Demographic and selective inference in great apes
Abstract/Contents
- Abstract
- Humans and other great apes have intricate evolutionary histories, shaped by numerous demographic and selective events. A wealth of new genomic data provides the foundation for key insights into some of this complexity. This thesis develops tools for population genetic analyses, provides genome-wide insights into gorilla population genetics, and delivers fine-scale understanding of a specific human disease resistance allele. The chapters of this thesis provide complementary genome-wide and localized insights into great ape evolutionary history. Chapter 2 details a genetic simulation software that generates large-scale genetic data in flexible scenarios. Chapter 3 describes a study on the demographic and selective history of gorillas; we find a significant population contraction during the last glacial maximum (20 kya) in western lowland gorillas and evidence of positive selection in genes related to heart function and bitter taste perception. Chapter 4 is an in-depth analysis of one of the most population differentiated loci in the human genome, the DARC gene, which is known to provide resistance to a malaria-causing protozoan. We explore this gene's population genetics, including its geographical distribution and signatures of natural selection, as well as infer the mode and magnitude of selection on the malaria resistance allele. These chapters emphasize the importance of population genetics at various scales. Genome-wide methods allow identification of global trends, while in-depth analyses of specific loci provide insights into specific events and selective pressures shaping our genomes, and complement our large-scale inferences. This dissertation develops generalizable methods, achieves novel biological insights, and broadens our understanding of great ape evolutionary history.
Description
| Type of resource | text |
|---|---|
| Form | electronic; electronic resource; remote |
| Extent | 1 online resource. |
| Publication date | 2015 |
| Issuance | monographic |
| Language | English |
Creators/Contributors
| Associated with | McManus, Kimberly | |
|---|---|---|
| Associated with | Stanford University, Department of Biology. | |
| Primary advisor | Bustamante, Carlos | |
| Thesis advisor | Bustamante, Carlos | |
| Thesis advisor | Montgomery, Stephen, 1979- | |
| Thesis advisor | Petrov, Dmitri Alex, 1969- | |
| Thesis advisor | Pritchard, Jonathan D | |
| Advisor | Montgomery, Stephen, 1979- | |
| Advisor | Petrov, Dmitri Alex, 1969- | |
| Advisor | Pritchard, Jonathan D |
Subjects
| Genre | Theses |
|---|
Bibliographic information
| Statement of responsibility | Kimberly McManus. |
|---|---|
| Note | Submitted to the Department of Biology. |
| Thesis | Thesis (Ph.D.)--Stanford University, 2015. |
| Location | electronic resource |
Access conditions
- Copyright
- © 2015 by Kimberly Faith McManus
- License
- This work is licensed under a Creative Commons Attribution Non Commercial 3.0 Unported license (CC BY-NC).
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