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Global and local ancestry estimation in a captive baboon colony
Christopher Kendall1, Jacqueline Robinson2, Guilherme Debortoli3
1Department of Anthropology, University of Toronto, Toronto, Ontario, Canada.
Plos One
|July 3, 2024
Summary
Genetic ancestry analysis of baboons reveals historical admixture and pedigree errors. This study provides updated genetic resources and ancestry informative markers for primate research.
Area of Science:
- Primate genetics
- Evolutionary biology
- Population genetics
Background:
- Hybridization studies are crucial for understanding primate evolution.
- Baboon (Papio) genetic research benefits from detailed ancestry information.
Purpose of the Study:
- To estimate genetic ancestry in captive baboons using dense genome data.
- To identify historical admixture and pedigree inaccuracies.
- To improve genetic resources for future baboon studies.
Main Methods:
- Utilized dense, full genome data from 881 baboons (Papio anubus, Papio cynocephalus, and hybrids).
- Performed genome imputation for low-coverage samples (n=830).
- Compared phasing/imputation pipelines and global ancestry estimation software.
Main Results:
- Detected historical admixture in supposedly purebred baboons.
- Identified errors in the Southwest National Primate Research Center pedigree.
- Found good agreement between global ancestry software (R2 > 0.88) but pipeline-dependent phase switch errors.
Conclusions:
- Genetic ancestry estimation can uncover hidden admixture and pedigree issues.
- Updated genetic maps and ancestry informative markers (n=1,747) are now available.
- This work enhances the genetic resources for baboon research and evolutionary studies.
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