Analytical inference of human demographic history using multiple individual genome sequences. H. Chen1, D. Reich2,3 1) Dept Epidemiology, Havard Sch Public Health, Boston, MA; 2) Department of Genetics, Harvard Medical School, Boston, MA 02115; 3) Broad Institute of Harvard and MIT, Cambridge, MA 02142.

   A central problem in human population genetics study is to infer the past demographic history using genetic polymorphism data from present-day humans. The whole-genomic sequence data generated by new sequencing technology provide an unprecedented opportunity for population genetic studies. We present a new approach that infers the joint ancient human demography of multiple populations using multiple genomes from divergent populations. We use coalescent theory to analytically derive the joint allele frequency spectrum of multiple populations that experienced different demographic histories. Compared with the recently developed approaches, such as diffusion process approximation (dadi), sequential Markov Coalescent method (PSMC), and coalescent-MCMC (Markov Chain Monte Carlo , GPhoCS) approaches, our method has several advantages: (1) the method is computationally efficient, as the coalescent likelihood for the joint pattern of multiple populations can be obtained analytically without relying on numerical approximation of diffusion (e.g., Gutenkunst et al 2009) or computationally intensive approaches (e.g. Gronau et al 2011); (2) the method jointly analyzes more than three populations, and multiple individuals from each population, whereas previous approaches were limit to three populations (Gutenkunst et al. 2009) or one individual from each population (Gronau et al 2011; Li and Durbin 2011); and (3) detailed demographic scenarios can be incorporated into the model, including temporally-varying population sizes. We apply the method to two data sets: the first data includes three Europeans, two Asians, three Yoruba and one San sequenced using Illumina technology; and the second data set includes eight East Asians, five Northern Europeans and seven Yoruba sequenced using Complete Genomics technology. We estimate that Eurasian populations split from ancient Africans at 58,000-120,800 years ago, and the divergence time of Europeans and Asians occurred at 35,750-70,500 years ago. The inferred demographic history is generally consistent with previous studies.

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