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Genome Res. 2016 Dec;26(12):1651-1662. Epub 2016 Oct 17.

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

Author information

1
Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA.
2
Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA.
3
University of Texas Health Science Center, Houston, Texas 77030, USA.
4
Southwest National Primate Research Center, San Antonio, Texas 78227, USA.
5
Department of Human Genetics, University of California, Los Angeles, California 90095, USA.
6
Oregon National Primate Research Center, Beaverton, Oregon 97006, USA.
7
North Carolina Museum of Natural Sciences, Raleigh, North Carolina 27601, USA.
8
Biological and Biomedical Sciences, North Carolina Central University, Durham, North Carolina 27707, USA.
9
Department of Evolutionary Anthropology, Duke University, Durham, North Carolina 27708, USA.
10
Yerkes National Primate Research Center, Atlanta, Georgia 30322, USA.
11
California National Primate Research Center, Davis, California 95616, USA.
12
School of Mathematical and Natural Sciences, Arizona State University, Phoenix, Arizona 85004, USA.
13
Tulane National Primate Research Center, Covington, Louisiana 70433, USA.
14
Center for Stem Cell and Translational Medicine, Anhui University, Anhui, China 230601.
15
Department of Neurobiology, Duke University, Durham, North Carolina 27708, USA.
16
Department of Neuroscience, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.
17
New England National Primate Research Center, Southborough, Massachusetts 01772, USA.
18
Wisconsin National Primate Research Center, Madison, Wisconsin 53711, USA.

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.

PMID:
27934697
PMCID:
PMC5131817
DOI:
10.1101/gr.204255.116
[Indexed for MEDLINE]
Free PMC Article

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