Massey Documents by Type
Permanent URI for this communityhttps://mro.massey.ac.nz/handle/10179/294
Browse
57 results
Search Results
Item Host phylogeny shapes viral transmission networks in an island ecosystem(Springer Nature Limited, 2023-11) French RK; Anderson SH; Cain KE; Greene TC; Minor M; Miskelly CM; Montoya JM; Wille M; Muller CG; Taylor MW; Digby A; Kākāpō Recovery Team; Holmes ECVirus transmission between host species underpins disease emergence. Both host phylogenetic relatedness and aspects of their ecology, such as species interactions and predator-prey relationships, may govern rates and patterns of cross-species virus transmission and hence zoonotic risk. To address the impact of host phylogeny and ecology on virus diversity and evolution, we characterized the virome structure of a relatively isolated island ecological community in Fiordland, New Zealand, that are linked through a food web. We show that phylogenetic barriers that inhibited cross-species virus transmission occurred at the level of host phyla (between the Chordata, Arthropoda and Streptophyta) as well as at lower taxonomic levels. By contrast, host ecology, manifest as predator-prey interactions and diet, had a smaller influence on virome composition, especially at higher taxonomic levels. The virus-host community comprised a 'small world' network, in which hosts with a high diversity of viruses were more likely to acquire new viruses, and generalist viruses that infect multiple hosts were more likely to infect additional species compared to host specialist viruses. Such a highly connected ecological community increases the likelihood of cross-species virus transmission, particularly among closely related species, and suggests that host generalist viruses present the greatest risk of disease emergence.Item Incorporating hydrology into climate suitability models changes projections of malaria transmission in Africa.(Springer Nature Limited, 2020-08-28) Smith MW; Willis T; Alfieri L; James WHM; Trigg MA; Yamazaki D; Hardy AJ; Bisselink B; De Roo A; Macklin MG; Thomas CJContinental-scale models of malaria climate suitability typically couple well-established temperature-response models with basic estimates of vector habitat availability using rainfall as a proxy. Here we show that across continental Africa, the estimated geographic range of climatic suitability for malaria transmission is more sensitive to the precipitation threshold than the thermal response curve applied. To address this problem we use downscaled daily climate predictions from seven GCMs to run a continental-scale hydrological model for a process-based representation of mosquito breeding habitat availability. A more complex pattern of malaria suitability emerges as water is routed through drainage networks and river corridors serve as year-round transmission foci. The estimated hydro-climatically suitable area for stable malaria transmission is smaller than previous models suggest and shows only a very small increase in state-of-the-art future climate scenarios. However, bigger geographical shifts are observed than with most rainfall threshold models and the pattern of that shift is very different when using a hydrological model to estimate surface water availability for vector breeding.Item Infection thresholds for two interacting pathogens in a wild animal population.(Elsevier B.V., 2024-07-17) Roberts MGWe present a model for the dynamics of two interacting pathogen variants in a wild animal host population. Using the next-generation matrix approach we define the invasion threshold for one pathogen variant when the other is already established and at steady state. We then provide explicit criteria for the special cases where: i) the two pathogen variants exclude each other; ii) one variant excludes the other; iii) the population dynamics of hosts infected with both variants are independent of the order of infection; iv) there is no interaction between the variants; and v) one variant enhances transmission of the other.Item Emerging advances in biosecurity to underpin human, animal, plant, and ecosystem health.(Elsevier B.V., 2023-09-15) Hulme PE; Beggs JR; Binny RN; Bray JP; Cogger N; Dhami MK; Finlay-Smits SC; French NP; Grant A; Hewitt CL; Jones EE; Lester PJ; Lockhart PJOne Biosecurity is an interdisciplinary approach to policy and research that builds on the interconnections between human, animal, plant, and ecosystem health to effectively prevent and mitigate the impacts of invasive alien species. To support this approach requires that key cross-sectoral research innovations be identified and prioritized. Following an interdisciplinary horizon scan for emerging research that underpins One Biosecurity, four major interlinked advances were identified: implementation of new surveillance technologies adopting state-of-the-art sensors connected to the Internet of Things, deployable handheld molecular and genomic tracing tools, the incorporation of wellbeing and diverse human values into biosecurity decision-making, and sophisticated socio-environmental models and data capture. The relevance and applicability of these innovations to address threats from pathogens, pests, and weeds in both terrestrial and aquatic ecosystems emphasize the opportunity to build critical mass around interdisciplinary teams at a global scale that can rapidly advance science solutions targeting biosecurity threats.Item The future of zoonotic risk prediction(The Royal Society, 2021-11-08) Carlson CJ; Farrell MJ; Grange Z; Han BA; Mollentze N; Phelan AL; Rasmussen AL; Albery GF; Bett B; Brett-Major DM; Cohen LE; Dallas T; Eskew EA; Fagre AC; Forbes KM; Gibb R; Halabi S; Hammer CC; Katz R; Kindrachuk J; Muylaert RL; Nutter FB; Ogola J; Olival KJ; Rourke M; Ryan SJ; Ross N; Seifert SN; Sironen T; Standley CJ; Taylor K; Venter M; Webala PWIn the light of the