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BIOLOGICAL SCIENCES / ANTHROPOLOGY
Statistical evaluation of alternative models of human evolution
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Laboratório de Biologia Genômica e Molecular, Faculdade de Biociências, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), 90619-900 Porto Alegre, RS, Brazil; Departamento de Genética, Universidade Federal do Rio Grande do Sul, 91501-970 Porto Alegre, RS, Brazil; Computational and Molecular Population Genetics (CMPG), Zoological Institute, University of Bern, CH-3012 Bern, Switzerland; ¶School of Animal and Microbial Sciences, University of Reading, Reading RG6 6AJ, United Kingdom; and ||Department of Ecology and Evolution, University of Lausanne, Biophore, CH-1015 Lausanne, Switzerland
Contributed by Francisco M. Salzano, August 31, 2007 (received for review August 1, 2007)
An appropriate model of recent human evolution is not only important to understand our own history, but it is necessary to disentangle the effects of demography and selection on genome diversity. Although most genetic data support the view that our species originated recently in Africa, it is still unclear if it completely replaced former members of the Homo genus, or if some interbreeding occurred during its range expansion. Several scenarios of modern human evolution have been proposed on the basis of molecular and paleontological data, but their likelihood has never been statistically assessed. Using DNA data from 50 nuclear loci sequenced in African, Asian and Native American samples, we show here by extensive simulations that a simple African replacement model with exponential growth has a higher probability (78%) as compared with alternative multiregional evolution or assimilation scenarios. A Bayesian analysis of the data under this best supported model points to an origin of our species 
141 thousand years ago (Kya), an exit out-of-Africa 51 Kya, and a recent colonization of the Americas 10.5 Kya. We also find that the African replacement model explains not only the shallow ancestry of mtDNA or Y-chromosomes but also the occurrence of deep lineages at some autosomal loci, which has been formerly interpreted as a sign of interbreeding with Homo erectus.
Bayesian analysis | DNA nuclear data | multiregional hypothesis | out of Africa hypothesis
The authors declare no conflict of interest.
Data deposition: Sequences reported in this paper have been deposited in the GenBank database (accession nos. EU105474–EU106045).
This article contains supporting information online at www.pnas.org/cgi/content/full/0708280104/DC1.
To whom correspondence may be addressed. E-mail: francisco.salzano{at}ufrgs.br, slbonatto{at}pucrs.br, or laurent.excoffier{at}zoo.unibe.ch
© 2007 by The National Academy of Sciences of the USA
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  D. Garrigan and M. F. Hammer Ancient lineages in the genome: A response to Fagundes et al. PNAS, January 15, 2008; 105(2): E3 - E3. [Full Text] [PDF]
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N. J. R. Fagundes, N. Ray, M. Beaumont, S. Neuenschwander, F. M. Salzano, S. L. Bonatto, and L. Excoffier Reply to Garrigan and Hammer: Ancient lineages and assimilation PNAS, January 15, 2008; 105(2): E4 - E4. [Full Text] [PDF]
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