Archaic human ancestry in East Asia

Edited by Richard G. Klein, Stanford University, Stanford, CA, and approved September 27, 2011 (received for review May 23, 2011)
October 31, 2011
108 (45) 18301-18306

Abstract

Recent studies of ancient genomes have suggested that gene flow from archaic hominin groups to the ancestors of modern humans occurred on two separate occasions during the modern human expansion out of Africa. At the same time, decreasing levels of human genetic diversity have been found at increasing distance from Africa as a consequence of human expansion out of Africa. We analyzed the signal of archaic ancestry in modern human populations, and we investigated how serial founder models of human expansion affect the signal of archaic ancestry using simulations. For descendants of an archaic admixture event, we show that genetic drift coupled with ascertainment bias for common alleles can cause artificial but largely predictable differences in similarity to archaic genomes. In genotype data from non-Africans, this effect results in a biased genetic similarity to Neandertals with increasing distance from Africa. However, in addition to the previously reported gene flow between Neandertals and non-Africans as well as gene flow between an archaic human population from Siberia (“Denisovans”) and Oceanians, we found a significant affinity between East Asians, particularly Southeast Asians, and the Denisova genome—a pattern that is not expected under a model of solely Neandertal admixture in the ancestry of East Asians. These results suggest admixture between Denisovans or a Denisova-related population and the ancestors of East Asians, and that the history of anatomically modern and archaic humans might be more complex than previously proposed.

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Acknowledgments

We thank Noah Rosenberg, Michael Blum, Anders Götherström, Carina Schlebusch, Sohini Ramachandran, and two anonymous reviewers for valuable comments. Financial support was provided by the Swedish Research Council and the Lawski Foundation. Computations were performed on Swedish National Infrastructure for Computing (SNIC) and Uppsala Multidisciplinary Center for Advanced Computational Science (UPPMAX) resources (Project b2010050).

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Information & Authors

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Published in

Go to Proceedings of the National Academy of Sciences
Go to Proceedings of the National Academy of Sciences
Proceedings of the National Academy of Sciences
Vol. 108 | No. 45
November 8, 2011
PubMed: 22042846

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Submission history

Published online: October 31, 2011
Published in issue: November 8, 2011

Keywords

  1. human origins
  2. ancient DNA

Acknowledgments

We thank Noah Rosenberg, Michael Blum, Anders Götherström, Carina Schlebusch, Sohini Ramachandran, and two anonymous reviewers for valuable comments. Financial support was provided by the Swedish Research Council and the Lawski Foundation. Computations were performed on Swedish National Infrastructure for Computing (SNIC) and Uppsala Multidisciplinary Center for Advanced Computational Science (UPPMAX) resources (Project b2010050).

Notes

This article is a PNAS Direct Submission.

Authors

Affiliations

Pontus Skoglund1 [email protected]
Department of Evolutionary Biology and
Mattias Jakobsson1 [email protected]
Department of Evolutionary Biology and
Science for Life Laboratory, Uppsala University, 75236 Uppsala, Sweden

Notes

1
To whom correspondence may be addressed. E-mail: [email protected] or [email protected].
Author contributions: P.S. and M.J. designed research; P.S. and M.J. performed research; P.S. analyzed data; and P.S. and M.J. wrote the paper.

Competing Interests

The authors declare no conflict of interest.

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    Archaic human ancestry in East Asia
    Proceedings of the National Academy of Sciences
    • Vol. 108
    • No. 45
    • pp. 18187-18566

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