Ostridge, Harrison James;
(2024)
Local genetic adaptation in chimpanzees.
Doctoral thesis (Ph.D), UCL (University College London).
Preview |
Text
Ostridge_10195599_thesis_ID_removed.pdf Download (49MB) | Preview |
Abstract
Chimpanzees, along with bonobos, are our closest living relatives and are endangered, with numbers continuing to decline. They inhabit a diversity of habitats in sub-Saharan Africa, from relatively cool and wet rainforest to hot and dry woodland-savannah. These environmental differences provide the opportunity for local genetic adaptations. Such adaptations would have important implications for conservation and our understanding of hominid evolution. However, studies of local adaptation in chimpanzees have been hindered by the difficulties associated with accessing genetic samples from endangered wild populations. This thesis investigates local genetic adaptation in chimpanzees for the first time by generating and analysing a new dataset of unprecedented scale and resolution, consisting of 828 exomes from non-invasive samples of wild individuals, together with newly collected environmental data. SNPs with exceptionally high population allele frequency differentiation (while accounting for population structure) provide limited evidence of local genetic adaptation. However, integrating a measure of habitat in a genotype-environment association (GEA) analysis results in increased power and finds evidence of local adaptation to habitat conditions on the genome-scale. Interestingly, candidate SNPs inferred to be beneficial in forest habitats are enriched for pathogen-related genes. Most notably, there is evidence for adaptation to malaria in lowland forests with selection targeting the same genes that underlie adaptation in humans. This work demonstrates the potential for population genomics using non-invasive samples to reveal fine-scale local adaptation in endangered wild populations.
| Type: | Thesis (Doctoral) |
|---|---|
| Qualification: | Ph.D |
| Title: | Local genetic adaptation in chimpanzees |
| Open access status: | An open access version is available from UCL Discovery |
| Language: | English |
| Additional information: | Copyright © The Author 2024. Original content in this thesis is licensed under the terms of the Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) Licence (https://creativecommons.org/licenses/by-nc/4.0/). Any third-party copyright material present remains the property of its respective owner(s) and is licensed under its existing terms. Access may initially be restricted at the author’s request. |
| UCL classification: | UCL UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences |
| URI: | https://discovery-pp.ucl.ac.uk/id/eprint/10195599 |
Archive Staff Only
 |
View Item |
