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Subject: search.filters.subject.Adélie penguin

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    Mitochondrial DNA diversity and variability in the Adélie penguin of Antarctica : a thesis presented in partial fulfilment of the requirements for the degree of Master of Science in Genetics at Massey University, Palmerston North, New Zealand
    (Massey University, 2003) Gibb, Gillian Claire
    In Antarctica, there are two distinct lineages of Adélie penguin (Pygoscelis adeliae) characterised by 8.3% divergence in mitochondrial DNA hypervariable region I (mt DNA HVR I). These two lineages are known as the Antarctic and Ross Sea lineages (A and RS respectively). This study aims to characterise aspects of mutation and variation as seen in HVR I of the Adélie penguin, by sequencing the DNA of individuals from different locations around Antarctica. The geographic distribution of the two lineages was examined in greater detail. A dramatic decrease in the RS lineage was discovered on the edge of the Ross Sea region of Antarctica. Because the two lineages have different geographic distributions, and are separated by 8.3% sequence divergence, this study also investigated the possibility that these two lineages were in fact cryptic species. Sequencing of mt DNA and microsatellite genotyping proved that individuals of the two lineages mate randomly and produce offspring. Recently, a rate of evolution based on serially preserved DNA from Adélie penguins was estimated at 0.96 substitutions/site/Million years. (0.53-1.43 s/s/Myr). This rate is four to seven times higher than previous avian control region evolution rates estimated by phylogenetic methods, and is more akin to rates of mutation determined by pedigree studies in other species such as humans. In the light of this higher direct estimate of the rate of evolution in Adélie penguins, this study also begins to determine a rate of mutation in Adélie penguins based on pedigree analysis. No new mutations were found, however three cases of inherited single point heteroplasmy were detected. The inclusion of heteroplasmy in mutation rate calculation is also addressed. One of the arguments as to why pedigree studies find a higher rate of mutation than phylogenetic studies is that pedigree studies preferentially find mutations at 'hot spots' in the DNA sequence. This study also seeks to characterise the distribution of variable sites in hypervariable region I in relation to the two mt DNA lineages, and also to geographic location. While the exact sites of variation differ between the two lineages, it was seen that the regions where variation was high or low is very similar in both lineages. This could be due to underlying physical constraints on DNA sequence variation. Looking towards future work in Adélie penguin mt DNA and an expansion of the studies undertaken here, the complete mitochondrial genome of the Adélie penguin was determined. This now provides the opportunity to estimate rates of change in the entire Adélie penguin mitochondrial genome, using ancient DNA from the extremely well preserved sub-fossil bones in Antarctica.
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    Microsatellite 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 Dawn
    Microsatellites 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.