Massey Documents by Type
Permanent URI for this communityhttps://mro.massey.ac.nz/handle/10179/294
Browse
8 results
Search Results
Item Population genetics and genomics of a marsupial species : analysis of native and invasive brushtail possum populations (Trichosurus vulpecula) : a dissertation presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Conservation Biology, Massey University, Manawatū Campus, New Zealand(Masey University, 2024-04-15) Pattabiraman, NimeshikaOne of the leading causes of global biodiversity decline is the introduction of invasive pest species that destroy native flora and compete with native fauna for food and other resources. Aotearoa New Zealand is one of the foremost countries in the world that has focussed on eradicating pest species and in particular exotic mammals from the archipelago, which lacks native, terrestrial mammals. The New Zealand Government recently set in train the ambitious task of removing all mustelids, rats, and possums from the terrestrial landscape by the year 2050. Brushtail possums (Trichosurus vulpecula) were introduced to Aotearoa New Zealand from Australia in the mid-1800s, after which they were translocated across the country and have become widespread, destroying indigenous habitat, eating native birds and invertebrates, and spreading bovine TB. Control efforts have seen possum numbers decline in the last two decades from close to 75 million in 2002 to 40 million in 2020. There is, however, a gap in the scientific understanding of possum populations with respect to their genetic composition and population structure across the country, and this knowledge could help us develop effective and dynamic management strategies to eradicate possums on a nationwide scale. In this thesis, I focus on three aspects of population structure and diversity of brushtail possums. First, I investigated a small geographical study area - The Kenepuru Peninsula - where I sought evidence of genetic correlations with geography, time and fur colour. I used two types of genetic markers that target the nuclear and mitochondrial regions of possum DNA with large population samples. In every case, it was determined that the possums comprised one freely interbreeding population at this scale. In particular I demonstrated that colour morphs associated with distinct subspecies in Australia, freely interbreed in New Zealand. I then increased the scale of sampling to include representation of populations across New Zealand and Australia, with the same genetic markers. This threw light on the heterogenous nature of possum diversity in New Zealand, and showed that even after ~110 generations, possums retained genetic separation among spatial groups. Additionally, the data showed evidence of multiple possum lineages across New Zealand that are derived from several Australian populations. High haplotype diversity in New Zealand suggests that the rapidly expanding population has retained novel haplotypes and the data thus far indicated a non-homogenous (metapopulation) distribution of possums without geographical concordance. As the project progressed, I was able to apply high-throughput genotyping-by-sequencing to generate a large genomic dataset. This dataset provided much more detail of the genotypic distribution of possums in Australia and among invasive metapopulations in New Zealand, as well as informing us of the relationship between them. This large, robust database of possum population structure and genetic diversity throughout Aotearoa New Zealand will support future studies in providing informed management decisions to eradicate brushtail possums.Item Understanding the population genetic structure of bovine mastitis-causing Staphylococcus aureus in New Zealand to identify potential vaccine candidates using reverse vaccinology : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Veterinary Science at Massey University, Palmerston North, New Zealand(Massey University, 2021) Nesaraj, JabinStaphylococcus aureus is one of the major causes of bovine mastitis in New Zealand and worldwide, causing severe economic loss to the dairy industry. With significant advances in whole-genome sequencing (WGS) and associated bioinformatics, S. aureus from bovine mastitis has been studied worldwide, but the understanding of the organism's genomics is still incomplete. To my knowledge, there have been no published WGS studies of S. aureus in dairy cattle in New Zealand to date. As WGS has become more affordable, and the concomitant bioinformatic analysis offers high-resolution indiscriminating betweenS. aureus lineages, WGS analysis was applied to a sample of S. aureus isolates obtained from dairy cattle in New Zealand. The work is undertaken in this thesis utilised advanced WGS analyses to study the genomic epidemiology ofS.aureusfrom dairy cattle over a period of 15 years. The findings from the analysis enabled a subsequent reverse vaccinology analysis that identified a number of conserved peptides potentially useful for incorporation in subunit vaccines for cattle. The first study analysed the population genetic structure of the pathogen using 188 bovineS. aureus isolates were collected from dairy farms across New Zealand in 2002-03, 2013-14, and 2017-18. Ruminant-specific and non-specific clonal complexes(CCs) were identified. CC1 was the dominant CC, a unique feature not observed in dairy cattle in other countries. CC1 was predominant in cattle in the three periods of isolate collection, suggesting a stable