day, whereas saltmarshes were primarily used at night and during high tides. Combining insights from research findings and existing literature, this thesis demonstrates that mangrove habitats play an important role in supporting banded rails. While mangroves are not a prerequisite for the survival of banded rail individuals, mangroves represent preferred habitats and support banded rail behaviours such as foraging and roosting. Viewed from a population perspective, mangroves help maintain banded rail populations by providing habitats to the majority of the country’s banded rail population. Three observations from this thesis are particularly relevant to conservationists and coastal managers in New Zealand: (1) mangroves are not uniform habitats; mangrove forests may appear structurally similar, but can be functionally different in their ability to support avifauna populations, (2) mangroves are more important to banded rails than previously understood or quantified; mangroves are preferred as foraging habitat to banded rails, can support roosting behaviours, and may make small patches of adjacent saltmarsh or terrestrial scrub viable breeding habitats, and (3) mangrove removal is likely to adversely affect local populations of banded rail, but more research is required to understand the nuances of these effects.
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    On kiwi (Apteryx mantelli) vocal behaviour and activity : relations to population densities and applications to conservation : a dissertation presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Zoology at Massey University, Manawatū, Aotearoa New Zealand
    (Massey University, 2021) De Rosa, Alberto
    According to the International Union for the Conservation of Nature (IUCN), over 38,500 species of living organisms assessed (27.8%) are currently threatened with extinction. Reducing this startling percentage requires cost–effective monitoring of populations of many and varied species. Information regarding population trends is crucial to allow decision makers to judiciously allocate unavoidably limited resources. Acoustic monitoring has long been employed to document the presence and estimate populations of vocal species for conservation purposes. Determining populations trends without the need of sighting or capturing animals can drastically reduce costs and improve welfare. However, as with many other indirect monitoring practices, acoustic surveys impose a series of assumptions about the detectability of the observed animals and their vocal behaviour. Whereas the variability in detection distances and other observer–induced effects can be minimised using acoustic recorders, enabling the delivery of animal abundances using acoustic monitoring requires detailed knowledge of the target species’ behaviours to relate numbers of detected acoustic cues to those of animals in an area. The iconic North Island Brown Kiwi (Apteryx mantelli, Bartlett 1851) is a flightless nocturnal bird species endemic to Aotearoa New Zealand, fragmentedly distributed across its mainland range and some of its offshore islands. North Island Brown Kiwi are known for their characteristic vocalisations which differ between sexes, with males emitting series of whistle-like syllables, and females producing series of hoarser and lower frequency syllables. Indeed, acoustic surveys are routinely employed by conservation groups and the Department of Conservation Te Papa Atawhai to monitor North Island Brown Kiwi. These surveys, known as Kiwi Call Counts, require observers to annotate sex, direction of arrival, and distance of the detected Kiwi vocalisations over a set period of time. However, little is known of North Island Brown Kiwi vocal behaviour and how this may relate to animal abundance and the development of more accurate and objective monitoring practices is included among the objectives of the Kiwi Recovery Plan (Germano et al., 2018). This thesis aimed to investigate North Island Brown Kiwi vocal behaviour and activity to build more objective and accurate acoustic monitoring protocols. Firstly, results from an extensive literature review on the acoustic playback technique — which has been shown to have the potential to enhance acoustic surveys in other species — led to the development of a set of recommendations to enable reproducibility when using playback. Secondly, results from playback experiments showed how single microphone acoustic recording units (ARUs) can be used to localise sound sources with reasonable degrees of uncertainty. This enables the potential transition of Kiwi Call Counts from relying on human observers to ARUs, which would allow for objective interpretation of the data while creating a potentially perpetual record. One of the thesis aims was to ascertain the potential of using playback to standardise the response of Kiwi populations. The results of experiments testing the effect of playback and environmental factors on kiwi vocal response show that there is no real relationship between the vocal activity of the target Kiwi community and playback. However, they corroborate and add to existing knowledge of Kiwi vocal behaviour by identifying relationships between the latter and external factors, such as lunar illumination and weather conditions. This thesis finally concentrated on the issue