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    Demographic inference using spectral methods on SNP data, with an analysis of the human out-of-Africa expansion

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    Genre
    Journal Article
    Date
    2012-01-01
    Author
    Lukic, S
    Hey, J
    Subject
    Africa
    African Continental Ancestry Group
    Demography
    Gene Frequency
    Genetics, Population
    Human Migration
    Humans
    Linkage Disequilibrium
    Models, Genetic
    Models, Theoretical
    Polymorphism, Single Nucleotide
    Population Groups
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    Permanent link to this record
    http://hdl.handle.net/20.500.12613/6016
    
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    DOI
    10.1534/genetics.112.141846
    Abstract
    We present an implementation of a recently introduced method for estimating the allele-frequency spectrum under the diffusion approximation. For single-nucleotide polymorphism (SNP) frequency data from multiple populations, the method computes numerical solutions to the allele-frequency spectrum (AFS) under a complex model that includes population splitting events, migration, population expansion, and admixture. The solution to the diffusion partial differential equation (PDE) that mimics the evolutionary process is found by means of truncated polynomial expansions. In the absence of gene flow, our computation of frequency spectra yields exact results. The results are compared to those that use a finite-difference method and to forward diffusion simulations. In general, all the methods yield comparable results, although the polynomial-based approach is the most accurate in the weak-migration limit. Also, the economical use of memory attained by the polynomial expansions makes the study of models with four populations possible for the first time. The method was applied to a four-population model of the human expansion out of Africa and the peopling of the Americas, using the Environmental Genome Project (EGP) SNP database. Although our confidence intervals largely overlapped previous analyses of these data, some were significantly different. In particular, estimates of migration among African, European, and Asian populations were considerably lower than those in a previous study and the estimated time of migration out of Africa was earlier. The estimated time of founding of a human population outside of Africa was 52,000 years (95% confidence interval: 36,000-80,800 years). © 2012 by the Genetics Society of America.
    Citation to related work
    Oxford University Press (OUP)
    Has part
    Genetics
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    ae974a485f413a2113503eed53cd6c53
    http://dx.doi.org/10.34944/dspace/5998
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