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Estimating Pan evolutionary history from nucleotide site patterns

View ORCID ProfileColin M. Brand, Frances J. White, View ORCID ProfileAlan R. Rogers, View ORCID ProfileTimothy H. Webster
doi: https://doi.org/10.1101/2022.01.07.475438
Colin M. Brand
1Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA, USA
2Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA
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  • ORCID record for Colin M. Brand
  • For correspondence: colin.brand@ucsf.edu timothy.h.webster@utah.edu
Frances J. White
3Department of Anthropology, University of Oregon, OR, USA
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Alan R. Rogers
4Department of Anthropology, University of Utah, UT, USA
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Timothy H. Webster
4Department of Anthropology, University of Utah, UT, USA
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  • ORCID record for Timothy H. Webster
  • For correspondence: colin.brand@ucsf.edu timothy.h.webster@utah.edu
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Abstract

Introgression appears increasingly ubiquitous in the evolutionary history of various taxa, including humans. However, accurately estimating introgression is difficult, particularly when 1) there are many parameters, 2) multiple models fit the data well, and 3) parameters are not simultaneously estimated. Here, we use the software Legofit to investigate the evolutionary history of bonobos (Pan paniscus) and chimpanzees (P. troglodytes) using whole genome sequences. This approach 1) ignores within-population variation, reducing the number of parameters requiring estimation, 2) allows for model selection, and 3) simultaneously estimates all parameters. We tabulated site patterns from the autosomes of 71 bonobos and chimpanzees representing all five extant Pan lineages. We then compared previously proposed demographic models and estimated parameters using a deterministic approach. We further considered sex bias in Pan evolutionary history by analyzing the site patterns from the X chromosome. Introgression from bonobos into the ancestor of eastern and central chimpanzees and from western into eastern chimpanzees best explained the autosomal site patterns. This second event was substantial with an estimated 0.21 admixture proportion. Estimates of effective population size and most divergence dates are consistent with previous findings; however, we observe a deeper divergence within chimpanzees at 987 ka. Finally, we identify male-biased reproduction in Pan evolutionary history and suggest that western to eastern chimpanzee introgression was driven by western males mating with eastern females.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • Email Addresses (in author order): fwhite{at}uoregon.edu, rogers{at}anthro.utah.edu

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted January 09, 2022.
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Estimating Pan evolutionary history from nucleotide site patterns
Colin M. Brand, Frances J. White, Alan R. Rogers, Timothy H. Webster
bioRxiv 2022.01.07.475438; doi: https://doi.org/10.1101/2022.01.07.475438
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Estimating Pan evolutionary history from nucleotide site patterns
Colin M. Brand, Frances J. White, Alan R. Rogers, Timothy H. Webster
bioRxiv 2022.01.07.475438; doi: https://doi.org/10.1101/2022.01.07.475438

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