of relating vocal activity to animal abundance by developing and trialling the use of animal-borne acoustic recorders in conjunction to fixed ARUs. Since using animal-borne acoustic recorders entails handling target animals, we first performed an experiment on post–handling vocal behaviour to ascertain whether the vocal activity of handled birds of our target community differed from that of birds that had never been handled. The results from this experiment showed that the vocal activity recorded from a gully inhabited by never handled Kiwi did not differ from that of a gully inhabited by birds that were handled during the survey — and have been regularly handled over the last 17 years — in any detectable way. This is encouraging both for animal welfare purposes, and for comparing acoustic surveys from both managed and more wild Kiwi populations. Finally, the results from employing the animal-borne acoustic recorders to inform density estimates showed how information about individual vocal activity informs more realistic and consistent population estimates than methods based only on community–level vocalisations. On all the occasions sampled, results of population estimates only accounting for environmentally recorded vocalisations delivered lower abundance expectations for both males and females. Repeated sampling results show how estimates that account for individual vocal activity are both more consistent and closer to real densities than traditional methods, as estimated by paired sampling with a specialised dog survey. Lastly, information from individual vocal activity in some populations informed more accurate estimates for other populations without individually tagged animals. Taking advantage of having multiple populations with tagged individuals, we estimated abundances of a target population with three different models: unmarked, tagged with animal-borne acoustic recorders, and with information from other populations’ tagged individuals. This last estimate was in between the unmarked and with animal-borne acoustic recorders and apparently more accurate than the unmarked model. This thesis provides methods and shows encouraging results to eventually employ passive acoustic monitoring to infer Kiwi abundance in a cost-effective and non–invasive fashion at large scale, and invites further employment of animal-borne acoustic recorders to confidently deliver abundance estimates, crucial information for conservation decision makers. Using animal-borne acoustic recorders and ARUs together as a way to estimate populations does involve some invasive trials, but has the potential to lead to fully non–invasive robust abundance estimates though passive acoustic monitoring.
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    Towards developing support tools for sustainable control of gastrointestinal nematodes in sheep : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Veterinary Science at Massey University, Palmerston North, Manawatū, New Zealand
    (Massey University, 2021) Ikurior, Seer
    Gastrointestinal nematode (GIN) parasitism is a major animal health challenge for sheep. Parasitized animals typically display a number of clinical signs, including a reduction in voluntary feed intake, altered grazing behaviour and lethargy. The aim of this thesis was to use remote sensing technologies to advance the development of a methodology where early changes in animal behaviour can be used to help identify sheep suffering ill effects of GIN parasitism, especially in a pre-clinical situation. It was hypothesised that lambs with even modest worm burdens will be less active, graze for less time and spend more time resting than those herd mates that were less heavily parasitized. The movement and behavioural activity of young and mature, infected and uninfected sheep were monitored in a series of studies using global positioning system (GPS) and tri-axial accelerometer sensors. Key behaviours were identified using machine learning techniques. Also assessed was the influence of host genotype on movement activity. Accelerometry data accurately identified grazing, resting and walking activities of sheep. The sensors were able to identify the effects of GIN parasitism on movement and behaviour in sheep. Clear evidence was found that GIN were associated with reduced movement and overall activity in growing lambs, with reductions in time spent ‘grazing’ and ‘walking’ occurring concomitantly with increases in ‘resting’ activity, and before effects were recorded on growth rates. Host genotype also had an effect on movement activity of lambs in untreated sheep, but not in treated individuals. Adult sheep, however, showed no consistent changes in movement and behaviour associated with parasitism, as measured by faecal egg counts. Overall, the findings in this thesis have demonstrated the potential value in remote monitoring of sheep as a diagnostic marker to detect the generally subtle behavioural changes associated with changing GIN infection status. Such monitoring could therefore be used as the basis for deciding whether animals need to be treated with anthelmintic on the basis of individual need, and such decisions could be taken early, i.e. before animals have failed to grow adequately or started to manifest more overt signs of clinical illness such as weight loss.
