Demographic histories and patterns of linkage disequilibrium in Chinese and Indian rhesus macaques

Ryan D. Hernandez, Melissa J. Hubisz, David A. Wheeler, David G. Smith, Betsy Ferguson, Jeffrey Rogers, Lynne Nazareth, Amit Indap, Traci Bourquin, John McPherson, Donna Muzny, Richard Gibbs, Rasmus Nielsen, Carlos D. Bustamante

    Research output: Contribution to journalArticle

    120 Citations (Scopus)

    Abstract

    To understand the demographic history of rhesus macaques (Macaca mulatta) and document the extent of linkage disequilibrium (LD) in the genome, we partially resequenced five Encyclopedia of DNA Elements regions in 9 Chinese and 38 captive-born Indian rhesus macaques. Population genetic analyses of the 1467 single-nucleotide polymorphisms discovered suggest that the two populations separated about 162,000 years ago, with the Chinese population tripling in size since then and the Indian population eventually shrinking by a factor of four. Using coalescent simulations, we confirmed that these inferred demographic events explain a much faster decay of LD in Chinese (r2 ≈ 0.15 at 10 kilobases) versus Indian (r2 ≈ 0.52 at 10 kilobases) macaque populations.

    Original languageEnglish (US)
    Pages (from-to)240-243
    Number of pages4
    JournalScience
    Volume316
    Issue number5822
    DOIs
    StatePublished - Apr 13 2007

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    Linkage Disequilibrium
    Macaca mulatta
    Demography
    Population
    Encyclopedias
    Population Genetics
    Macaca
    Single Nucleotide Polymorphism
    History
    Genome
    DNA

    ASJC Scopus subject areas

    • General

    Cite this

    Hernandez, R. D., Hubisz, M. J., Wheeler, D. A., Smith, D. G., Ferguson, B., Rogers, J., ... Bustamante, C. D. (2007). Demographic histories and patterns of linkage disequilibrium in Chinese and Indian rhesus macaques. Science, 316(5822), 240-243. https://doi.org/10.1126/science.1140462

    Demographic histories and patterns of linkage disequilibrium in Chinese and Indian rhesus macaques. / Hernandez, Ryan D.; Hubisz, Melissa J.; Wheeler, David A.; Smith, David G.; Ferguson, Betsy; Rogers, Jeffrey; Nazareth, Lynne; Indap, Amit; Bourquin, Traci; McPherson, John; Muzny, Donna; Gibbs, Richard; Nielsen, Rasmus; Bustamante, Carlos D.

    In: Science, Vol. 316, No. 5822, 13.04.2007, p. 240-243.

    Research output: Contribution to journalArticle

    Hernandez, RD, Hubisz, MJ, Wheeler, DA, Smith, DG, Ferguson, B, Rogers, J, Nazareth, L, Indap, A, Bourquin, T, McPherson, J, Muzny, D, Gibbs, R, Nielsen, R & Bustamante, CD 2007, 'Demographic histories and patterns of linkage disequilibrium in Chinese and Indian rhesus macaques', Science, vol. 316, no. 5822, pp. 240-243. https://doi.org/10.1126/science.1140462
    Hernandez, Ryan D. ; Hubisz, Melissa J. ; Wheeler, David A. ; Smith, David G. ; Ferguson, Betsy ; Rogers, Jeffrey ; Nazareth, Lynne ; Indap, Amit ; Bourquin, Traci ; McPherson, John ; Muzny, Donna ; Gibbs, Richard ; Nielsen, Rasmus ; Bustamante, Carlos D. / Demographic histories and patterns of linkage disequilibrium in Chinese and Indian rhesus macaques. In: Science. 2007 ; Vol. 316, No. 5822. pp. 240-243.
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    abstract = "To understand the demographic history of rhesus macaques (Macaca mulatta) and document the extent of linkage disequilibrium (LD) in the genome, we partially resequenced five Encyclopedia of DNA Elements regions in 9 Chinese and 38 captive-born Indian rhesus macaques. Population genetic analyses of the 1467 single-nucleotide polymorphisms discovered suggest that the two populations separated about 162,000 years ago, with the Chinese population tripling in size since then and the Indian population eventually shrinking by a factor of four. Using coalescent simulations, we confirmed that these inferred demographic events explain a much faster decay of LD in Chinese (r2 ≈ 0.15 at 10 kilobases) versus Indian (r2 ≈ 0.52 at 10 kilobases) macaque populations.",
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