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

doi:10.1126/science.1140462

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

Oregon National Primate Research Center

Research output: Contribution to journal › Article › peer-review

138 Scopus citations

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 language	English (US)
Pages (from-to)	240-243
Number of pages	4
Journal	Science
Volume	316
Issue number	5822
DOIs	https://doi.org/10.1126/science.1140462
State	Published - Apr 13 2007

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Hernandez, R. D., Hubisz, M. J., Wheeler, D. A., Smith, D. G., Ferguson, B., Rogers, J., Nazareth, L., Indap, A., Bourquin, T., McPherson, J., Muzny, D., Gibbs, R., Nielsen, R., & 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

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title = "Demographic histories and patterns of linkage disequilibrium in Chinese and Indian rhesus macaques",

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.",

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

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AU - Hernandez, Ryan D.

AU - Hubisz, Melissa J.

AU - Wheeler, David A.

AU - Smith, David G.

AU - Ferguson, Betsy

AU - Rogers, Jeffrey

AU - Nazareth, Lynne

AU - Indap, Amit

AU - Bourquin, Traci

AU - McPherson, John

AU - Muzny, Donna

AU - Gibbs, Richard

AU - Nielsen, Rasmus

AU - Bustamante, Carlos D.

PY - 2007/4/13

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

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