Statistical evaluation of alternative models of human evolution

doi:10.1073/pnas.0708280104

Statistical evaluation of alternative models of human evolution

^†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)

Abstract

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.

Footnotes

^††To whom correspondence may be addressed. E-mail: francisco.salzano{at}ufrgs.br, slbonatto{at}pucrs.br, or laurent.excoffier{at}zoo.unibe.ch
Author contributions: S.L.B. and L.E. designed research; N.J.R.F. and N.R. performed research; N.R., M.B., S.N., F.M.S., and L.E. contributed new reagents/analytic tools; N.J.R.F., N.R., and L.E. analyzed data; and N.J.R.F., N.R., M.B., F.M.S., S.L.B., and L.E. wrote the paper.
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.
Abbreviations:

ABC,

approximate Bayesian computation;

AFREG,

African replacement with exponential population growth;

ASEG,

assimilation with exponential population growth;

Kya,

thousand years ago;

MRE,

multiregional evolution;

MREBIG,

MRE with bottleneck and instantaneous population growth;

TMRCA,

time to the most recent common ancestor.