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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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    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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    Ecology of sharks and human attitudes towards shark conservation in the Galapagos Marine Reserve : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Ecology at Massey University, Albany, New Zealand
    (Massey University, 2018) Acuña Marrero, David
    In this thesis, I used a multi-disciplinary approach to study both the spatial ecology of coastal sharks and human attitudes towards sharks at the Galapagos Marine Reserve (GMR). Benthic and pelagic baited remote underwater stereo-video systems recorded coastal shark assemblages that displayed high spatial variation, with the relative importance of environmental and biological drivers differing among shark species according to their mobility. Telemetry data (both acoustic and satellite) from tagged tiger sharks (Galeocerdo cuvier) showed a high degree of philopatry, with movements of adult tiger sharks concentrating at the most important nesting areas for sea turtles at the GMR. Using diver-operated stereo-video systems (DOVs) I demonstrated that non-instantaneous surveys yield estimates of shark densities that can almost double the ones obtained from instantaneous surveys. Furthermore, I proposed a new methodological approach to study attitudes towards sharks that proved to be reliable and informative, showing that attitudes were shaped by a range of psychological factors, such as aesthetics, and also by the socio-economic context of individual respondents. Strong correlations were found between attitudes and behavioural responses, such as tolerance or support for shark protection. In conclusion, I demonstrated that sharks at the GMR have species-specific and size-specific spatial requirements for particular habitats and food resources. Indeed, the presence of a predictable source of prey and suitable habitats at the GMR might reduce the spatial extent of the potential areas used by large and highly mobile shark species, such as tiger sharks, thereby enhancing the potential effectiveness of the GMR for their protection. I also propose the use of non-instantaneous DOV surveys to provide more accurate estimates of shark densities than underwater visual techniques. In addition, the multivariate methods used here for the first time to study human perspectives on sharks allowed me to identify specific attitudes and associated factors having the greatest influence on human behaviours towards shark conservation. In summary, with mounting anthropogenic pressures on shark populations, this thesis provides timely and critical information for the global objective of identifying effective strategies for the management and conservation of sharks to ensure their long-term survival.
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    Spatial ecology of delphinids in Queen Charlotte Sound, New Zealand : Implications for conservation management : a thesis submitted in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Marine Ecology Massey University, Albany, New Zealand
    (Massey University, 2019) Cross, Cheryl Lynne
    Understanding species’ ecological interactions and area usage depends on clear insight into their temporal and spatial patterns. Such information combined with recognition of regional human-invested interests, is crucial for developing conservation management efforts. Queen Charlotte Sound (QCS), South Island, New Zealand is a unique environment inhabited by diverse marine life, including several cetacean species. The area is subject to rising levels of anthropogenic activity inclusive of marine farming, tourism and vessel traffic. With conservation management in mind, this thesis focused on three key delphinid species: Hector’s (Cephalorhynchus hectori), bottlenose (Tursiops truncatus) and dusky dolphins (Lagenorhynchus obscurus). Specifically, this study sought to: 1) explore long-term historical temporal and spatial trends in delphinid occurrence 2) identify recent patterns in delphinid distribution, density and range 3) investigate delphinid species’ habitat use 4) initiate research of regional swim-with-dolphin tourism. Dolphin sighting data were: 1) collated from tour vessel logbooks spanning 1995–2011 and 2) collected during dedicated surveys aboard opportunistic platforms from 2011–2014. Dynamic and static environmental variables were sourced from local government agency databases to use in analyses with both datasets. Historical delphinid presence (from logbook data) was correlated with dynamic environmental variables during two separate time frames (1995–2002; 2003–2011), using Generalized Additive Models (GAMs) and Generalized Linear Models (GLMs). Spatial patterns of these sightings were explored across temporal periods (i.e., seasons; blocks of year). Dedicated survey data were used to generate kernel density estimates and to determine species’ range and central range. These dolphin density estimates were correlated with static and dynamic habitat parameters using (GAMs). Spatial predictions were then generated from the resultant significant variables. Bottlenose dolphin engagement in swim-with-dolphin encounters was assessed according to several proxies using Linear Models (LMs) and GLMs. A total of 5,295 historical records consisting of 6,055 delphinid sightings were compiled, demonstrating a long-term presence of the focal species. Of these, Hector’s dolphins consistently had the highest trip encounter rate. Seasonal patterns indicated peaks in occurrence for Hector’s during summer/autumn, bottlenose during autumn/winter and dusky dolphins during winter/spring. Further investigation with GAMs suggested that each species’ presence was associated with a unique set or range of dynamic variables. Annual variation occurred amongst all species. During both historical