RT Journal
A1 Xue, Cheng
A1 Raveendran, Muthuswamy
A1 Harris, R. Alan
A1 Fawcett, Gloria L.
A1 Liu, Xiaoming
A1 White, Simon
A1 Dahdouli, Mahmoud
A1 Rio Deiros, David
A1 Below, Jennifer E.
A1 Salerno, William
A1 Cox, Laura
A1 Fan, Guoping
A1 Ferguson, Betsy
A1 Horvath, Julie
A1 Johnson, Zach
A1 Kanthaswamy, Sree
A1 Kubisch, H. Michael
A1 Liu, Dahai
A1 Platt, Michael
A1 Smith, David G.
A1 Sun, Binghua
A1 Vallender, Eric J.
A1 Wang, Feng
A1 Wiseman, Roger W.
A1 Chen, Rui
A1 Muzny, Donna M.
A1 Gibbs, Richard A.
A1 Yu, Fuli
A1 Rogers, Jeffrey
T1 The population genomics of rhesus macaques (Macaca mulatta) based on whole-genome sequences
JF Genome Research 
JO Genome Research 
YR 2016 
FD December 01 
VO 26 
IS 12 
SP 1651 
OP 1662 
DO 10.1101/gr.204255.116 
UL http://genome.cshlp.org/content/26/12/1651.abstract 
AB Rhesus macaques (Macaca mulatta) are the most widely used nonhuman primate in biomedical research, have the largest natural geographic distribution of any nonhuman primate, and have been the focus of much evolutionary and behavioral investigation. Consequently, rhesus macaques are one of the most thoroughly studied nonhuman primate species. However, little is known about genome-wide genetic variation in this species. A detailed understanding of extant genomic variation among rhesus macaques has implications for the use of this species as a model for studies of human health and disease, as well as for evolutionary population genomics. Whole-genome sequencing analysis of 133 rhesus macaques revealed more than 43.7 million single-nucleotide variants, including thousands predicted to alter protein sequences, transcript splicing, and transcription factor binding sites. Rhesus macaques exhibit 2.5-fold higher overall nucleotide diversity and slightly elevated putative functional variation compared with humans. This functional variation in macaques provides opportunities for analyses of coding and noncoding variation, and its cellular consequences. Despite modestly higher levels of nonsynonymous variation in the macaques, the estimated distribution of fitness effects and the ratio of nonsynonymous to synonymous variants suggest that purifying selection has had stronger effects in rhesus macaques than in humans. Demographic reconstructions indicate this species has experienced a consistently large but fluctuating population size. Overall, the results presented here provide new insights into the population genomics of nonhuman primates and expand genomic information directly relevant to primate models of human disease.