Bayesian inference of ancient human demography from individual genome sequences
Open Access
- 18 September 2011
- journal article
- research article
- Published by Springer Science and Business Media LLC in Nature Genetics
- Vol. 43 (10), 1031-1034
- https://doi.org/10.1038/ng.937
Abstract
Adam Siepel and colleagues estimate key parameters for ancient human demography using a Bayesian analysis of the whole-genome sequences of six individuals from diverse populations. They present new methods for coalescent-based inference of demographic parameters as well as a custom pipeline for genotype inference. Whole-genome sequences provide a rich source of information about human evolution. Here we describe an effort to estimate key evolutionary parameters based on the whole-genome sequences of six individuals from diverse human populations. We used a Bayesian, coalescent-based approach to obtain information about ancestral population sizes, divergence times and migration rates from inferred genealogies at many neutrally evolving loci across the genome. We introduce new methods for accommodating gene flow between populations and integrating over possible phasings of diploid genotypes. We also describe a custom pipeline for genotype inference to mitigate biases from heterogeneous sequencing technologies and coverage levels. Our analysis indicates that the San population of southern Africa diverged from other human populations approximately 108–157 thousand years ago, that Eurasians diverged from an ancestral African population 38–64 thousand years ago, and that the effective population size of the ancestors of all modern humans was ∼9,000.Keywords
This publication has 45 references indexed in Scilit:
- Inference of human population history from individual whole-genome sequencesNature, 2011
- A map of human genome variation from population-scale sequencingNature, 2010
- Fast and accurate short read alignment with Burrows–Wheeler transformBioinformatics, 2009
- Accurate whole human genome sequencing using reversible terminator chemistryNature, 2008
- The diploid genome sequence of an Asian individualNature, 2008
- Statistical evaluation of alternative models of human evolutionProceedings of the National Academy of Sciences of the United States of America, 2007
- A second generation human haplotype map of over 3.1 million SNPsNature, 2007
- Measurement of the human allele frequency spectrum demonstrates greater genetic drift in East Asians than in EuropeansNature Genetics, 2007
- A Geographically Explicit Genetic Model of Worldwide Human-Settlement HistoryAmerican Journal of Human Genetics, 2006
- Mitochondrial DNA and human evolutionNature, 1987