and successful clonal lineage. Interestingly, CC1is also the predominant CC in humans in New Zealand, and is mainly associated with humans in other countries and is not commonly reported in cattle. The second study compared the genomes of the bovineS. aureus isolates from the first study with genomes of quasi-contemporaneous human, canine and feline(n=59), and small ruminant (n=30) isolates also collected in New Zealand. Comparative genomic analyses of the core and accessory genomes were used to assess the effect of the host species of origin on the phylogenetic clustering of the isolates, and to identify host-specific/host-adaptive genomic signatures. Comparative analysis of CC1isolates identified marked phylogenetic segregations of both the core and accessory genomes among cattle and humans, and the presence of previously described ruminant-adaptive genes in bovine isolates, but not in human isolates. To my knowledge, this is the first report of ruminant host adaptation within CC1. The third study compared the antimicrobial resistance results obtained using the Disk Diffusion test (DD) with a resistome analysis, to assess the potential usefulness of WGS analysis to predict the antimicrobial resistance phenotype of bovineS. aureus. The antimicrobial resistance genes identified were: theβ-lactamase geneblaZ, the erythromycin resistance gene ermC, the streptomycin resistance gene str, and the fusidic acid resistance gene fusC. WGS identification of theblaZgene had a sensitivity of 71% and a specificity of 100% in predicting resistance when the DD test was considered the reference standard. Similar analyses could not be performed with other antimicrobials due to the low frequency of other resistance genes in the sample. Finally, the information obtained from the first two studies was used to construct a reverse vaccinology bioinformatic pipeline to identify potential vaccine candidate (PVC) proteins for S. aureus mastitis. Eighteen PVC proteins were identified using a range of bioinformatics tools. Some of these proteins have previously been shown to be immunogenic through in vitro and animal studies, providing cross-validation to the pipeline, while others have not yet been tested. In summary, this thesis presents a detailed description of the population genetic structure of bovine mastitis-causing S. aureus in New Zealand over 15 years. The work provides new insights into the complex mechanisms of S. aureus host-adaptation to ruminants and identifies some obstacles for the successful application of genomic analysis for the prediction of the antimicrobial resistance phenotype of clinical S. aureus isolates. Potentially useful proteins to be included in subunit vaccines for cattle are also reportedItem A study of some aspects of the genetic variation and covariation of fertility in a flock of New Zealand Romney ewes : being a thesis presented in partial fulfilment of the requirements for the degree of M.Agr.Sc, Massey Agricultural College, University of New Zealand, May 1955(Massey University, 1955) Ch'ang, Tang Seng"Fertility" is a term generally used to denote the expression of reproductive performance. Any precise definition of "Fertility", however, must depend ultimately on the purpose for which it is intended and the criterion by which it is measured. For the present purpose "Fertility" may be regarded as the rate of reproduction which is measured by some form of a lambing percentage. The economic importance of fertility in sheep production has not been, until recently, fully appreciated, but still less has its significance in the genetic improvement of sheep been realised. [FROM INTRODUCTION]Item Modeling the role of social structures in population genetics : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Statistics at Massey University, Manawatu, New Zealand(Massey University, 2015) Guillot, Elsa GratianneBuilding on a theoretical framework, population genetics has been widely applied to diverse organisms, from bacteria to animals. On humans, this has led to the reconstruction of history, the timing of settlements, and migration between populations. Mostly based on the coalescent theory, modern population genetic studies are challenged by human social structures, which are difficult to incorporate into analytically models. The implications of social structure on population genetics are mostly unknown. This work presents new modeling and inference methods to model the role of social structure in poulation genetics. The applications of these new techniques permit to gain better understanding of the history and practices of a number of Indonesian island communities. This thesis comprises three published, organized as sequential chapters. The Introduction describes population genetic models and the statistical tools that are used to make inferences. The second chapter presents the first paper, which measures the change of population size through time on four Indonesian islands structured by history and geography. The third chapter presents SMARTPOP, a new simulation tool to study social structure, including mating systems and genetic diversity. The fourth chapter focuses on Asymmetric Prescriptive Alliance, a famous kinship system linking the migration of women between communities with cousin alliance. The fifth chapter presents a conclusion and future directions. In combination, this body of work shows the importance of including social structure in population genetics and proposes new ways to reconstruct