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 Douglas 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
Externally publishedYes

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

ASJC Scopus subject areas

  • Medicine(all)
  • 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 Douglas; 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, JD, 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 RD, Hubisz MJ, Wheeler DA, Smith DG, Ferguson B, Rogers J et al. Demographic histories and patterns of linkage disequilibrium in Chinese and Indian rhesus macaques. Science. 2007 Apr 13;316(5822):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 Douglas ; 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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