Abstract
BackgroundEstimating 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.Methodology/Principal FindingsWe 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.Conclusions/SignificanceOur 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.
Highlights
The evolution, origins and geographic dispersals of modern humans remain among the most hotly debated issues in many disciplines, including paleoanthropology, archeology, linguistics and genetics
The number of haplotypes and the levels of nucleotide diversity were the highest in the African sample, an observation that is expected under the out-of-Africa model (Table 1)
Investigating the out of Africa Models of Dispersal(s) We investigated the mode in which the different population dispersals out of Africa occurred to colonize Eurasia, by relaxing the assumption of single major dispersal event followed by the Eurasian split (Figure 4A)
Summary
The evolution, origins and geographic dispersals of modern humans remain among the most hotly debated issues in many disciplines, including paleoanthropology, archeology, linguistics and genetics. Because past demographic events, such as changes in population sizes, geographic range expansions, and varying levels of gene flow, have produced specific patterns of genetic diversity, the study of genetic variation in present-day human populations allows inference of the general demographic models best explaining neutral genetic variability [9]. Evaluation of these demographic scenarios is needed to disentangle the mimicking effects of population demography and natural selection on genome diversity [10,11,12,13,14]. 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
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