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

TitleDemographic histories and patterns of linkage disequilibrium in Chinese and Indian rhesus macaques.
Publication TypeJournal Article
Year of Publication2007
AuthorsHernandez, RD, Hubisz, MJ, Wheeler, DA, Smith, DG, Ferguson, B, Rogers, J, Nazareth, L, Indap, A, Bourquin, T, McPherson, J, Muzny, DM, Gibbs, R, Nielsen, R, Bustamante, CD
JournalScience
Volume316
Issue5822
Pagination240-3
Date Published2007 Apr 13
ISSN1095-9203
KeywordsAnimals, China, Demography, DNA, Mitochondrial, Genetics, Medical, Humans, India, Linkage Disequilibrium, Macaca mulatta, Polymorphism, Single Nucleotide
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 (r(2) approximately 0.15 at 10 kilobases) versus Indian (r(2) approximately 0.52 at 10 kilobases) macaque populations.

DOI10.1126/science.1140462
Alternate JournalScience
PubMed ID17431170
Grant List1R01HG003229 / HG / NHGRI NIH HHS / United States
NSF0516310 / / PHS HHS / United States
RR00163 / RR / NCRR NIH HHS / United States
RR015383 / RR / NCRR NIH HHS / United States
RR05090 / RR / NCRR NIH HHS / United States