The population genomics of rhesus macaques (Macaca mulatta) based on whole-genome sequences.

TitleThe population genomics of rhesus macaques (Macaca mulatta) based on whole-genome sequences.
Publication TypeJournal Article
Year of Publication2016
AuthorsXue, C, Raveendran, M, R Harris, A, Fawcett, GL, Liu, X, White, S, Dahdouli, M, Deiros, DRio, Below, JE, Salerno, W, Cox, L, Fan, G, Ferguson, B, Horvath, J, Johnson, Z, Kanthaswamy, S, H Kubisch, M, Liu, D, Platt, M, Smith, DG, Sun, B, Vallender, EJ, Wang, F, Wiseman, RW, Chen, R, Muzny, DM, Gibbs, RA, Yu, F, Rogers, J
JournalGenome Res
Volume26
Issue12
Pagination1651-1662
Date Published2016 Dec
ISSN1549-5469
Abstract

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.

DOI10.1101/gr.204255.116
Alternate JournalGenome Res.
PubMed ID27934697
PubMed Central IDPMC5131817
Grant ListP51 OD011092 / OD / NIH HHS / United States
R01 EY026045 / EY / NEI NIH HHS / United States
U54 HG003273 / HG / NHGRI NIH HHS / United States
P30 EY002520 / EY / NEI NIH HHS / United States
P51 OD011133 / OD / NIH HHS / United States
R24 OD011173 / OD / NIH HHS / United States