Vincent Plagnol * , Jeffrey D. Wall
1 Department of Molecular and Computational Biology, University of Southern California, Los Angeles, California, United States of America
Abstract
Determining the evolutionary relationships between fossil hominid groups such as Neanderthals and modern humans has been a question of enduring interest in human evolutionary genetics. Here we present a new method for addressing whether archaic human groups contributed to the modern gene pool (called ancient admixture), using the patterns of variation in contemporary human populations. Our method improves on previous work by explicitly accounting for recent population history before performing the analyses. Using sequence data from the Environmental Genome Project, we find strong evidence for ancient admixture in both a European and a West African population (p ≈ 10−7), with contributions to the modern gene pool of at least 5%. While Neanderthals form an obvious archaic source population candidate in Europe, there is not yet a clear source population candidate in West Africa.
Synopsis
Determining the evolutionary relationships between modern humans and fossil hominine groups such as Neanderthals has been a question of enduring interest in human evolutionary genetics. In this paper, Plagnol and Wall present a new method for addressing whether archaic human groups contributed to the modern gene pool. Using sequence data from the Environmental Genome Project, they find strong evidence for ancient admixture in both a European and a West African population, with contributions to the modern gene pool of at least 5%. While Neanderthals form an obvious archaic source population candidate in Europe, there is not yet a clear source population candidate in West Africa. The authors' results have direct implications for the competing models of modern human origins. In particular, their estimates of non-negligible contributions of archaic populations to the modern gene pool are inconsistent with strict forms of the Recent African Origin model, which posits that modern humans evolved in a single location in Africa and from there spread and replaced all other existing hominines.
Citation: Plagnol V, Wall JD (2006) Possible Ancestral Structure in Human Populations. PLoS Genet 2(7): e105. doi:10.1371/journal.pgen.0020105
Editor: Anna Di Rienzo, University of Chicago, United States of America
Received: February 17, 2006; Accepted: May 26, 2006; Published: July 28, 2006
Copyright: © 2006 Plagnol and Wall. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Funding: This work was supported by NSF grant BCS-0423123 to JDW.
Competing interests: The authors have declared that no competing interests exist.
Abbreviations: ARG, ancestral recombination graph; CEPH, Centre d'Etude du Polymorphisme Humain 1980 database of people living in Utah with ancestry from Northern and Western Europe; EGP, Environmental Genome Project; RAO, recent African origin
* To whom correspondence should be addressed. E-mail: vincent.plagnol@normalesup.org
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