Applying genomic approaches to address ecological, evolutionary, and clinical questions
Abstract/Contents
- Abstract
- Technological developments in genomics over the past two decades have allowed biologists to address long-standing questions in ecology, evolutionary biology, and medicine, but also pose a substantial challenge for analysis and interpretation. This thesis addresses these challenges by developing and testing novel genomic tools and resources as well as leveraging them to address basic biological questions. The thesis chapters are united in their focus on the origin and maintenance of natural genetic variation as well as its influence on phenotypic variation. The first introductory chapter expands upon the unifying themes and briefly outlines the history of the study of genetic variation, with a specific focus on aneuploidy. The second chapter focuses on reference genome assembly by identifying advantages and limitations of a new synthetic long-read technology for de novo genome reconstruction. The third chapter introduces a low-cost method to survey genetic variation in non-model species by simultaneously building a transcriptome reference and discovering expressed single nucleotide polymorphisms from a population sample. These genomic data are then used to infer the demographic history of an introduced checkerspot butterfly, achieving parameter estimates that are consistent with the known population history. The final two chapters focus on application of high-throughput genomic technologies in a clinical setting, specifically in the context of preimplantation genetic screening (PGS) during in vitro fertilization. PGS data are then analyzed to study variation in chromosome copy number (i.e. aneuploidy) which is prevalent in early human development, but rarely survives to live birth. The fourth chapter contrasts the incidences of various forms of aneuploidy at different stages of preimplantation development, demonstrating that mitotic-origin aneuploidies are strongly selected against at the onset of zygotic genome activation. The final chapter provides evidence that a maternal genetic variant influences aneuploidy risk, identifying a promising candidate gene in the region. Together, these dissertation chapters develop and apply novel genomic approaches to achieve new biological insights and pave the way for future genomic studies.
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 | McCoy, Rajiv Champion | |
|---|---|---|
| Associated with | Stanford University, Department of Biology. | |
| Primary advisor | Boggs, Carol | |
| Primary advisor | Petrov, Dmitri Alex, 1969- | |
| Thesis advisor | Boggs, Carol | |
| Thesis advisor | Petrov, Dmitri Alex, 1969- | |
| Thesis advisor | Fraser, Hunter B | |
| Thesis advisor | Palumbi, Stephen R | |
| Advisor | Fraser, Hunter B | |
| Advisor | Palumbi, Stephen R |
Subjects
| Genre | Theses |
|---|
Bibliographic information
| Statement of responsibility | Rajiv Champion McCoy. |
|---|---|
| Note | Submitted to the Department of Biology. |
| Thesis | Thesis (Ph.D.)--Stanford University, 2015. |
| Location | electronic resource |
Access conditions
- Copyright
- © 2015 by Rajiv Champion McCoy
- License
- This work is licensed under a Creative Commons Attribution Non Commercial 3.0 Unported license (CC BY-NC).
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