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Science 13 April 2007:
Vol. 316. no. 5822, pp. 240 - 243
DOI: 10.1126/science.1140462
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Reports

Demographic Histories and Patterns of Linkage Disequilibrium in Chinese and Indian Rhesus Macaques

Ryan D. Hernandez,1 Melissa J. Hubisz,2 David A. Wheeler,3 David G. Smith,4,5 Betsy Ferguson,6,7 Jeffrey Rogers,8 Lynne Nazareth,3 Amit Indap,1 Traci Bourquin,3 John McPherson,3 Donna Muzny,3 Richard Gibbs,3 Rasmus Nielsen,9 Carlos D. Bustamante1*

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 {approx} 0.15 at 10 kilobases) versus Indian (r2 {approx} 0.52 at 10 kilobases) macaque populations.

1 Biological Statistics and Computational Biology, Cornell University, Ithaca, NY 14850, USA.
2 Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA.
3 Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA.
4 Department of Anthropology, Davis, CA, USA.
5 California National Primate Research Center, Davis, CA, USA.
6 Genetics Research and Informatics Program, Oregon National Primate Research Center, Oregon Health and Sciences University, Beaverton, OR 97006, USA.
7 Washington National Primate Research Center, University of Washington, Seattle, WA 98195, USA.
8 Department of Genetics, Southwest Foundation for Biomedical Research, and Southwest National Primate Research Center, San Antonio, TX 78227, USA.
9 Center for Comparative Genomics, Department of Biology, University of Copenhagen, Universitetsparken 15, 2100 Kbh Ø, Denmark.

* To whom correspondence should be addressed. E-mail: cdb28{at}cornell.edu

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