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    Extrapolating incomplete animal population and surveillance data for use in national disease control : examples from Myanmar and New Zealand : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Veterinary Epidemiology, School of Veterinary Science at Massey University, Manawatu, New Zealand
    (Massey University, 2019) van Beest van Andel, Mary
    National level databases of animal numbers, locations, and movements provide the essential foundations for disease outbreak investigations, disease control, and disease preparedness activities. These activities are particularly important for managing and mitigating the risks of high impact exotic disease outbreaks like foot-and-mouth disease (FMD) as well as other economically important endemic diseases, which can significantly impact international trade and food security. However, many countries worldwide either lack national animal databases entirely or have multiple, fragmented databases that provide an incomplete picture of animal demographics. Consequently, there has been growing interest in developing novel methods to infer missing information on animal populations from other data sources, to quantify the extent of missing information, and to understand the impacts of missing information on the predictions made from national disease simulation models. This thesis explores these issues in the context of an FMD free country (New Zealand) as well as a country with endemic FMD (Myanmar). In Chapter 3, regression models were used to predict farm-level animal populations in New Zealand based on available data on farm type and location. When the results were compared against a subset of validated animal population data, the predictions at the farm level were found to be inaccurate especially for small-scale farms that keep animals for personal consumption or as a hobby. These properties are of particular interest to animal health authorities as they have been identified as at risk for exotic disease outbreaks. In Chapter 4, the impacts of having inaccurate herd size data on the predictions made by an FMD disease spread simulation model were explored. The results were analysed using cox proportional hazard models and logistic regression models, which showed that simulations run using actual animal population data indicated different optimal control strategies for FMD than models run with imperfect data and these effects differed by the region in New Zealand where the hypothetical disease outbreak was seeded. In Chapter 5, high-resolution local survey data and low-resolution national remote sensor data were used alone and in combination to predict the location of FMD positive villages in Myanmar, which were identified by serological sampling conducted as part of a large OIE funded research project in 2016. The performance of both random forest models and logistic regression models were explored using training and testing data sets. Bovine populations and proximity to cattle markets were found to be significant risk factors for FMD seropositivity and the logistic regression models performed as well as machine learning techniques. Chapter 6 compared verbal reports of FMD outbreaks from village headman and householders against the serological test results from their villages to determine whether using public reports is a viable alternative to conducting resource intensive serological surveys for estimating FMD prevalence in Myanmar. Although village headmen proved to be a better source of FMD reports compared to householders, the verbal reports were still not as accurate as serological tests in an endemic situation where both sensitivity and specificity of observing clinical signs can be complicated by endemic stability and concurrent outbreaks of other diseases. The work in both chapters 5 and 6 was carried out using data from activities of the Livestock Breeding and Veterinary Department and the OIE and as such separate human ethics approval was not required for the surveys described. Chapter 7 addressed the issue of estimating the scale of missing data in a national database by comparing intensively collected interview information with recorded movements at the farm level for farms involved in New Zealand’s Mycoplasma bovis eradication programme. The results showed that dairy farmers often failed to record almost half of high risk movements including leased bulls, calves sent offsite for rearing, and adult cattle sent away for winter grazing. It was also estimated that approximately 60% of animals arriving at abattoirs in New Zealand have multiple movements missing from their life history in the National Animal Identification and Tracing system (NAIT) database. This missing information had a significant impact on the ability of government and industry to effectively respond to the outbreak. However, a positive finding from this study was that the rates of missing data are decreasing over time. Overall, this thesis demonstrated the importance of enhancing efforts to collect accurate and up-to- date national animal population and movement data. For New Zealand, the changes required to improve the national farm animal data landscape include improving compliance with the legislated requirements to record animal movements and modifying the existing databases to record information on the health status of animals against a unique animal identifier. A unique farm identifier is required at the national level and should be agreed upon by industry representatives, government and researchers. The combination of animal health data associated with the unique animal identifier and a single current farm identifier for all farms will result in a robust animal health and biosecurity system.
