Genomewide ancestry and divergence patterns from low-coverage sequencing data reveal a complex history of admixture in wild baboons

Jeffrey D. Wall, Stephen A. Schlebusch, Susan C. Alberts, Laura A. Cox, Noah Snyder-Mackler, Kimberly A. Nevonen, Lucia Carbone, Jenny Tung

Research output: Contribution to journalArticle

26 Citations (Scopus)

Abstract

Naturally occurring admixture has now been documented in every major primate lineage, suggesting its key role in primate evolutionary history. Active primate hybrid zones can provide valuable insight into this process. Here, we investigate the history of admixture in one of the best-studied natural primate hybrid zones, between yellow baboons (Papio cynocephalus) and anubis baboons (Papio anubis) in the Amboseli ecosystem of Kenya. We generated a new genome assembly for yellow baboon and low-coverage genomewide resequencing data from yellow baboons, anubis baboons and known hybrids (n = 44). Using a novel composite likelihood method for estimating local ancestry from low-coverage data, we found high levels of genetic diversity and genetic differentiation between the parent taxa, and excellent agreement between genome-scale ancestry estimates and a priori pedigree, life history and morphology-based estimates (r2 = 0.899). However, even putatively unadmixed Amboseli yellow individuals carried a substantial proportion of anubis ancestry, presumably due to historical admixture. Further, the distribution of shared vs. fixed differences between a putatively unadmixed Amboseli yellow baboon and an unadmixed anubis baboon, both sequenced at high coverage, is inconsistent with simple isolation–migration or equilibrium migration models. Our findings suggest a complex process of intermittent contact that has occurred multiple times in baboon evolutionary history, despite no obvious fitness costs to hybrids or major geographic or behavioural barriers. In combination with the extensive phenotypic data available for baboon hybrids, our results provide valuable context for understanding the history of admixture in primates, including in our own lineage.

Original languageEnglish (US)
Pages (from-to)3469-3483
Number of pages15
JournalMolecular Ecology
Volume25
Issue number14
DOIs
StatePublished - Jul 1 2016

Fingerprint

Papio cynocephalus
Papio
ancestry
primate
Primates
divergence
History
history
hybrid zone
genome
Papio anubis
Genome
genome assembly
genetic variation
Kenya
Pedigree
genetic differentiation
pedigree
Ecosystem
life history

Keywords

  • admixture
  • Amboseli baboons
  • genome resequencing
  • hybridization
  • local ancestry

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Genetics

Cite this

Wall, J. D., Schlebusch, S. A., Alberts, S. C., Cox, L. A., Snyder-Mackler, N., Nevonen, K. A., ... Tung, J. (2016). Genomewide ancestry and divergence patterns from low-coverage sequencing data reveal a complex history of admixture in wild baboons. Molecular Ecology, 25(14), 3469-3483. https://doi.org/10.1111/mec.13684

Genomewide ancestry and divergence patterns from low-coverage sequencing data reveal a complex history of admixture in wild baboons. / Wall, Jeffrey D.; Schlebusch, Stephen A.; Alberts, Susan C.; Cox, Laura A.; Snyder-Mackler, Noah; Nevonen, Kimberly A.; Carbone, Lucia; Tung, Jenny.

In: Molecular Ecology, Vol. 25, No. 14, 01.07.2016, p. 3469-3483.

Research output: Contribution to journalArticle

Wall, JD, Schlebusch, SA, Alberts, SC, Cox, LA, Snyder-Mackler, N, Nevonen, KA, Carbone, L & Tung, J 2016, 'Genomewide ancestry and divergence patterns from low-coverage sequencing data reveal a complex history of admixture in wild baboons', Molecular Ecology, vol. 25, no. 14, pp. 3469-3483. https://doi.org/10.1111/mec.13684
Wall, Jeffrey D. ; Schlebusch, Stephen A. ; Alberts, Susan C. ; Cox, Laura A. ; Snyder-Mackler, Noah ; Nevonen, Kimberly A. ; Carbone, Lucia ; Tung, Jenny. / Genomewide ancestry and divergence patterns from low-coverage sequencing data reveal a complex history of admixture in wild baboons. In: Molecular Ecology. 2016 ; Vol. 25, No. 14. pp. 3469-3483.
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