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. 2005 Dec 20;102(51):18508-13.
doi: 10.1073/pnas.0507325102. Epub 2005 Dec 13.

Interrogating multiple aspects of variation in a full resequencing data set to infer human population size changes

Benjamin F Voight  1 , Alison M Adams, Linda A Frisse, Yudong Qian, Richard R Hudson, Anna Di Rienzo
Affiliations

Interrogating multiple aspects of variation in a full resequencing data set to infer human population size changes

Benjamin F Voight et al. Proc Natl Acad Sci U S A. .

Abstract

We present an expanded data set of 50 unlinked autosomal noncoding regions, resequenced in samples of Hausa from Cameroon, Italians, and Chinese. We use these data to make inferences about human demographic history by using a technique that combines multiple aspects of genetic data, including levels of polymorphism, the allele frequency spectrum, and linkage disequilibrium. We explore an extensive range of demographic parameters and demonstrate that our method of combining multiple aspects of the data results in a significant reduction of the compatible parameter space. In agreement with previous reports, we find that the Hausa data are compatible with demographic equilibrium as well as a set of recent population expansion models. In contrast to the Hausa, when multiple aspects of the data are considered jointly, the non-Africans depart from an equilibrium model of constant population size and are compatible with a range of simple bottleneck models, including a 50-90% reduction in effective population size occurring some time after the appearance of modern humans in Africa 160,000-120,000 years ago.

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Figures

Fig. 1.
Fig. 1.
Power of combining multiple summary statistics. The power to reject a constant size demographic model for combined summaries with an NA of 10,659 under bottleneck models with a 70% reduction in NA and a total time of 40,000 years for various bottleneck durations (tdur) (a) and a bottleneck duration of 20,000 years for a total demographic epoch of 40,000 years for various bottleneck severities (b). The type-I error rate was held at 5%.
Fig. 2.
Fig. 2.
Confidence sets for a bottleneck with tstart of 40,000 years. Results are shown for the Italian (a–c) and Chinese (d–f) data sets for NA values of 9,450 (a and d), 10,659 (b and e), and 12,300 (c and f). The combined statistics are formula image. The contours represent the confidence region of parameter space with P values of 0.1, 0.05, 0.02, and 0.01 from innermost to outermost, with darker shading indicating lower P values.
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