Massey Documents by Type

Permanent URI for this communityhttps://mro.massey.ac.nz/handle/10179/294

Browse

Subject: search.filters.subject.Huia

Search Results

Now showing 1 - 3 of 3
  • Thumbnail Image
    Item
    Nuclear and mitochondrial DNA evolution in Adélie penguins : studies of modern and ancient populations : a thesis presented in partial fulfillment of the requirements for the degree of Doctor of Philosophy (PhD) in Genetics, Allan Wilson Centre for Molecular Ecology and Evolution, Institute for Natural Sciences, Massey University, Auckland, New Zealand
    (Massey University, 2012) Beans Picón, Gabrielle Angela
    The Adélie penguin of Antarctica (Pygoscelis adeliae) breeds on the Antarctic continent and on offshore islands. Its evolutionary history has been, and its current biology remains, dependent on a range of climate variables. Over geological time, glacial warming and cooling periods have resulted in Adélie penguin populations decreasing and expanding. Therefore, understanding Adélie penguin population dynamics at a genetic level can provide insights into how the species responds to changing climates, one reason why Adélie penguins are an important natural model species. In addition, sub-fossil bone deposits of this species below modern and abandoned colonies provide an excellent source of ancient DNA that can bring a temporal dimension to population studies of the species. In combination, these attributes enable us to address some fundamental questions regarding evolutionary change. Making use of known mitochondrial DNA mutation rates and current population sizes, a positive and significant correlation between population size and modern mitochondrial control region diversity was detected. This finding supports the use of mitochondrial DNA for population inferences. Effective population sizes of breeding colonies are shown to have increased since the late Pleistocene. To extend current tools available for understanding Adélie penguins, six nuclear intron loci were recovered from a wide range of introns that can be applied to population genetics and phylogenetic studies of penguins. Five introns were used to investigate the persistence of the mitochondrial Antarctic (A) and Ross Sea (RS) lineages. No evidence for the existence of these lineages was found in the nuclear loci sequenced. A signature of historical population expansion, preceding the mitochondrial one, was detected. The utility of four introns in resolving penguin phylogenetic signals was also determined. Non-coding nuclear sequence of one intron were obtained from ancient sub-fossil remains of Adélie penguins using multiplex PCR enrichment, followed by second-generation sequencing of a barcoded library. A shift in haplotype frequencies was detected between ancient and modern intron sequences in Adélie penguins, despite a small sample size. In the future, advancing the current methodologies and extending sampling to additional introns as well as older samples, is likely to provide a new level of understanding of this remarkable species.
  • Thumbnail Image
    Item
    The molecular ecology of the extinct New Zealand Huia
    (Public Library of Science, 2009) Lambert D; Shepherd L; Huynen L; Beans Picon G; Walter G; Millar C
    The extinct Huia (Heteralocha acutirostris) of New Zealand represents the most extreme example of beak dimorphism known in birds. We used a combination of nuclear genotyping methods, molecular sexing, and morphometric analyses of museum specimens collected in the late 19th and early 20th centuries to quantify the sexual dimorphism and population structure of this extraordinary species. We report that the classical description of Huia as having distinctive sex-linked morphologies is not universally correct. Four Huia, sexed as females had short beaks and, on this basis, were indistinguishable from males. Hence, we suggest it is likely that Huia males and females were indistinguishable as juveniles and that the well-known beak dimorphism is the result of differential beak growth rates in males and females. Furthermore, we tested the prediction that the social organisation and limited powers of flight of Huia resulted in high levels of population genetic structure. Using a suite of microsatellite DNA loci, we report high levels of genetic diversity in Huia, and we detected no significant population genetic structure. In addition, using mitochondrial hypervariable region sequences, and likely mutation rates and generation times, we estimated that the census population size of Huia was moderately high. We conclude that the social organization and limited powers of flight did not result in a highly structured population.
  • Thumbnail Image
    Item
    Ancient 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 Dawn
    Ancient 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.