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. 2017 Jul;206(3):1549-1567.
doi: 10.1534/genetics.117.200493. Epub 2017 May 11.

Inferring the Joint Demographic History of Multiple Populations: Beyond the Diffusion Approximation

Affiliations

Inferring the Joint Demographic History of Multiple Populations: Beyond the Diffusion Approximation

Julien Jouganous et al. Genetics. 2017 Jul.

Abstract

Understanding variation in allele frequencies across populations is a central goal of population genetics. Classical models for the distribution of allele frequencies, using forward simulation, coalescent theory, or the diffusion approximation, have been applied extensively for demographic inference, medical study design, and evolutionary studies. Here we propose a tractable model of ordinary differential equations for the evolution of allele frequencies that is closely related to the diffusion approximation but avoids many of its limitations and approximations. We show that the approach is typically faster, more numerically stable, and more easily generalizable than the state-of-the-art software implementation of the diffusion approximation. We present a number of applications to human sequence data, including demographic inference with a five-population joint frequency spectrum and a discussion of the robustness of the out-of-Africa model inference to the choice of modern population.

Keywords: demographic inference; diffusion approximation; joint allele frequency spectrum; moments equations.

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Figures

Figure B1
Figure B1
Illustration of two types of multiple coalescence. Dots represent individuals, arrows represent shared descendance.
Figure 1
Figure 1
Moments predictions for finite-genome frequency spectrum for a population of constant size N=10,000 with reversible mutation rates u=v=2×106 (●), compared to theoretical expectations obtained by integrating equations 5.70 and 5.72 in Ewens (2004) (solid lines).
Figure 2
Figure 2
Inferred ancestral population sizes (width of blue lines) and migration rates (width of black arrow) for populations of African (YRI), Asian (CHB), and European (CEU) ancestry.
Figure 3
Figure 3
Inferred ancestral population sizes (width of blue lines) and migration rates (width of black arrow) for populations of African (YRI), Asian (CHB and JPT), and European (CEU) ancestry.

References

    1. 1000 Genomes Project , 2015. A global reference for human genetic variation. Nature 526: 68–74. - PMC - PubMed
    1. Baolin Z., Wenzhi L., 1994. On alternating segment Crank-Nicolson scheme. Parallel Comput. 20: 897–902.
    1. Bhaskar A., Clark A. G., Song Y. S., 2014. Distortion of genealogical properties when the sample is very large. Proc. Natl. Acad. Sci. USA 111: 2385–2390. - PMC - PubMed
    1. Bryant D., Bouckaert R., Felsenstein J., Rosenberg N. A., RoyChoudhury A., 2012. Inferring species trees directly from biallelic genetic markers: bypassing gene trees in a full coalescent analysis. Mol. Biol. Evol. 29: 1917–1932. - PMC - PubMed
    1. Coffman A. J., Hsieh P. H., Gravel S., Gutenkunst R. N., 2016. Computationally efficient composite likelihood statistics for demographic inference. Mol. Biol. Evol. 33: 591–593. - PMC - PubMed

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