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    Behavior changes in grazing dairy cows during the transition period are associated with risk of disease : a dissertation presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Animal Science at Massey University, Manawatū, New Zealand
    (Massey University, 2020) Hendriks, Stacey
    There is growing interest in the use of behavior data derived from accelerometers as a potential measure of animal health, however, research determining the optimal use of these devices and the interpretation of data derived from them, is lacking, particularly in grazing systems. The aims of this thesis were to understand: 1) data management considerations that need to be taken into account when using accelerometer devices to measure behavior in a research setting; 2) environmental and other potentially-confounding variables that can influence cow behavior and, therefore, the interpretation of behavior data; 3) ‘normal’ behavior of clinically-healthy grazing dairy cows during the transition period, and; 4) changes to behavior of grazing dairy cows experiencing varying degrees of hypocalcemia and hyperketonemia. To do this, data from 4 separate parent experiments were collated to generate a database containing detailed phenotype data, including, but not limited to, measures of cow performance (e.g., milk production and composition, body weight and body condition score), cow health (e.g., energy and protein metabolites, minerals, liver enzymes, and immune markers in blood), and cow behavior (e.g., lying behavior and activity derived from triaxial accelerometers). My review of the appropriate use of leg-mounted accelerometers to monitor lying behaviors of dairy cows indicated that applying editing criteria to remove errors in lying behavior data caused by erroneous movements of the leg (e.g., scratching and kicking) can improve the accuracy of data derived from accelerometers for recording daily lying bouts (LB); however, has little to no impact on the accuracy of lying time. Lying behavior data must be edited using a suitable LB criterion where the interest is in studying both lying time and LB. My results indicated that inclement weather, parity, and physiological state are important variables that influence behavior in their own right and must be considered in subsequent analyses. Interestingly, when comparing my results with lying behaviors previously reported in housed cows, my results indicated that grazing dairy cows engage in similar lying behaviors to housed cows before and at the time of calving, while postcalving, grazing cows spend less time lying. Furthermore, grazing dairy cows displayed greater behavioral synchrony (i.e., cows engaged in the same behaviors simultaneously) compared with reports in housed cows. These postcalving differences highlight the importance of assessing behavior within the farming system of interest. My results also indicated that cows alter their behavior in response to ill health, whereby grazing dairy cows experiencing clinical hypocalcemia (without paresis) and hyperketonemia [with severe negative energy balance (NEB)] altered their behavior before, at the time of, and after disease diagnosis compared with healthy cows. My results indicated that behavioral differences between cows classified into 3 blood calcium groups [clinically-hypocalcemic (without paresis), subclinically-hypocalcemic, and normocalcemic] were transient. On the day of calving, clinically-hypocalcemic cows (without paresis), were less active, spent more time lying, and had more frequent LB compared with subclinically-hypocalcemic and normocalcemic cows; however, changes in behavior were short lived and were no longer present by 2 d postcalving. My results indicate that observed differences in behavior associated with hypocalcemia are small and may not be biologically significant as a metric to discriminate between hypocalcemic and normocalcemic cows. On the contrary, changes in behavior over time and within cow may allow differences between hypocalcemic and normocalcemic cows to be more easily discerned than using mean values of lying behavior and activity at a specific time point. My findings indicated that a relative increase in the number of steps taken within cow compared with a baseline period 2 wk precalving was positively associated with blood calcium concentrations postcalving. Further, my results indicated the behavioral differences between cows classified into 3 energy status groups [Hi–Hi = high non-esterified fatty acids (NEFA) and high β-hydroxybutyrate (BHB); Hi–Lo = high NEFA and low BHB, and; Lo–Lo = low NEFA and low BHB] occurred up to 2 wk before calving. During the 2 wk before calving, cows identified as Hi–Hi were more active, spent less time lying, and had fewer LB than the other 2 energy status groups. Interestingly, similar to the hypocalcemia work, my results indicated that a relative increase in the number of steps taken within cow during the 2 wk before calving was associated with lower odds of developing hyperketonemia with NEB; therefore, greater increases in activity before calving were associated with improved health outcomes postcalving in both studies. My results suggest that relative changes in behavior, in particular, step activity, might be an improved metric to discriminate between clinically-healthy grazing cows and cows experiencing a subclinical metabolic disease. My research provides an improved understanding of the associations between cow behavior and health, particularly for grazing dairy cows. This information provides a base for further exploring the potential for behavior and activity measures to identify cows experiencing ill health during the transition period. Future work should focus on continuing to improve our understanding of associations between behavior and disease, particularly in grazing dairy cows. Using within-cow behavior measures and determining how these data could be interpreted so that farmers could be alerted to sick animals and make actionable decisions on farm, should be the focus of future studies.
