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Whole genome sequence analyses of Western Central African Pygmy hunter-gatherers reveal a complex demographic history and identify candidate genes under positive natural selection

PingHsun Hsieh, Krishna R. Veeramah, Joseph Lachance, Sarah A. Tishkoff, Jeffrey D. Wall, Michael F. Hammer, Ryan N. Gutenkunst
doi: https://doi.org/10.1101/022194
PingHsun Hsieh
1Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ
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Krishna R. Veeramah
2Arizona Research Laboratories Division of Biotechnology, University of Arizona, Tucson, AZ
6Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY
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Joseph Lachance
4Department of Biology and Genetics, University of Pennsylvania, Philadelphia, PA
7School of Biology, Georgia Institute of Technology, Atlanta, GA
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Sarah A. Tishkoff
4Department of Biology and Genetics, University of Pennsylvania, Philadelphia, PA
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Jeffrey D. Wall
5Institute for Human Genetics, University of California, San Francisco, CA
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Michael F. Hammer
1Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ
2Arizona Research Laboratories Division of Biotechnology, University of Arizona, Tucson, AZ
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  • For correspondence: mfh@email.arizona.edu rgutenk@email.arizona.edu
Ryan N. Gutenkunst
1Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ
3Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ
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  • For correspondence: mfh@email.arizona.edu rgutenk@email.arizona.edu
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Abstract

African Pygmies practicing a mobile hunter-gatherer lifestyle are phenotypically and genetically diverged from other anatomically modern humans, and they likely experienced strong selective pressures due to their unique lifestyle in the Central African rainforest. To identify genomic targets of adaptation, we sequenced the genomes of four Biaka Pygmies from the Central African Republic and jointly analyzed these data with the genome sequences of three Baka Pygmies from Cameroon and nine Yoruba famers. To account for the complex demographic history of these populations that includes both isolation and gene flow, we fit models using the joint allele frequency spectrum and validated them using independent approaches. Our two best-fit models both suggest ancient divergence between the ancestors of the farmers and Pygmies, 90,000 or 150,000 years ago. We also find that bi-directional asymmetric gene-flow is statistically better supported than a single pulse of unidirectional gene flow from farmers to Pygmies, as previously suggested. We then applied complementary statistics to scan the genome for evidence of selective sweeps and polygenic selection. We found that conventional statistical outlier approaches were biased toward identifying candidates in regions of high mutation or low recombination rate. To avoid this bias, we assigned P-values for candidates using whole-genome simulations incorporating demography and variation in both recombination and mutation rates. We found that genes and gene sets involved in muscle development, bone synthesis, immunity, reproduction, cell signaling and development, and energy metabolism are likely to be targets of positive natural selection in Western African Pygmies or their recent ancestors.

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Posted July 08, 2015.
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Whole genome sequence analyses of Western Central African Pygmy hunter-gatherers reveal a complex demographic history and identify candidate genes under positive natural selection
PingHsun Hsieh, Krishna R. Veeramah, Joseph Lachance, Sarah A. Tishkoff, Jeffrey D. Wall, Michael F. Hammer, Ryan N. Gutenkunst
bioRxiv 022194; doi: https://doi.org/10.1101/022194
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Whole genome sequence analyses of Western Central African Pygmy hunter-gatherers reveal a complex demographic history and identify candidate genes under positive natural selection
PingHsun Hsieh, Krishna R. Veeramah, Joseph Lachance, Sarah A. Tishkoff, Jeffrey D. Wall, Michael F. Hammer, Ryan N. Gutenkunst
bioRxiv 022194; doi: https://doi.org/10.1101/022194

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