aspects of social history.Item A population genetics approach to species delimitation in the genus Selliera (Goodeniaceae) : a thesis submitted in partial fulfilment of the requirements for the degree of Master of Science in Plant Biology at Massey University, Palmerston North, New Zealand(Massey University, 2014) Pilkington, Kay MargaretCurrently there is only one internationally recognised species of Selliera, Selliera radicans. In New Zealand, three species have been described based on morphology and geographic location although there is disagreement about whether these actually constitute different species. Selliera rotundifolia is distinguished from S. radicans by rounder leaves and a preferred dune habitat compared to the estuary habitat of S. radicans. Selliera microphylla is distinguished from S. radicans by a smaller size and inland location. However, S. microphylla reverts to a size similar to S. radicans when grown in the same environment, but a single chromosome count for S. microphylla on the Central Volcanic Plateau is 2n=56. Both S. rotundifolia and S. radicans have chromosome counts of 2n=16. Species delimitation is important in biology, conservation, and evolutionary studies but remains a difficult task. I applied a population genetics approach combined with morphological analysis of leaves and existing karyotype data to determine the species boundaries within Selliera. Microsatellite markers are ideal for use in population genetics due to the higher mutation rate, genotyping ease and their co-dominant nature. No microsatellite markers previously existed for use in Selliera. In this study, next generation sequencing was used to develop microsatellite markers for Selliera. From 8,101 independent sequence contigs, 107 microsatellite loci were detected and primer pairs designed for these. Forty-three of these primer pairs were chosen to be screened and nine of these were reliably amplifiable and polymorphic. These nine markers were genotyped over 618 samples from Selliera comprising the three described species. Populations within all three described species showed high differentiation and S. radicans was variable for population structure. Leaf morphological analyses suggested there was a distinct difference between the three species. Microsatellite data revealed two genetic clusters in S. microphylla which clustered into the North Island and South Island populations. Two genetic clusters were also observed in S. rotundifolia which each clustered with different S. radicans populations suggesting round leaves may have had multiple origins. Hybridization was observed at one sympatric site between S. radicans and S. rotundifolia and apparent reproductive isolation for S. rotundifolia was observed at another site. These results suggest that the South Island S. microphylla population may be an inland variant of S. radicans which may continue to diverge if it remains isolated, while the North Island populations should retain the S. microphylla name due to the 2n=56 chromosome count, geographic isolation and genetic distinction although this needs further review. There is evidence of reproductive isolation for S. rotundifolia at one of the sympatric sites suggesting this is a distinct species but it appears round leaves may have had multiple origins so may not be suitable to describe the species according to the lineage species concept. This study provides insights into the population structure within and between the described species and has identified interesting areas of future study.Item One- and two- locus inbreeding for recurrent selection and overlapping generations selection schemes : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Statistics at Massey University(Massey University, 1978) Choy, SamInbreeding coefficients at one and two loci are evaluated for recurrent selection and overlapping generations selection schemes. These mating schemes have found great use in plant and animal breeding. The inbreeding coefficients are derived in terms of probability measures that genes are identical by descent. The procedures demonstrated here can be applied to any regular system of mating between individuals or groups of individuals. For individual mating systems, two digametic individual measures are defined and employed in the derivation of a recurrence formula for the one-locus inbreeding coefficients. Two further classes of individual measures, trigametic and quadrigametic, are required for transition from one generation to the previous one to allow the calculation of the inbreeding coefficients for the two-locus case. This process is illustrated for the case of recurrent selection. For recurrent selection populations with various imposed assumptions, numerical values of the average inbreeding coefficients at the end of the breeding cycles are listed to demonstrate the effects of linkage and population size on the accrual of inbreeding and hence of homozygosity. For group mating systems, gametic set measures are needed in addition to the average individual measures. Transition equations relating values in successive generations of gametic set measures are established for the calculation of the group inbreeding coefficients. As an illustration of this process, the one- and two-locus inbreeding coefficients for populations with overlapping generations are evaluated. Both monoecious and dioecious populations of diploids are considered and family size is not restricted to being Poisson. Inbreeding effective numbers