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Model-based analyses of whole-genome data reveal a complex evolutionary history involving archaic introgression in Central African Pygmies

Model-based analyses of whole-genome data reveal a complex evolutionary history involving archaic introgression in Central African Pygmies

  1. Michael F. Hammer3
  1. 1Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, USA;
  2. 2Graduate Interdisciplinary Program in Genetics, University of Arizona, Tucson, Arizona 85721, USA;
  3. 3Arizona Research Laboratories Division of Biotechnology, University of Arizona, Tucson, Arizona 85721, USA;
  4. 4Institute for Human Genetics, University of California, San Francisco, California 94143, USA;
  5. 5Department of Biology and Genetics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA;
  6. 6Department of Biology, Georgia Institute of Technology, Atlanta, Georgia 30332, USA;
  7. 7Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona 85721, USA
  1. Corresponding author: mfh{at}email.arizona.edu

Abstract

Comparisons of whole-genome sequences from ancient and contemporary samples have pointed to several instances of archaic admixture through interbreeding between the ancestors of modern non-Africans and now extinct hominids such as Neanderthals and Denisovans. One implication of these findings is that some adaptive features in contemporary humans may have entered the population via gene flow with archaic forms in Eurasia. Within Africa, fossil evidence suggests that anatomically modern humans (AMH) and various archaic forms coexisted for much of the last 200,000 yr; however, the absence of ancient DNA in Africa has limited our ability to make a direct comparison between archaic and modern human genomes. Here, we use statistical inference based on high coverage whole-genome data (greater than 60×) from contemporary African Pygmy hunter-gatherers as an alternative means to study the evolutionary history of the genus Homo. Using whole-genome simulations that consider demographic histories that include both isolation and gene flow with neighboring farming populations, our inference method rejects the hypothesis that the ancestors of AMH were genetically isolated in Africa, thus providing model-based whole genome-level evidence of African archaic admixture. Our inferences also suggest a complex human evolutionary history in Africa, which involves at least a single admixture event from an unknown archaic population into the ancestors of AMH, likely within the last 30,000 yr.

Footnotes

  • Received July 7, 2015.
  • Accepted January 19, 2016.

This article is distributed exclusively by Cold Spring Harbor Laboratory Press for the first six months after the full-issue publication date (see http://genome.cshlp.org/site/misc/terms.xhtml). After six months, it is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.

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