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Gigascience. 2018 Sep 1;7(9). doi: 10.1093/gigascience/giy106.

Population genomics of wild Chinese rhesus macaques reveals a dynamic demographic history and local adaptation, with implications for biomedical research.

Author information

1
Chinese Academy of Sciences Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beichen West Road, Chaoyang District, Beijing, 100101, China.
2
University of Chinese Academy of Sciences, Yuquan Road, Shijingshan District, Beijing, 100049, China.
3
School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff CF10 3AX, United Kingdom.
4
Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA.
5
Novogene Bioinformatics Institute, Jiuxianqiao North Road, Chaoyang District, Beijing, 100083, China.
6
Institute of Physical Science and Information Technology, Anhui University, Jiulong Road, Hefei, 230601, China.
7
College of Life Science, Sichuan Agricultural University, Xinkang Road, Yucheng District, Ya'an, 625014, China.
8
School of Sociology and Anthropology, Sun Yat-sen University, Xingang Xi Road, Guang Zhou, 510275, China.
9
College of Life Science and Technology, Central South University of Forestry and Technology, Shaoshan South Road, Changsha, 410004, China.
10
School of Life Sciences, Anhui University, Jiulong Road, Hefei, 230601, China.
11
Gene Bank of Primates and Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Kellnerweg 4, Göttingen, 37077, Germany.
12
Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China.

Abstract

Background:

The rhesus macaque (RM, Macaca mulatta) is the most important nonhuman primate model in biomedical research. We present the first genomic survey of wild RMs, sequencing 81 geo-referenced individuals of five subspecies from 17 locations in China, a large fraction of the species' natural distribution.

Results:

Populations were structured into five genetic lineages on the mainland and Hainan Island, recapitulating current subspecies designations. These subspecies are estimated to have diverged 125.8 to 51.3 thousand years ago, but feature recent gene flow. Consistent with the expectation of a larger body size in colder climates and smaller body size in warmer climates (Bergman's rule), the northernmost RM lineage (M. m. tcheliensis), possessing the largest body size of all Chinese RMs, and the southernmost lineage (M. m. brevicaudus), with the smallest body size of all Chinese RMs, feature positively selected genes responsible for skeletal development. Further, two candidate selected genes (Fbp1, Fbp2) found in M. m. tcheliensis are involved in gluconeogenesis, potentially maintaining stable blood glucose levels during starvation when food resources are scarce in winter. The tropical subspecies M. m. brevicaudus showed positively selected genes related to cardiovascular function and response to temperature stimuli, potentially involved in tropical adaptation. We found 118 single-nucleotide polymorphisms matching human disease-causing variants with 82 being subspecies specific.

Conclusions:

These data provide a resource for selection of RMs in biomedical experiments. The demographic history of Chinese RMs and their history of local adaption offer new insights into their evolution and provide valuable baseline information for biomedical investigation.

PMID:
30165519
PMCID:
PMC6143732
DOI:
10.1093/gigascience/giy106
[Indexed for MEDLINE]
Free PMC Article

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