Browsing by Author "Shepherd, Lara Dawn"
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- ItemAncient DNA studies of the New Zealand kiwi and wattlebirds : evolution, conservation and culture : a thesis presented in fulfilment of the requirements of Doctor of Philosophy in Molecular BioSciences at Massey University, Albany, New Zealand(Massey University, 2006) Shepherd, Lara DawnAncient DNA was used to provide a temporal perspective for examining a number of evolutionary, conservation and cultural questions involving members of the New Zealand avifauna. Ancient mitochondrial DNA (mtDNA) sequences were used to examine the past levels and patterns of genetic diversity in the five species of New Zealand kiwi (Apterygidae). Brown kiwi, particularly in the South Island, exhibited high levels of genetic structuring with nearly every population exhibiting private mitochondrial haplotypes. The extinction of a large number of brown kiwi populations has, therefore, led to the loss of a large amount of genetic variation in these species. The past ranges of great spotted kiwi and the three brown kiwi species, whose bones are morphologically indistinguishable, were determined. This information can aid conservation programmes aiming to re-introduce kiwi to regions where they are now extinct. In contrast to the high level of genetic structuring in South Island brown kiwi, the majority of little spotted kiwi samples from the South Island shared a common haplotype. The difference in phylogeography between brown kiwi and little spotted kiwi is hypothesised to relate to differences in their dispersal behaviour and/or their population histories. The addition of ancient samples of little spotted kiwi from the North Island indicated a complex relationship with great spotted kiwi. Nuclear microsatellite DNA markers were isolated from North Island brown kiwi and tested for cross amplification in the other kiwi species. Five loci were polymorphic in all kiwi species. Preliminary analyses of genotyping results indicated that the kiwi species were distinguished by assignment tests and that subdivision may occur within several of the species. An extensive reference database of modern and ancient mtDNA sequences was used to determine species and provenance of a number of unlabelled museum subfossil bones and skins. This method was also used to examine provenance of brown kiwi feathers from Maori artefacts (cloaks and baskets). Ancient DNA methodology was also used in a molecular examination of the relationships of a second endemic avian family, the New Zealand wattlebirds (Callaeatidae). Analyses of nuclear gene sequences, c-mos and RAG-1, revealed kokako, saddleback and huia comprised a strongly supported monophyletic group. A divergence time estimate for the New Zealand wattlebirds indicated that they are more likely to have arrived by transoceanic dispersal than have a Gondwanan origin. Sequences from three mtDNA genes, 12S, ND2 and cytochrome b, were also analysed but could not resolve the relationships between the three genera. Microsatellite DNA from the extinct New Zealand huia exhibited considerable genetic variation, exceeding that found in extant North Island saddleback, from which the loci were isolated. Assignment tests indicated no genetic structuring within huia, although interpretation was complicated by a lack of provenance details for many of the skins. The results presented here suggest that ancient DNA can not only provide information about the relationships of extinct taxa but also demonstrates the importance of placing the present day genetic diversity found in endangered taxa within the context of past patterns and levels of genetic variation.
- ItemMicrosatellite evolution and population genetics of ancient and living Adélie penguins in Antarctica : a thesis presented in partial fulfilment of the requirements for the degree of Master of Science in Biological Sciences at Massey University(Massey University, 2001) Shepherd, Lara DawnMicrosatellites are widely used as genetic markers for examining a variety of biological questions. Despite their widespread use, little is known about the processes by which they evolve. An accurate understanding of these processes is essential for their correct use as population genetic markers. In this study, microsatellite loci from both living and cryopreserved (AMS 14C dated at up to 6424 years BP ±80) Antarctic Adélie penguins (Pygoscelis adeliae) were examined in order to gain insights into temporal population genetics and the evolution of microsatellite loci. Firstly, ancient DNA extracted from Adélie penguin subfossil bones was found to be extremely well-preserved and readily allowed the amplification of single-copy nuclear microsatellite DNA. Genotyping six microsatellite loci in ancient and living samples from three populations of Adélie penguins in the Terra Nova Bay region allowed a comparison of genetic change over time. Although the ancient sample sizes were limiting, several statistical tests indicated that the ancient and living populations from Inexpressible Island were genetically distinct. In addition, differentiation was also inferred between the three ancient populations that were examined, which is in contrast to the lack of differentiation found between the living populations. These genetic changes may be a result of population expansion out of ice-age refugia since the Last Glacial Maximum. To study microsatellite evolution over a substantial time period, up to 500 living and 100 cryopreserved Adélie penguins were genotyped at six microsatellite loci. No novel electromorph alleles were detected in the ancient samples. Numerous alleles were sequenced from four of these loci in both Adélie penguins and several other species of penguin (Spheniscidae). Analysis of these sequences provided an insight into the mutational processes occurring at these loci. In particular, these allele sequences revealed extensive size homoplasy, both within Adélie penguins and between penguin species. At one locus, variation in the flanking region allowed discrimination between the mechanisms proposed for length change at microsatellite loci. Slippage was the most plausible mechanism for length change. In this same locus, instability was observed in the region bordering the repeat tract with a transversional bias predominating. This bias may be a caused by inaccurate DNA replication resulting from structural features of DNA.