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    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, Nimeshika
    One 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.
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    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 Gratianne
    Building 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.
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    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, Sam
    Inbreeding 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.
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    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 Martin
    Data 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.