urgency raised by the COVID-19 pandemic, global investment in wildlife virology is likely to increase, and new surveillance programmes will identify hundreds of novel viruses that might someday pose a threat to humans. To support the extensive task of laboratory characterization, scientists may increasingly rely on data-driven rubrics or machine learning models that learn from known zoonoses to identify which animal pathogens could someday pose a threat to global health. We synthesize the findings of an interdisciplinary workshop on zoonotic risk technologies to answer the following questions. What are the prerequisites, in terms of open data, equity and interdisciplinary collaboration, to the development and application of those tools? What effect could the technology have on global health? Who would control that technology, who would have access to it and who would benefit from it? Would it improve pandemic prevention? Could it create new challenges?Item Field measurements of a massive Porites coral at Goolboodi (Orpheus Island), Great Barrier Reef(Springer Nature Limited, 2021-08-19) Smith A; Cook N; Cook K; Brown R; Woodgett R; Veron J; Saylor VAn exceptionally large coral Porites sp. has been identified and measured at Goolboodi (Orpheus Island), Great Barrier Reef (GBR). This coral was measured in March 2021 during citizen science research of coral reefs in the Palm Islands group. We conducted a literature review and consulted scientists to compare the size, age and health of the Porites with others in the GBR and internationally. This is the largest diameter Porites coral measured by scientists and the sixth highest coral measured in the GBR. The health of the Porites was assessed as very good with over 70% live coral cover and minor percentages of sponge, live coral rock and macroalgae. An estimated age of 421-438 years was calculated based on linear growth models. Manbarra Traditional Owners were consulted and suggested that the Porites be named Muga dhambi (big coral) to communicate traditional knowledge, language and culture to indigenous, tourists, scientists and students.Item Population ecology and foraging behaviour of yellow-eyed penguins in New Zealand’s subantarctic Auckland Islands : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Veterinary Science and Ecology, Massey University, Manawatū, New Zealand(Massey University, 2022) Muller, ChristopherPenguins and other seabirds rely on healthy, functioning marine systems, and are vulnerable to human-induced changes. Accurate long-term monitoring of a threatened species’ population size and trend is therefore important for conservation management. The endangered yellow-eyed penguin (Megadyptes antipodes) is found only in New Zealand waters, with separate northern (mainland New Zealand and offshore islands) and southern (subantarctic) breeding populations. The northern population is declining, believed to be due to threats at sea including direct mortality, as well as changes to food supply, and the effects of climate change. The southern population was previously estimated to comprise at least 60% of the species. Despite this, the subantarctic has been little studied, with one previous population estimate at the Auckland Islands in 1989, two at Campbell Island, and no recent data or measurement of population trends. To address this data gap, this research studied the population and foraging behaviour (diving, foraging location, and diet) of breeding yellow-eyed penguins on Enderby Island, Auckland Islands, from 2015–2017. The first step for this research was locating cryptic yellow-eyed penguin nests hidden in thick vegetation, as ground searches are inefficient, time-consuming, and potentially hazardous for researchers in subantarctic terrain. I utilised a drone fitted with a novel multi-frequency VHF receiver which located nests in only 3% of the time for traditional search methods, facilitating my other research. Next, I defined methods for surveying populations in the subantarctic, and estimated a mean of 577 breeding pairs at the Auckland Islands, although the population and number of breeders fluctuated annually, and may have declined since 1989. My foraging research showed that 62% of foraging trips, and over 86% of all southern yellow-eyed penguin dives were pelagic (mid-water), unlike the predominantly benthic (seabed) dives of the northern population. Maximum dive depth was 134 m for benthic dives, and 115 m for pelagic dives, which is deeper than many northern penguins dive. The proportion of pelagic dives increased during La Niña years, likely influenced by climate conditions and prey availability. Foraging distance also varied, with a maximum distance of 47 km from shore, further than many northern birds travel. Foraging area size was greater for females and for pelagic foragers, although benthic foragers travelled further from shore on average. Diet also varied, and during El Niño conditions comprised lower trophic level prey, which were more benthic, and found closer to shore than during La Niña years. Diet results showed some individuals maintained consistent foraging behaviour, although foraging plasticity was also evident. Some individuals changed their foraging behaviour between years, and even within a breeding season. Variable breeding success in the subantarctic, along with variable foraging behaviour and diet suggests that prey availability is likely limiting the southern population in some years. Prey availability is therefore expected to be a major influence on survival and breeding success in the future, particularly if the effects of climate change become more pronounced.Item Systematics, bionomics and distribution of the plant bug Nysius huttoni White (Heteroptera : Lygaeidae) : a thesis presented in partial fulfilment of the requirements for the degree of Master of Agricultural Science