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

Dataset type: Genomic
Data released on August 16, 2018

Liu Z; Tan X; Orozco-terWenge P; Zhou X; Zhang L; Tian S; Yan Z; Xu H; Ren B; Zhang P; Xiang Z; Sun B; Roos C; Bruford MW; Li M (2018): Supporting data for "Population genomics of wild Chinese rhesus macaques reveals a dynamic demographic history and local adaptation, with implications for biomedical research" GigaScience Database. http://dx.doi.org/10.5524/100484

DOI10.5524/100484

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.
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 SNPs matching human disease-causing variants with 82 being subspecies-specific.
These data provide a resource for selection of RMs in biomedical experiments. The demographic history of Chinese RMs, and their history of local adaption offers new insights into their evolution and provides valuable baseline information for biomedical investigation.

Additional details

Read the peer-reviewed publication(s):

Liu, Z., Tan, X., Orozco-terWengel, P., Zhou, X., Zhang, L., Tian, S., … Li, M. (2018). Population genomics of wild Chinese rhesus macaques reveals a dynamic demographic history and local adaptation, with implications for biomedical research. GigaScience, 7(9). doi:10.1093/gigascience/giy106

Accessions (data included in GigaDB):

BioProject: PRJNA345528





Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
C_rhe_19544Rhesus macaqueRhesus monkeyMacaca mulatta Description:Transcriptomics of the Pomacea canalic...
Description:DNA from the blood of Macaca mulatta s...
Common name:Rhesus macaque
...
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C_rhe_109544Rhesus macaqueRhesus monkeyMacaca mulatta Environment (feature):paddy field [ENVO:00000297]
Description:DNA from the blood of Macaca mulatta s...
Common name:Rhesus macaque
...
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C_rhe_119544Rhesus macaqueRhesus monkeyMacaca mulatta Isolate:biologilca replicate 3
Description:DNA from the blood of Macaca mulatta s...
Common name:Rhesus macaque
...
+
C_rhe_129544Rhesus macaqueRhesus monkeyMacaca mulatta Description:DNA from the blood of Macaca mulatta s...
Common name:Rhesus macaque
Geographic location (country and/or sea,region):Ch...
...
+
C_rhe_139544Rhesus macaqueRhesus monkeyMacaca mulatta Description:DNA from the blood of Macaca mulatta s...
Common name:Rhesus macaque
Geographic location (country and/or sea,region):Ch...
...
+
C_rhe_149544Rhesus macaqueRhesus monkeyMacaca mulatta Description:DNA from the blood of Macaca mulatta s...
Common name:Rhesus macaque
Geographic location (country and/or sea,region):Ch...
...
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C_rhe_159544Rhesus macaqueRhesus monkeyMacaca mulatta Collection date:42638
Description:DNA from the blood of Macaca mulatta s...
Common name:Rhesus macaque
...
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C_rhe_169544Rhesus macaqueRhesus monkeyMacaca mulatta Description:DNA from the blood of Macaca mulatta s...
Common name:Rhesus macaque
Geographic location (country and/or sea,region):Ch...
...
+
C_rhe_179544Rhesus macaqueRhesus monkeyMacaca mulatta Description:DNA from the blood of Macaca mulatta s...
Common name:Rhesus macaque
Geographic location (country and/or sea,region):Ch...
...
+
C_rhe_189544Rhesus macaqueRhesus monkeyMacaca mulatta Description:Transcriptomics of the Pomacea canalic...
Description:DNA from the blood of Macaca mulatta s...
Common name:Rhesus macaque
...
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Displaying 1-10 of 79 Sample(s).




File NameSample IDData TypeFile FormatSizeRelease Date 
OtherUNKNOWN1.25 KB2018-08-07
OtherUNKNOWN75.88 KB2018-08-07
OtherUNKNOWN1.28 KB2018-08-07
AlignmentsFASTA390.77 MB2018-08-07
TextTEXT20.56 KB2018-08-07
ImagePNG17.78 KB2018-08-07
Tabular dataUNKNOWN0.3 KB2018-08-07
Mixed archiveTAR15.21 MB2018-08-07
Mixed archiveTAR5.33 MB2018-08-07
file_typeUNKNOWN3.27 KB2018-08-07
Displaying 1-10 of 16 File(s).
Funding body Awardee Award ID Comments
National Natural Science Foundation of China Z Liu 31471989
National Key Technology R&D Program of China M Li 2016YFC0503200
National Natural Science Foundation of China M Li 31530068
Chinese Academy of Sciences M Li XDA19050202 Strategic Priority Research Program
Chinese Academy of Sciences M Li XDB31000000 Strategic Priority Research Program
National Natural Science Foundation of China M Li 2018JZ0008 Creative Research Group Project
National Natural Science Foundation of China M Li Creative Research Group Project
Date Action
August 16, 2018 Dataset publish
August 28, 2018 Manuscript Link added : 10.1093/gigascience/giy106