10.1101/gr.3708505Access the most recent version at doi: 2005 15: 1161-1167 Genome Res. Nicolas Ray, Mathias Currat, Pierre Berthier and Laurent Excoffier realistic and spatially explicit simulationsRecovering the geographic origin of early modern humans by dataSupplementary http://www.genome.org/cgi/content/full/15/8/1161/DC1 "Supplemental Research Data" References http://www.genome.org/cgi/content/full/15/8/1161#otherarticlesArticle cited in: http://www.genome.org/cgi/content/full/15/8/1161#ReferencesThis article cites 43 articles, 19 of which can be accessed free at: serviceEmail alerting click heretop right corner of the article or Receive free email alerts when new articles cite this article - sign up in the box at the Notes http://www.genome.org/subscriptions/ go to: Genome ResearchTo subscribe to © 2005 Cold Spring Harbor Laboratory Press on September 22, 2006 www.genome.orgDownloaded fromRecovering the geographic origin of early modernhumans by realistic and spatially explicit simulationsNicolas Ray,1Mathias Currat, Pierre Berthier, and Laurent ExcoffierComputational and Molecular Population Genetics Lab, Zoological Institute, University of Bern, 3012 Bern, SwitzerlandMost genetic and archeological evidence argue in favor of a recent and unique origin of modern humans insub-Saharan Africa, but no attempt has ever been made at quantifying the likelihood of this model, relative toalternative hypotheses of human evolution. In this paper, we investigate the possibility of using multilocus geneticdata to correctly infer the geographic origin of humans, and to distinguish between a unique origin (UO) and amultiregional evolution (ME) model. We introduce here an approach based on realistic simulations of the geneticdiversity expected after an expansion process of modern humans into the Old World from different possible areasand their comparison to observed data. We find that the geographic origin of the expansion can be correctlyrecovered provided that a large number of independent markers are used, and that precise information on pastdemography and potential places of origins is available. In that case, it is also possible to unambiguously distinguishbetween a unique origin and a multiregional model of human evolution. Application to a real human data set of 377STR markers tested in 22 populations points toward a unique but surprising North African origin of modernhumans. We show that this result could be due to ascertainment bias in favor of markers selected to be polymorphicin Europeans. A new estimation modeling this bias explicitly reveals that East Africa is the most likely place of originfor modern humans.[Supplemental material is available online at www.genome.org.]The problems of human origins are far from being settled, and nocomplete agreement has been reached on the process by whichanatomically modern humans (Homo sapiens sapiens) appearedand occupied their present range. Current archeological, anthro-pological, and genetic evidence globally favor a complete re-placement of previous representatives of the genus Homo by earlymodern humans having originated in Africa (the recent Africanorigin [RAO] model) (see, e.g., Harpending and Rogers 2000;Kaessmann and Paabo 2002; Stringer 2002; Cavalli-Sforza andFeldman 2003; Currat and Excoffier 2004). This is mainly basedon the observation of earliest forms of anatomically modern hu-mans in Africa (White et al. 2003) and a very recent commonancestry of mitochondrial (Vigilant et al. 1991; Ingman et al.2000) and Y-chromosome (Donnelly et al. 1996; Pritchard et al.1999) genes for which the ancestral form is found in Africa. Thisview is also supported by the overall larger extent of geneticdiversity (Excoffier 2002; Tishkoff and Williams 2002) and lowerlevels of linkage disequilibrium (e.g., Tishkoff et al. 1996; Gabrielet al. 2002) in Africa, as well as the persistence in Africa of mostancestral forms of nuclear genes (Takahata et al. 2001; Satta andTakahata 2004). This RAO model is challenged by the persistenceof morphological characters from Homo erectus to modern hu-mans on different continents (Wolpoff 1989; Wolpoff et al. 2000;but see Brauer et al. 2004), by the old ancestry of several nucleargenes (Hawks et al. 2000), or the inference of pre-H. sapiens rangeexpansions from current patterns of molecular diversity (e.g.,Templeton 2002).While the RAO model or one of its extensions seems themost likely (Excoffier 2002), it has not been formally testedagainst competing models. Alternative models could either beother locations for a recent and unique origin (UO) of modernhumans, an incomplete replacement of H. erectus individuals bymodern humans, or the multiregional evolution model (MEmodel) (see, e.g., Wolpoff 1989; Wolpoff et al. 2000). The lattermodel postulates that there was a gradual and simultaneous tran-sition from H. erectus to modern forms on different continents,and that this synchronized process was possible because of con-tinuous migrations between continents. While the exact param-eters of this model have never been really defined, a very fewattempts have been made to evaluate the relative likelihood ofthe UO and the ME models (Takahata et al. 2001; Satta and Ta-kahata 2004). The observed prevalence of ancestral genes in Af-rica was found incompatible with the ME model, unless the Af-rican population size was much larger than that of the othercontinents (Takahata et al. 2001). More recently, it was alsoshown that a more explicit spatial model would better fit the data(Satta and Takahata 2004).In the present study, we introduce a new approach to testbetween alternative models of human evolution. It consists ofcomparing the observed pattern of genetic diversity betweenpopulations to that expected under various models of humanevolution obtained from spatially explicit simulations takinginto account geographic and/or environmental constraints (Cur-rat et al. 2004). We thus simulate a range expansion process un-der the UO model from arbitrary geographic origins or an MEmodel assuming various continental sizes, environmental het-erogeneity, and different rates of exchange between continents,and see whether the patterns of genetic diversity allow one todistinguish between UO and ME models. Simulated data are firstused to validate our approach, and we then apply our testingprocedure to a data set of 377 short tandem repeat (STR) loci(Rosenberg et al. 2002).1Corresponding author.E-mail [email protected];
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