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    Estimating the population size of two critically endangered South Pacific parakeets : the Tasman Parakeet and Malherbe's Parakeet : a thesis submitted in partial fulfilment of the requirements for the degree of Master of Science in Conservation Biology, Massey University, New Zealand
    (Massey University, 2018) Skirrow, Michael John Adam
    The Cyanoramphus parakeets are a cryptically coloured group of birds that are distributed across the islands of the South Pacific region. Due to their restricted range and island distributions, species belonging to this genus are considered vulnerable to extinction. However, the extent to which these parrot species are threatened is difficult to determine due to an absence of accurate and reliable population estimates. This research aims to contribute to the conservation of two critically endangered Cyanoramphus parakeets by evaluating the survey methods currently used to estimate population densities. This thesis details the precision and efficiency of distance sampling methods used for monitoring low density parrot populations on small islands. Specifically, examining the annual variation in population size for the critically endangered Tasman Parakeet (Cyanoramphus cookii) and their introduced competitor, the Crimson Rosella (Platycercus elegans), to evaluate the effectiveness of conservation management and species control on Norfolk Island. In addition, the size of three translocated populations of the critically endangered Malherbe’s Parakeet (Cyanoramphus malherbi) were examined to identify if this endemic New Zealand parrot requires further management. Of the distance sampling methods used to monitor parrots, the fixed point survey method was the most suitable method for surveying Tasman Parakeets. This method yielded the highest number of parakeet detections per survey and offered the greatest count precision of the methods examined. On Norfolk Island, the Tasman Parakeet population increased by 126% over four years of intense predator management and nest provisioning. In comparison, the Crimson Rosella population remained stable, despite regular culling to control the population which competes with the Tasman Parakeet. In New Zealand, Malherbe’s Parakeets were detected with varying degrees of success. On Maud Island, no parakeets were detected; however, they were detected on both Blumine Island and Chalky Island. On Blumine Island, the Malherbe’s Parakeet population was moderately abundant, consisting of 202 ± 67 individuals distributed through the mature forest. In comparison, the Chalky Island population of Malherbe’s Parakeet was less extensive and consisted of 84 ± 58 parakeets. This research illustrates the importance of regularly monitoring the size of threatened parrot populations for conservation.
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    Understanding movement and habitat selection of the lesser short-tailed bat to infer potential encounters with anticoagulant bait : a thesis presented in partial fulfilment of the requirements for the Degree of Master of Science in Zoology at Massey University, Manawatū, New Zealand
    (Massey University, 2019) Bennett, Ruby Sam
    The lesser short-tailed bat (Mystacina tuberculata) and the long-tailed bat (Chalinolobus tuberculatus) are New Zealand’s only extant endemic land-dwelling mammals. Both species are listed as nationally endangered by the IUCN, with numbers declining due to widespread habitat destruction and other human interferences. Short-tailed bats have been an unintentional victim of toxins used for pest control in New Zealand, being particularly susceptible to poisoning due to their diverse diet and ground-feeding habits. To manage toxin use to minimize bat exposure it is necessary to understand their movements and area usage behaviours. Movements and habitat use of the short-tailed bat were studied on the area of farmland between Pikiariki and Waipapa Ecological Area, Pureora Forest Park, New Zealand. Bats using the area between the two large forests were studied using acoustic monitoring and radio telemetry techniques to determine which routes they use, how they utilise the farmland and forest fragments along the way, and how they interact with obstacles such as open farmland and roads. Evidence of foraging was more often observed near forest fragments than open areas. While levels of habitat preference varied among individuals, forest was consistently selected over open areas throughout their commutes over farmland. 50% of the radio tracked bats were commuting directly between Pikiariki and Waipapa, while a further 25% were deemed to forage or rest throughout the trip. These results confirm that short-tailed bats utilise marginal habitats on private land, suggesting a need for the implementation of safe pest control in areas near known colonies on both public and conservation land. Stronger toxins are often used on private land so the risks to short-tailed bats could be higher. The results also provide information on how short-tailed bats make use of a fragmented environment, and whether we need to create forest bridges across open farmland to assist the nightly commute of bats.
