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Inference of human population history from individual whole-genome sequences

Abstract

The history of human population size is important for understanding human evolution. Various studies1,2,3,4,5 have found evidence for a founder event (bottleneck) in East Asian and European populations, associated with the human dispersal out-of-Africa event around 60 thousand years (kyr) ago. However, these studies have had to assume simplified demographic models with few parameters, and they do not provide a precise date for the start and stop times of the bottleneck. Here, with fewer assumptions on population size changes, we present a more detailed history of human population sizes between approximately ten thousand and a million years ago, using the pairwise sequentially Markovian coalescent model applied to the complete diploid genome sequences of a Chinese male (YH)6, a Korean male (SJK)7, three European individuals (J. C. Venter8, NA12891 and NA12878 (ref. 9)) and two Yoruba males (NA18507 (ref. 10) and NA19239). We infer that European and Chinese populations had very similar population-size histories before 10–20 kyr ago. Both populations experienced a severe bottleneck 10–60 kyr ago, whereas African populations experienced a milder bottleneck from which they recovered earlier. All three populations have an elevated effective population size between 60 and 250 kyr ago, possibly due to population substructure11. We also infer that the differentiation of genetically modern humans may have started as early as 100–120 kyr ago12, but considerable genetic exchanges may still have occurred until 20–40 kyr ago.

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Figure 1: Illustration of the PSMC model and its application to simulated data.
Figure 2: PSMC estimate on simulated data.
Figure 3: PSMC estimate on real data.

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Acknowledgements

We are grateful to D. Bentley (Illumina) and J. Wang (Beijing Genomics Institute) for early access to the sequencing data. We thank A. Coghlan for the idea of bootstrapping, and N. Patterson, M. Przeworski, D. Reich, and members of the Durbin research group for discussions and critiques. This work was funded by Wellcome Trust grant WT077192.

Author information

Authors and Affiliations

Authors

Contributions

R.D. proposed the basic strategy and designed the overall study. H.L. developed the theory, implemented the algorithm and analysed results. R.D. and H.L. wrote the manuscript.

Corresponding authors

Correspondence to Heng Li or Richard Durbin.

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Competing interests

The authors declare no competing financial interests.

Additional information

The PSMC software package is freely available at http://github.com/lh3/psmc.

Supplementary information

Supplementary Information

The file contains Supplementary Text, Supplementary Figures 1-13, Supplementary Tables 1-2 and additional references. (PDF 730 kb)

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Li, H., Durbin, R. Inference of human population history from individual whole-genome sequences. Nature 475, 493–496 (2011). https://doi.org/10.1038/nature10231

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