in the University of New Zealand(Massey University, 1958) Eyles, Alan CharlesNysius huttoni White, endemic to new Zealand is a member of an almost cosmopolitan genus which shows remarkable adaption throughout the world. As it is the only Nysius species so far recorded from this country, some attention to it is surely due, if for no other reason. There are, however, other valid reasons which prompted this study, ands these are as follows. Relatively little work has been carried out on N. huttoni, there being only one study (by Gurr, 1957) specifically on this insect; the immature stages have not been described; no illustrations of any of the instars either nymphal or imaginal have been published, except for one photomicrograph by Blair and Morrison (1949) of a balsam-mounted image, but it is so distorted as to be unrecognisable; the systematics of the insect has not been fully studied, for Usinger (1945) states that two species may be represented; the number of broods per year is not known, but Myers (1926) states that there is probably more than one. An attempt has been made to elucidate the subject along these lines. Further, the insect occurs in large numbers and is easily caught, which two factors contribute much to the suitability of the insect for study material. Thus N. huttoni presents ample for a general study on the bionomics of an animal [From Introduction]Item Genetic and phenotypic variation used to identify populations of endangered green gecko (Naultinus) found in the north-west South Island, New Zealand : a thesis submitted in fulfilment of the requirements for the degree of Master of Science in Conservation Biology, Massey University, Albany and Palmerston North. EMBARGOED until further notice.(Massey University, 2018) King, Samantha J.Two species of green gecko (Naultinus stellatus and Naultinus tuberculatus) found in the north and west South Island are endemic to New Zealand and are classified as Nationally Vulnerable (Hitchmough et al. 2016). Detailed information about the ecology, morphology and distribution of these geckos is limited, including what traits are diagnostic, details of their geographic range and it is unknown whether both species hybridise in the wild. My research aimed to investigate if the Denniston and Stockton Plateaus in New Zealand’s South Island represent a putative contact zone between N. stellatus and N. tuberculatus and if natural hybridisation occurs. Naultinus species are known to reproduce with each other in captivity and a few wild caught individuals (n=5) have led to an inference of introgressive hybridisation. In addition, I aimed to collect basic data on the ecology and morphology of both species and a putative hybrid to determine the extent of inter and intraspecific variation in phenotypic traits. I did not find evidence of a contact zone or hybridisation occurring between N. tuberculatus and N. stellatus; all geckos sampled in this study from Denniston and Stockton plateaux were morphologically and genetically part of N. tuberculatus. My results show significant intraspecific phenotypic variation between populations for each species. For example, body colour patterns of some populations are more similar between species than within. However, concordance between genetic markers and colour combinations of mouth and tongue provided evidence of clear species differences, and traits to distinguish the species, despite intraspecific variation of other traits. Finally, I recorded detailed habitat parameters for each individual and documented variation in perch height, both within populations and between sex. This information helps conservation practitioners to implement best practice techniques for green gecko conservation management by determining ecotypes and habitat use, population variance, which can prevent the further decline of both genetic variation and risk to species. Specifically, this research aids the mitigation of negative impacts by mining operations and development, such as is the current threat to the Denniston and Stockton plateaux.--Shortened abstractItem Quantifying bed stability : the missing tool for establishing mechanistic hydrological limits : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Geography at Massey University, Palmerston North, New Zealand(Massey University, 2018) Neverman, Andrew J.Sediment transport processes are a key mechanism of ecological change in riverine systems, and certain levels of sediment flux are necessary for healthy ecosystem functioning. Altered flow regimes and sediment mobility are contributing to a global problem of higher substrate embeddedness reducing the frequency of substrate scour events and leading to increases in periphyton accrual. Excess periphyton accrual leads to fish and invertebrate kills from oxygen depletion, degraded ecological health, altered sediment dynamics, deterioration in water taste, and odour nuisance. In recent decades, reports of toxic periphyton proliferations have increased and are linked with health problems in humans including asthma, skin rashes, liver damage, and the death of domestic dogs. Excess periphyton accrual is prominent in impounded catchments where dams have a considerable impact on flow and sediment regimes. With at least 3,700 large dams currently under construction or in the planning phase the problem is set to increase in the foreseeable future. Hydrological limits are widely implemented by authorities in an attempt to manage periphyton accrual. Hydrological limits are frequently based on flow-ecology relationships but are often ineffective. Sediment transport thresholds have been found to have a better relationship with periphyton accrual than hydrological metrics. Flow-ecology relationships do not account for the mechanisms of periphyton removal (scour, abrasion, and molar action) which are likely to vary between sites at