Guillaume Laval1,2, Etienne Patin1¤a, Luis B. Barreiro1¤b,Lluís Quintana-Murci1,2*
1 Human Evolutionary Genetics, Institut Pasteur, Paris, France, 2 Centre National de la Recherche Scientifique, URA3012, Paris, France
Estimating the historical and demographic parameters that characterize modern human populations is a fundamental part of reconstructing the recent history of our species. In addition, the development of a model of human evolution that can best explain neutral genetic diversity is required to identify confidently regions of the human genome that have been targeted by natural selection.
We have resequenced 20 independent noncoding autosomal regions dispersed throughout the genome in 213 individuals from different continental populations, corresponding to a total of ~6 Mb of diploid resequencing data. We used these data to explore and co-estimate an extensive range of historical and demographic parameters with a statistical framework that combines the evaluation of multiple models of human evolution via a best-fit approach, followed by an Approximate Bayesian Computation (ABC) analysis. From a methodological standpoint, evaluating the accuracy of the parameter co-estimation allowed us to identify the most accurate set of statistics to be used for the estimation of each of the different historical and demographic parameters characterizing recent human evolution.
Our results support a model in which modern humans left Africa through a single major dispersal event occurring ~60,000 years ago, corresponding to a drastic reduction of ~5 times the effective population size of the ancestral African population of ~13,800 individuals. Subsequently, the ancestors of modern Europeans and East Asians diverged much later, ~22,500 years ago, from the population of ancestral migrants. This late diversification of Eurasians after the African exodus points to the occurrence of a long maturation phase in which the ancestral Eurasian population was not yet diversified.
Citation: Laval G, Patin E, Barreiro LB, Quintana-Murci L (2010) Formulating a Historical and Demographic Model of Recent Human Evolution Based on Resequencing Data from Noncoding Regions. PLoS ONE 5(4): e10284. doi:10.1371/journal.pone.0010284
Editor: John Relethford, State University of New York College at Oneonta, United States of America.
Received: November 3, 2009; Accepted: March 27, 2010; Published: April 22, 2010
Copyright: © 2010 Laval et al. 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: Financial support was provided by Institut Pasteur, by the Centre National de la Recherche Scientifique (CNRS), and by the Agence Nationale de la Recherche (ANR) research grant (ANR-05-JCJC-0124-01) to L.Q.-M. L.B.B. was supported by a ‘Fundação para a Ciência e a Tecnologia’ fellowship (SFRH/BD/18580/2004), and E.P. by the “Fondation pour la Recherche Médicale” (FRM). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Competing interests: The authors have declared that no competing interests exist.
* E-mail: firstname.lastname@example.org
¤a Current address: Human Genetics of Infectious Diseases, INSERM U550, Paris, France
¤b Current address: Department of Human Genetics, University of Chicago, Chicago, United States of America