Comparative and population genomics of large carnivores
Abstract/Contents
- Abstract
- The combined effects of land-use change, habitat loss, and climate change have placed incredible stress on species living through the Anthropocene. For charismatic megafauna, especially predators, these affects are exacerbated by additional losses from poaching and human-wildlife conflict. An open question in conservation biology and genomics, concerns how these declines manifest at the genomic level, and whether we can distinguish between populations that are on the precipice of extinction, compared to those which are simply small. In addition, there are several open questions as to how we can best manage these populations into the future; should low-diversity populations be mixed to maximize adaptive potential, or should the populations be managed separately to maintain unique lineages? Can genomics tell us something about recent and historic declines? In order to answer these questions, genome-level resources for the species in question are preferred, since patterns in the genome (such as heterozygosity and the accuracy of run of homozygosity detection) rely on highly-continguous assemblies and large amounts of whole-genome resequencing data. Here, I focus on the generation of high quality genomic data for members of the order which have experienced substantial declines over the last 100 years. I generate high-quality genome assemblies from several members of the Panthera group, including the lion, the snow leopard, the African leopard, and the tiger, in addition to high-quality genomes for several African wild dogs. I examine how using different reference assemblies can lead to biased estimates of various statistics of interest, such as heterozygosity and runs of homozygosity. I then focus on the tiger, detailing the patterns of variation and demographic history in the wild tiger, with a focus on individuals from India, where a previous lack of sampling has inhibited our evolutionary inference. Together, this scholarship provides an abundance of genomic data for species where little to no data existed, investigates the biases and pitfalls of genomic data, and uses range-wide sampling of a species of conservation concern to generate management recommendations based on signals of recent demographic declines.
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 | 2021; ©2021 |
| Publication date | 2021; 2021 |
| Issuance | monographic |
| Language | English |
Creators/Contributors
| Author | Armstrong, Ellie Elizabeth |
|---|---|
| Degree supervisor | Hadly, Elizabeth Anne, 1958- |
| Degree supervisor | Petrov, Dmitri Alex, 1969- |
| Thesis advisor | Hadly, Elizabeth Anne, 1958- |
| Thesis advisor | Petrov, Dmitri Alex, 1969- |
| Thesis advisor | Campana, Michael |
| Thesis advisor | Rosenberg, Noah |
| Degree committee member | Campana, Michael |
| Degree committee member | Rosenberg, Noah |
| Associated with | Stanford University, Department of Biology |
Subjects
| Genre | Theses |
|---|---|
| Genre | Text |
Bibliographic information
| Statement of responsibility | Ellie Elizabeth Armstrong. |
|---|---|
| Note | Submitted to the Department of Biology. |
| Thesis | Thesis Ph.D. Stanford University 2021. |
| Location | https://purl.stanford.edu/dk510pt1621 |
Access conditions
- Copyright
- © 2021 by Ellie Elizabeth Armstrong
- License
- This work is licensed under a Creative Commons Attribution Non Commercial 3.0 Unported license (CC BY-NC).
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