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Bayesian inference of ancient human demography from individual genome sequences

Abstract

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.

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Figure 1: Population phylogeny and genealogies.
Figure 2: Results of the simulation study.
Figure 3: Parameter estimates from real data.

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Acknowledgements

This research was supported by a Packard Fellowship (to A.S.), National Science Foundation grant DBI-0644111 and National Institutes of Health training grant T32HD052471 (to C.G.D.). We thank S. Schuster, W. Miller, D. Reich, G. Coop, J. Hey, J. Wall, R.S. Wells, A. Keinan, A.G. Clark, S.C. Choi, C.D. Bustamante, B. Henn and others for helpful discussions and feedback.

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Authors and Affiliations

Authors

Contributions

A.S. conceived of and designed the study. I.G. implemented G-PhoCS and applied it to both simulated and real data. B.G. implemented BSNP and applied it to the individual genomes. I.G., M.J.H., B.G., C.G.D. and A.S. performed additional statistical analyses. I.G. and A.S. wrote the paper with review and contributions by all authors.

Corresponding author

Correspondence to Adam Siepel.

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The authors declare no competing financial interests.

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Supplementary Figures 1–13, Supplementary Tables 1–7 and Supplementary Note. (PDF 3609 kb)

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Gronau, I., Hubisz, M., Gulko, B. et al. Bayesian inference of ancient human demography from individual genome sequences. Nat Genet 43, 1031–1034 (2011). https://doi.org/10.1038/ng.937

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