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    Species delimitation and the population genetics of rare plants : a case study using the New Zealand native pygmy forget-me-not group (Myosotis; Boraginaceae) : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Plant Biology at Massey University, Manawatū, New Zealand
    (Massey University, 2016) Prebble, Jessica Mary
    Myosotis L., the forget-me-nots, is a genus of about 100 species distributed in the Northern and Southern Hemispheres. There are two centres of diversity, Eurasia and New Zealand. The New Zealand species are a priority for taxonomic revision, as they comprise many threatened species and taxonomically indeterminate entities. This thesis includes a taxonomic revision of the native New Zealand Myosotis pygmaea subgroup, followed by an exploration of the genetic effects of rarity, and implications for conservation management. Species delimitation follows the general lineage model, in which multiple lines of evidence are analysed to identify evolutionary lineages. The morphological data collected from herbarium specimens and live plants grown in a common garden were used to delineate the M. pygmaea group and identify several groups within it that nearly matched the current taxonomy. High levels of plasticity were also uncovered. Microsatellite loci were developed as polymorphic markers for the M. pygmaea group for species delimitation and conservation genetics. Over 500 individuals were genotyped, mostly focusing on the M. pygmaea group but including several outgroup species for comparison. Several genetic clusters were identified showing morphological or geographic patterns. Considering both the genetic and morphological data, as well as novel ecological niche modelling, there is evidence for three main lineages within the M. pygmaea group which are formally recognised as M. antarctica, M. brevis and M. glauca. M. antarctica is further subdivided into two subspecies based on allopatry and morphology, namely subsp. antarctica and subsp. traillii (formerly M. drucei + M. antarctica and M. pygmaea, respectively). Using this new taxonomic framework to explore genetic variation relative to rarity shows very little difference among species. This is most likely due to the confounding effect of high levels of self-fertilization and low dispersal, which means that the majority of genetic variation within these species is partitioned between, rather than within populations. The implication for conservation is that each population is equally important in terms of their contribution to the genetic diversity of each species. This thesis represents a major increase in our knowledge of the evolution, systematics, taxonomy, rarity and conservation of New Zealand native forget-me-nots.
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    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 Margaret
    Currently 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.
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    Rates of molecular evolution and gene flow : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Zoology, Massey University, New Zealand.
    (Massey University, 2013) Dowle, Eddy Jocelyn
    Species diversity is driven by speciation, extinction and immigration. In this thesis I explore species diversity among regions and the process of speciation via four related studies. The latitudinal biodiversity gradient (LBG) describes the pattern of higher diversity levels towards the tropics. One of the popular hypotheses to explain the LBG is the evolutionary speed hypothesis, which suggests that species in the tropical regions are evolving faster than those in temperate regions. I demonstrate that current work on the LBG often focuses on describing the pattern as distinct from understanding the process that might drive the LBG (chapter 1). Second, I show that the most popular method used to measure differences in rate of molecular evolution between taxa from different regions, the sister-species method, does not give consistent results and estimated rates of molecular evolution can vary widely depending on outgroup selection and gene analysed. The inherent problems revealed within the current approaches raise questions as to the validity of inferences made from putative variation in rate of molecular evolution between high and low latitudinal taxa. In particular, I show that studies of the LBG that use very close sister-species pairs, rely on the most problematic datasets and should therefore be treated with considerable scepticism (chapter 2). A phenomenon such as the LBG must derive from small-scale processes in population dynamics. Species are sometimes defined as reproductively isolated units, with hybridisation viewed as evidence of failure to speciate. But it is now increasingly acknowledged that speciation is a dynamic process during which species and populations can exchange alleles. I found relatively high levels of admixture and gene flow between morphologically distinct biological entities in two very different study systems: insects and snails. Analyses of a pair of grasshopper species provided no evidence of deviation from random mating in the region where they are sympatric. However, analysis of morphological traits provided no evidence for hybrid phenotypes between these Sigaus grasshoppers. I infer that some loci associated with these morphological characters are subject to strong natural selection but neutral genetic material is being extensively shared between the two species (chapter 3). A similar situation was found in terrestrial snails that I studied, but in this case there was a clear association of neutral genetic makers with phenotype. The mtDNA haplotypes, 3,764 SNP loci and morphometric data revealed two clear genotypic clusters among New Caledonian Placostylus, despite strong evidence for gene flow (chapter 4). Although it is convenient and popular to define species on the basis of their reproductive isolation, a more dynamic model that allows for the possibility of gene flow is closer to reality for these taxa. Speciation can be complex and our current understanding of the process of speciation does not suggest it is limited by the genomes' rate of molecular evolution. Results from my research shows, in support of other recent research, that the process of speciation is often the product of adaptation.
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