equivalent flows, and the species-specific resistance to each mechanism also likely varies. Abrasion and molar action result from transport of sediment. Improving the effectiveness of hydrological limits as a tool for river management therefore relies on setting flows with the aim of inducing sediment transport to initiate mechanisms of periphyton scour. This will require models which can accurately predict the flow required to induce different phases of sediment transport. The research presented in this thesis focuses on improving the estimation of gravel entrainment to advance entrainment models as a means of setting hydrological limits to induce molar action and improve the effectiveness of periphyton removal. A literature review of methods for estimating gravel particle entrainment thresholds in natural channels revealed a considerable gap in methods being available to quantify substrate characteristics to calculate resistance thresholds. The review also found significant challenges in identifying the onset of gravel transport in natural channels, and difficulty obtaining corresponding hydrodynamic data to identify entrainment thresholds. Further, the review found seepage was an important component of hydrodynamic forces for inducing particle entrainment in flumes, but seepage is not considered in conventional entrainment formulae, and is not measured alongside bedload transport data in the field. A suite of tools is identified and developed to improve the quantification of substrate structure and resistance, identification of incipient motion, and quantification of entrainment thresholds in natural gravel beds to advance the assessment of bed mobility. Optical and ranging techniques are compared to identify an optimal approach to remotely quantify substrate structure. Both approaches were found to produce a comparable quantification of surface roughness using point cloud elevations, but identified different trends in surface layer development. Quantification of surface layer development was found to be sensitive to the cell size used to grid the data, and this sensitivity increased with higher-order statistical moments which were used to describe armouring. Airborne optical sensors were found to be the most versatile method for remote characterisation of gravel-bed surface structure, with a larger range of metrics being derivable from the same dataset to quantify a wider range of substrate structural and textural characteristics. Whilst quantifying bed structure is critical for developing bed mobility models, measuring the resistive force of the bed created by the structural arrangement of particles is required for model calibration and empirical data collection. A protocol was developed to use a modified penetrometer to quantify the resistive force of the armour (active) layer in gravel-bed channels. The modifications made to the penetrometer made it sensitive to variations in armour layer compactness, and allowed for adaptive penetration depths enabling variations in armour layer thickness to be accounted for. The protocol and modified penetrometer provide a significant advancement in the ability to empirically quantify bed resistance and relate bed structure to potential bed mobility, and build on the remote sensing methods to provide a suite of bed resistance parameters for entrainment models. Measurement of bed mobility is also critical for calibrating entrainment models and relating ecological metrics to bed mobility thresholds. Both direct and indirect measurement of bed mobility have benefits for research and river management. Tick-box indices are frequently used in ecological studies to provide an indirect assessment of substrate (in)stability (i.e. bed mobility). These indices often provide a poor approximation of bed mobility, and do not relate well with biotic communities, but their low-cost and rapidity make them a valuable tool for research and management. An improved index is developed to provide rapid, low-cost assessment of bed mobility. This index improves on previous methods by focusing on objective measurements of parameters where low-cost approaches are available, or providing a framework for scoring parameters where visual assessment is required. The index scores correlated well with tracer particle data, and were found to relate to accrual of Phormidium biomass. This index therefore provides a means to rapidly and cost-effectively estimate bed mobility and predict periphyton accrual. Direct measurement of bed mobility is also required to provide an empirical dataset for the calibration of particle entrainment and transport models, and for the empirical derivation of hydrological limits. A multi-sensor system was developed to measure the onset of particle movement, and record corresponding hydrodynamic data, including bed seepage, to identify hydraulic entrainment thresholds in natural channels, and therefore address the challenges of identifying bedload entrainment thresholds identified in the literature review. A pilot study testing the system identified bed seepage and turbulence intensity as key predictors of particle entrainment, and discharge and mean velocity as the worst predictors. These findings challenge the use of discharge and mean velocity as the metrics used to set hydrological limits if mechanistic limits based on bed mobility-ecology relationships are to be established effectively. These tools provide a means for scientists to study bedload entrainment and transport, identify their thresholds, and relate the frequency and magnitude of these processes to benthic community dynamics. This research will form the basis for establishing the mechanisms required to achieve removal of excess periphyton and establish hydrological limits to ensure these mechanisms function and effective removal of periphyton is achieved to maintain ecosystem health.
