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Dissertation/Thesis Abstract

Inference of Recent Demographic History of Population Isolates Using Genome-Wide High Density SNP Arrays and Whole Genome Sequences
by Gladstein, Ariella, Ph.D., The University of Arizona, 2018, 298; 10839026
Abstract (Summary)

In this dissertation I addressed the problem of SNP array bias when finding runs of ho- mozygosity. I demonstrated the pitfalls of using uninformed methods for finding runs of homozygosity and provide better alternatives, including a more reliable algorithm for identi- fying runs of homozygosity than the most commonly used program. I then provide a review of Ashkenazi population genetics. Next, I developed software to efficiently run millions of whole chromosome simulations, which is publicly available through GitHub, DockerHub, and on the CyVerse Discovery Environment. I applied my computational method to use Approximate Bayesian Computation to test models of Ashkenazi Jewish demographic his- tory. I found that the Ashkenazi Jews are comprised of genetically distinct subgroups from Eastern and Western Europe, as a result of massive population growth in the Eastern Ashkenazi Jews, but not in the Western Ashkenazi Jews. I further confirmed that the Ashkenazi Jews do not primarily originate from Khazaria. Finally, I created a correction for SNP array ascertainment bias in the median and total length of runs of homozygosity, and applied this correction to world-wide human populations. However, I found that ascertainment bias plays a minor role compared to SNP array bias in human populations.

Indexing (document details)
Advisor: Hammer, Michael
Commitee: Barker, Michael, Gutenkunst, Ryan, Walsh, Bruce
School: The University of Arizona
Department: Ecology & Evolutionary Biology
School Location: United States -- Arizona
Source: DAI-B 79/12(E), Dissertation Abstracts International
Subjects: Genetics
Keywords: Computational biology, Genomics, Population genetics
Publication Number: 10839026
ISBN: 978-0-438-19098-6
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