Inverse problems in the Pacific : ancestry deconvolution and dimensionality reduction for reconstructing human settlement in Oceania
Abstract/Contents
- Abstract
- The settlement of Polynesia represents a uniquely structured final chapter in the historical founding events of the human species; however, the population history of its many islands remains largely unknown. Resolving the detailed sequences of islands settled and dates of settlement requires careful attention to both haplotype and genetic drift based methodologies. These must be developed within a framework that accounts for the confounding effects of subsequent waves of complex admixture. I will describe the novel methods I have developed for a dataset consisting of hundreds of human DNA samples sequenced at seven hundred thousand genomic sites each and spanning the Pacific in order to unravel the peopling of this region, and the timing of island interactions, for the first time from a genomic perspective. I will discuss an algorithm for reconstructing the ancestral migration graph based on combining directionality measures with dissimilarity measures, a method for dating settlement based on haplotypes, and a matrix completion based method for visualizing ancestry specific patterns of population differentiation. Based on these new methods I will present findings about the origin and timing of specific events, including strong evidence for a complex pre-European admixture event between Polynesians and Native Americans within several of the easternmost island populations.
Description
| Type of resource | text |
|---|---|
| Form | electronic resource; remote; computer; online resource |
| Extent | 1 online resource. |
| Place | California |
| Place | [Stanford, California] |
| Publisher | [Stanford University] |
| Copyright date | 2018; ©2018 |
| Publication date | 2018; 2018 |
| Issuance | monographic |
| Language | English |
Creators/Contributors
| Author | Ioannidis, Alexander |
|---|---|
| Degree supervisor | Bustamante, Carlos |
| Thesis advisor | Bustamante, Carlos |
| Thesis advisor | Feldman, Marcus W |
| Thesis advisor | Moreno-Estrada, Andrés |
| Degree committee member | Feldman, Marcus W |
| Degree committee member | Moreno-Estrada, Andrés |
| Associated with | Stanford University, Institute for Computational and Mathematical Engineering. |
Subjects
| Genre | Theses |
|---|---|
| Genre | Text |
Bibliographic information
| Statement of responsibility | Alexander Ioannidis. |
|---|---|
| Note | Submitted to the Institute for Computational and Mathematical Engineering. |
| Thesis | Thesis Ph.D. Stanford University 2018. |
| Location | electronic resource |
Access conditions
- Copyright
- © 2018 by Alexander Ioannidis
- License
- This work is licensed under a Creative Commons Attribution Non Commercial 3.0 Unported license (CC BY-NC).
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