Please use this identifier to cite or link to this item: http://hdl.handle.net/2440/120205
Type: Thesis
Title: Inferring the Characteristics of Ancient Populations using Bioinformatic Analysis of Genome-wide DNA Sequencing Data
Author: Gower, Graham Richard
Issue Date: 2019
School/Discipline: School of Biological Sciences
Abstract: In this thesis, I apply, evaluate, and develop methods for learning about past populations from genome-wide sequencing data. Specifically, I: • apply methods based on random genetic drift between populations, to determine that pre-Holocene gene flow occurred between the ancestors of domestic cattle (Bos primigenius) and European bison (Bison priscus), and that the contribution of Bos genealogy to the bison lineage was less than 10 %; • use simulations to assess the impact of short genomic scaffolds when inferring past populations sizes with the pairwise sequentially Markov coalescent, and show that population size inferences can be robust for scaffold lengths as short as 100 kb; • perform genetic sex determination of ancient DNA specimens to show that bison (Bison spp.) and brown bear (Ursus arctos) specimens are approximately 75% male, and that male-biased observations likely stem from the ecological and social structures of the populations; • and develop a suite of software tools for processing hairpin bisulfite sequencing data, which can be used to investigate genome-wide DNA methylation levels in ancient DNA.
Advisor: Cooper, Alan
Llamas, Bastien
Mitchel, Kieren
Dissertation Note: Thesis (Ph.D.) -- University of Adelaide, School of Biological Sciences, 2019
Keywords: Ancient DNA
bioinformatics
population genetics
Provenance: This electronic version is made publicly available by the University of Adelaide in accordance with its open access policy for student theses. Copyright in this thesis remains with the author. This thesis may incorporate third party material which has been used by the author pursuant to Fair Dealing exceptions. If you are the owner of any included third party copyright material you wish to be removed from this electronic version, please complete the take down form located at: http://www.adelaide.edu.au/legals
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