found by the exact treatment here are compared to various previous approximate results.Item A study of the variability of estimates of heritability and their standard errors derived by paternal half-sib techniques using simulated data : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Animal Science at Massey University(Massey University, 1989) Rendel, John MartinData sets were generated that varied in the number of sires (20, 50, 100, 150 and 200) and progeny per sire (a mean of 20, 50, 70 and 100). These data sets were generated far balanced data and, in an effort to approximate actual flock data, unbalanced data based on a normal distribution of progeny per sire with standard deviations of 2, 5 and 7. In addition, data sets were generated with a standard deviation of 14, 25 and 29 progeny per sire, but for data set size of 100 sires with a mean of 100 progeny per sire, only. Also, numbers of progeny per sire and numbers of sires from 6 actual flocks were used to generate data sets. The sets were generated to conform with a 1-way random model with, the sire variance set at 0.6783 and error variance at 11.0106, giving a paternal half-sib heritability of 0.2321. Each combination of number of sire and progeny per sire was generated 100 times (i.e. 100 replicates) at each level of unbalance. Sire and error variances and heritabilities were estimated, as well as their standard errors, for each replicate using Henderson's Method 1 (HM), Maximum Likelihood (ML) and Restricted Maximum Likelihood (REML). There was good agreement between the population heritabilities and sire and error variances, and the corresponding mean of the replicates that made up each data set. There was also little difference between the results of the 3 methods of estimating the variance components. The Mean Squared Error (MSE) was similar for each method except for the data sets based on the flocks where the MSE of the sire variances for HM was larger than those for ML and REML. The MSE was largest for data sets consisting of 20 sires and 50 sires with a mean of 20 progeny per sire. The standard errors of the heritability and sire and error variances appear to be good indicators of the variation of estimates within data sets regardless of the level of unbalance or method of estimation. The differences between heritability estimates from 31 flocks for weaning weight of Coopworth lambs was shown to be greater than that estimated by the standard error. The implications of this are discussed with respect to the problems of pooling estimates from various sources.Item Population genetics, biogeography and ecological interactions of the New Zealand bellbird (Anthornis melanura) and their avian malaria parasites : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy (Ph.D.) in Zoology at Massey University, Albany, New Zealand(Massey University, 2011) Baillie, Shauna MaureenHabitat loss and redistribution of species has lead to population declines and loss of genetic diversity with serious implications to species survival on ecological and evolutionary scales. While there is no doubt that rapidly dwindling endangered populations require our immediate attention, studies on common species are equally important. The purpose of this thesis is to investigate the genetic connectivity, biogeographical relationships and host-parasite interactions of a common and widely distributed bird species, mainly because we want common species to remain common. Furthermore, I illustrate how studies such as this provide invaluable comparisons for sympatric endangered species. In this thesis, patterns of genetic variation of the New Zealand bellbird (Anthornis melanura) are delineated to assess their re-colonization potential among fragmented landscapes. Using a phylogeographic perspective I show how dispersal ability and secondary contact among isolated population fragments shape the evolutionary trajectory of a species. I also determine the biogeographical relationships between the bellbird host and its malaria parasites with key emphasis on host-parasite specificity. Finally, immunological trade-offs are investigated in disease epidemiology by examining host factors that influence malaria prevalence. I show that an immense capacity for dispersal has prevented divergence and shaped the high levels of genetic diversity and connectivity in bellbirds today. However, substantial genetic differentiation among subpopulations reflects recent habitat fragmentation. Based on these findings I conclude that continued habitat loss can lead to further reductions in gene flow, despite dispersal. Though restricted to northern populations, I provide evidence that the most abundant avian malaria lineage infecting bellbirds is likely an endemic Plasmodium (Novyella). This parasite exhibits bimodal seasonality and male-biased infections, but these relationships vary among subpopulations. Malaria prevalence appears to be governed by food availability and territory stability, thus habitat disturbance has repercussions to immune phenotype. With this thesis I advocate a re-thinking of conservation strategies toward spatial planning that enables ‘natural’ secondary contact among habitat fragments. Translocation is not necessary for all species. In addition to being the first study on seasonal and host factors affecting malaria patterns in the Southern Hemisphere, this thesis makes major contributions to science by elucidating some ecological relationships that underpin the evolution of immunity.