time frames (1995–2002 and 2003–2011), Hector’s dolphin occurrence was associated with higher SST values. Bottlenose dolphins displayed an association with mid-low SST (during 1995–2002) and with high turbidity (during 2003–2011). Dusky dolphins were influenced by low SST (during both time frames) and from 2003–2011 were also influenced by low turbidity and mid-value tidal range. Spatial patterns illustrated that Hector’s and dusky dolphins have become more restricted in their use of QCS over time. Finally, logbook data indicated an increased prevalence of swim-with-dolphin encounters, suggesting an expansion of local tourism from 2004–2011. A total of 677 dedicated opportunistic surveys were completed. These equalled 1,613 hrs of search effort spanning 263 km2. Sighting rate calculations indicated that Hector’s and bottlenose dolphins occurred more frequently than dusky dolphins. Seasonality was particularly notable amongst Hector’s dolphins, whereas the sighting and encounter rates were higher during summer and autumn. The collective range of all species suggests that delphinids utilized most of QCS. However, both the range and central range of Hector’s dolphins were more limited. Notable spatial patterns included peaks in Hector’s dolphin density mid-Sound, during summer/autumn and peaks in bottlenose dolphin density toward the outer Sound during summer/autumn. Temporal overlap was relatively high for bottlenose and Hector’s dolphins (0.67) and low for Hector’s and dusky dolphins (0.22), while spatial overlap was quite low for all species combinations. The patterns explored here offer evidence of temporal and spatial multi-species habitat partitioning within QCS. This may be due to the broader ecological trends within New Zealand and is likely attributed to the availability and movement of prey. Habitat models (GAMs) indicated a unique set of significant drivers associated with dolphin density for each species. Hector’s dolphins displayed an association with dynamic and static variables (SST, fluorescence, depth, slope and distance to the closest marine farm). Dusky dolphins were influenced by the same variables, as well as year. Consistency with the earlier models in the association with SST for Hector’s (higher values) and dusky dolphins (lower values) was detected. Bottlenose dolphins were only influenced by static variables (depth, slope and distance to the closest marine farm) and year. The habitat differences suggested by these models offer further insight to the ecological meaning of dolphin spatial patterns in QCS. In particular, these findings offer additional evidence of delphinid resource partitioning, specifically on a trophic scale. This likely occurred because all three species exhibit both dietary and foraging plasticity. While similarities were observed between comparable studies in other areas, the presence of some variation is likely due to unique physical and hydrographic regional characteristics. Spatial predictions that were generated from significant model variables were valuable in estimating potential locations of dolphin density beyond sighting locations, including areas that they previously occupied. Data representing animal area usage, like those presented here, are integral to conservation management, especially amidst growing anthropogenic influences, like tourism. This first ever tourism-based study in QCS indicated bottlenose dolphins as the main target species for swim-with-dolphin activity. A total of 190 bottlenose dolphin swim encounters were assessed according to several proxies. Interactions were very short (𝑥̅=4.2 min), with most dolphin reactions neutral (82.9 %), suggesting animal disinterest. Swim encounters occurred regularly, irrespective of group composition or behavioural state. Furthermore, tour operators travelled great distances (𝑥̅=11.7 km) amongst dolphin groups to complete swim encounters, demonstrating pursuit of interaction. Collectively, these proxies suggest a lack of dolphin engagement in swim activity. This thesis encompassed the first multi-species comprehensive assessment of delphinid density, range, habitat use and swim-with-dolphin tourism in QCS. It established a baseline of data, contributing to regional ecological knowledge. Detailed evidence of when and where three sympatric dolphin species utilized QCS was provided. Moreover, this work established an understanding of delphinid inter-specific interactions and associations with habitat variables. Applications of the findings presented here include contributions to developing comprehensive conservation management and further research. Periods and regions of high density and predicted density may be considered in regional management decisions regarding anthropogenic use of the Sound and during the design of future surveys.
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    Development of a low-cost automated sample presentation and analysis system for counting and classifying nematode eggs : a thesis presented in partial fulfilment of the requirements for the degree of Master of Engineering in Mechatronics at Massey University, Manawatu, New Zealand
    (Massey University, 2017) Pedersen, Benjamin
    This thesis discusses the concept development and design of a low-cost, automated, sample presentation system for faecal egg counting, and classification. The system developed uses microfluidics to present nematode eggs for digital imaging to produce images suitable for image analysis and classification. The system costs are kept low by using simple manufacturing methods and commonly available equipment to produce microfluidic counting chambers, which can be interfaced with conventional microscopes. This thesis includes details of the design and implementation of the software developed to allow capture and processing of images from the presentation system. This thesis also includes details on the measures taken to correct for the optical aberrations introduced by the sample presentation system.