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
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):
(PubMed: 30165519)
Accessions (data generated as part of this study):
BioProject:
PRJNA345528
Sample ID | Taxonomic ID | Common Name | Genbank Name | Scientific Name | Sample Attributes |
---|---|---|---|---|---|
C_rhe_1 | 9544 | Rhesus macaque | Rhesus monkey | Macaca mulatta | Description:Transcriptomics of the Pomacea canalic... Description:DNA from the blood of Macaca mulatta s... Common name:Rhesus macaque ... + |
C_rhe_10 | 9544 | Rhesus macaque | Rhesus monkey | Macaca mulatta | Environment (feature):paddy field [ENVO:00000297] Description:DNA from the blood of Macaca mulatta s... Common name:Rhesus macaque ... + |
C_rhe_11 | 9544 | Rhesus macaque | Rhesus monkey | Macaca mulatta | Isolate:biologilca replicate 3 Description:DNA from the blood of Macaca mulatta s... Common name:Rhesus macaque ... + |
C_rhe_12 | 9544 | Rhesus macaque | Rhesus monkey | Macaca mulatta | Description:DNA from the blood of Macaca mulatta s... Common name:Rhesus macaque Geographic location (country and/or sea,region):Ch... ... + |
C_rhe_13 | 9544 | Rhesus macaque | Rhesus monkey | Macaca mulatta | Description:DNA from the blood of Macaca mulatta s... Common name:Rhesus macaque Geographic location (country and/or sea,region):Ch... ... + |
C_rhe_14 | 9544 | Rhesus macaque | Rhesus monkey | Macaca mulatta | Description:DNA from the blood of Macaca mulatta s... Common name:Rhesus macaque Geographic location (country and/or sea,region):Ch... ... + |
C_rhe_15 | 9544 | Rhesus macaque | Rhesus monkey | Macaca mulatta | Collection date:42638 Description:DNA from the blood of Macaca mulatta s... Common name:Rhesus macaque ... + |
C_rhe_16 | 9544 | Rhesus macaque | Rhesus monkey | Macaca mulatta | Description:DNA from the blood of Macaca mulatta s... Common name:Rhesus macaque Geographic location (country and/or sea,region):Ch... ... + |
C_rhe_17 | 9544 | Rhesus macaque | Rhesus monkey | Macaca mulatta | Description:DNA from the blood of Macaca mulatta s... Common name:Rhesus macaque Geographic location (country and/or sea,region):Ch... ... + |
C_rhe_18 | 9544 | Rhesus macaque | Rhesus monkey | Macaca mulatta | Description:Transcriptomics of the Pomacea canalic... Description:DNA from the blood of Macaca mulatta s... Common name:Rhesus macaque ... + |