|Title:||Evolutionary Analysis of Ancient DNA Sequences|
|Publisher:||University of Sydney.|
School of Biological Sciences.
|Abstract:||Studies of genetic data from old specimens – ancient DNA – offer a unique possibility to explore evolutionary history. Ancient DNA allows examination of past populations, extinct prehistoric species, and even large-scale analyses of past ecosystems. Since the beginnings of ancient DNA research in the mid 1980s, the field has undergone major technological and methodological transitions. However, investigations of the theory and methods used to analyse ancient DNA sequences have not kept up with the rapid pace of data generation. This thesis investigates a number of issues associated with the evolutionary analysis of ancient DNA. First, I built a model of post-mortem DNA degradation and examined its potential effects on the resulting sequence data (Chapter 2). Second, I conducted a large-scale study of time-dependent rates in order to look into their causes, characteristics, and ubiquity (Chapter 3). Third, I explored the impact of incorporating uncertainties associated with sample age into phylogenetic analysis (Chapters 4 and 5). Fourth, I evaluated the performance of Bayesian skyline plots in detecting recent population bottlenecks (Chapter 6). Finally, I combined several of these developments in a biogeographical analysis of the extinct cave bear (Chapter 7). My thesis shows that many of the common practices in ancient DNA studies, such as employing sequence-authentication criteria or ignoring age uncertainty in phylogenetic analyses, appear to be effective and to produce reliable results. However, there are areas in which more caution is needed when interpreting the results of DNA analyses. These include estimations of evolutionary rates, which are highly sensitive to the calibration points that are used; and the poor performance of Bayesian skyline reconstructions of recent population-size changes. The results of my studies improve our understanding of ancient DNA research and will serve as a useful guide for future evolutionary analyses of ancient DNA sequences.|
|Description:||Includes published papers co-authored with others|
|Access Level:||Access is restricted to staff and students of the University of Sydney . UniKey credentials are required. Non university access may be obtained by visiting the University of Sydney Library.|
|Rights and Permissions:||The author retains copyright of this thesis. It may only be used for the purposes of research and study. It must not be used for any other purposes and may not be transmitted or shared with others without prior permission.|
|Type of Work:||PhD Doctorate|
|Type of Publication:||Doctor of Philosophy Ph.D.|
|Appears in Collections:||Sydney Digital Theses (University of Sydney Access only)|
|molak_me_thesis.pdf||PhD thesis||5.36 MB||Adobe PDF|
Items in Sydney eScholarship Repository are protected by copyright, with all rights reserved, unless otherwise indicated.