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    The ecology of bottlenose dolphins (Tursiops truncatus) in the Hauraki Gulf, New Zealand : a thesis presented in partial fulfilment of the requirements for the degree of Master of Science in Conservation Biology, Massey University, New Zealand
    (Massey University, 2018) Outhwaite, Blair R.
    Bottlenose dolphins (Tursiops truncatus) are one of the most studied cetacean species in the world. In New Zealand, this species is classified as Nationally Endangered and studies are generally limited to just a few known core areas. Herein, I examine the use of social media in citizen science as a means of collecting occurrence data of bottlenose dolphins in the inner Hauraki Gulf. A dedicated research vessel was employed to verify data collected by citizen scientists. This study also investigated the habitat selection of bottlenose dolphins at Great Barrier Island, an area only recently described for its importance to the north-eastern North Island population. Data collected for a behavioural budget and whistle repertoire were recorded on a dedicated research vessel with the aim of understanding habitat selection. Environmental variables were used to model behavioural states in order to determine how habitats were utilised by the dolphins. The whistle repertoire was assessed to understand how it correlated with behavioural states and group dynamics. A total of 260 sightings of bottlenose dolphins were reported by citizen scientists between April 2015 and July 2016. Only 42 of these were independent reports. Of the total number of reports, 73.5% did not identify a dolphin species. Citizen scientists identified three species of cetacean. Killer whales (Orcinus orca) were often reported correctly, however all five reports of common dolphins (Delphinus delphis) were misidentified, and 33.3% (n=5) of the reports identifying bottlenose dolphin were either unconfirmed or misclassified. Researchers’ verifying the identity of the species reported was the most useful method of confirming citizen science reports in this study (34.8%). Citizen scientists failed to detect dolphins on only three occasions that the research vessel or platform of opportunity did. Yet, citizen scientists were able to detect bottlenose dolphins more often than either the research vessel or platform of opportunity. The number of independent citizen science reports, research vessel encounters and platform of opportunity encounters for bottlenose dolphins were similar over each austral season. Notably, only the platform of opportunity had encounters over summer, both of which were in deeper water, outside of the study area. Bottlenose dolphin group size was often underestimated by citizen scientists in this study, though rigid comparisons were not possible for group size or behavioural state due to small sample sizes. The proportion of total reports varied temporally between seasons, and was highest in the mornings for autumn and winter, but peaked during the afternoons in spring. Bottlenose dolphins did not appear to use the study area frequently and were usually recorded travelling. The majority of behavioural observations at Great Barrier Island were made during winter and spring. Bottlenose dolphins were recorded between 13.5 and 24.1°C and in depths of 1.8 to 55.3m. The largest group sizes were recorded in autumn while the smallest group sizes were recorded most often in spring and summer. While the largest group sizes were recorded in the warmest sea surface temperatures and greatest depths, there was no significant difference between group size categories. Resting made up the largest proportion of the behavioural budget (32.1%), while foraging (8.2%) and socialising (9%) were rarely recorded. The models predicted that the behavioural budgets at Great Barrier Island were determined primarily by abiotic factors (e.g. depths and sea surface temperature). The mean whistle rate, calculated as the number of whistles per minute per dolphin, recorded at Great Barrier Island for bottlenose dolphins was 0.50 (SD=0.53) and the highest whistle rate was recording during foraging (1.17, SD=0.98). There was no significant difference in whistle rates between group size categories. Whistles recorded lasted on average 0.84s (SD=0.52), with a mean frequency of 11.6kHz (SD=2.34). The parameters with the highest variation were the number of inflection points, length, and frequency range of whistles. The Ascending whistle type was the most commonly recorded, and particular whistle types were correlated to behavioural state and group size category. This study represents the first instance that citizen science utilised social media in the Hauraki Gulf and suggests there is potential for continued monitoring of bottlenose dolphins with citizen science, if recommendations are applied. It also presents the first behavioural budget and whistle repertoire for bottlenose dolphins at Great Barrier Island. This study reported a unique behavioural budget and acoustic parameters that imply its importance for the north-eastern North Island population. Continued monitoring of this population is recommended to ensure this population is managed appropriately.