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. https://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):
- Liu, Z., Tan, X., Orozco-terWengel, P., Zhou, X., Zhang, L., Tian, S., Yan, Z., Xu, H., Ren, B., Zhang, P., Xiang, Z., Sun, B., Roos, C., Bruford, M. W., & 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). https://doi.org/10.1093/gigascience/giy106 (PubMed:30165519)
Accessions (data included in GigaDB):
BioProject: PRJNA345528
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Table SettingsSample ID | Common Name | Scientific Name | Sample Attributes | Taxonomic ID | Genbank Name |
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C_rhe_51 | Macaca mulatta lasiotus | Description:DNA from the blood of Macaca mulatta l... Environment (biome):area of cropland [ENVO:0100089... Common name:Rhesus macaque ... |
1449913 | ||
C_rhe_39 | Macaca mulatta lasiotus | Environment (feature):paddy field [ENVO:00000297] Description:DNA from the blood of Macaca mulatta l... Common name:Rhesus macaque ... |
1449913 | ||
C_rhe_57 | Macaca mulatta lasiotus | Isolate:biologilca replicate 3 Description:DNA from the blood of Macaca mulatta l... Common name:Rhesus macaque ... |
1449913 | ||
C_rhe_6 | Rhesus macaque | Macaca mulatta | Alternative accession-BioProject:PRJNA345528 Alternative names:apple snail Infra specific name:subspecies ... |
9544 | Rhesus monkey |
C_rhe_7 | Rhesus macaque | Macaca mulatta | Specific host:N/A Description:DNA from the blood of Macaca mulatta s... Common name:Rhesus macaque ... |
9544 | Rhesus monkey |
C_rhe_2 | Rhesus macaque | Macaca mulatta | Alternative accession-SRA Sample:SRS1762018 Host taxid:N/A Description:DNA from the blood of Macaca mulatta s... ... |
9544 | Rhesus monkey |
C_rhe_3 | Rhesus macaque | Macaca mulatta | Description:DNA from the blood of Macaca mulatta s... Common name:Rhesus macaque Geographic location (country and/or sea,region):Ch... ... |
9544 | Rhesus monkey |
C_rhe_4 | Rhesus macaque | Macaca mulatta | Description:DNA from the blood of Macaca mulatta s... Common name:Rhesus macaque Geographic location (country and/or sea,region):Ch... ... |
9544 | Rhesus monkey |
C_rhe_5 | Rhesus macaque | Macaca mulatta | Description:DNA from the blood of Macaca mulatta s... Common name:Rhesus macaque Geographic location (country and/or sea,region):Ch... ... |
9544 | Rhesus monkey |
C_rhe_1 | Rhesus macaque | Macaca mulatta | Alternative names:M16 Description:Transcriptomics of the Pomacea canalic... Description:DNA from the blood of Macaca mulatta s... ... |
9544 | Rhesus monkey |
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Table SettingsFile Name | Description | Sample ID | Data Type | File Format | Size | Release Date | File Attributes | Download |
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Readme | TEXT | 3.47 kB | 2018-08-07 | MD5 checksum: d5a31c4985025f22f950a4cb26696ec3 |
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pairwise sequential Markovian coalescent (PSMC) output fies | Other | TAR | 13.88 kB | 2018-08-07 | MD5 checksum: fec8ca9290f52094c924704b64544246 |
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Fastsimcoal output - estimation (.est) file | Other | UNKNOWN | 1.27 kB | 2018-08-07 | MD5 checksum: d26ddfa48210e49e107f88ddad9ffdc5 |
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Fastsimcoal output - site frequency spectrum (SFS) file | Other | UNKNOWN | 77.70 kB | 2018-08-07 | MD5 checksum: 89bd4991b2e664f2258f11b28d7613de |
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Fastsimcoal output - template (.tpl) file | Other | UNKNOWN | 1.31 kB | 2018-08-07 | MD5 checksum: ea0fbef0d24f55b2a0d13348f95ab292 |
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Fastsimcoal output - the results of 100 bootstraps | Text | TEXT | 21.05 kB | 2018-08-07 | MD5 checksum: c956359b6102d26ece79b26ff4d6a6e3 |
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Fastsimcoal output - the results of 50 replicates | Text | TEXT | 10.57 kB | 2018-08-07 | MD5 checksum: 0a89b86e41262a482997ad0f7bcb983c |
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TW test result (pca output file) | Tabular data | UNKNOWN | 308 B | 2018-08-07 | MD5 checksum: d171cae35bb57889dc491b871dd6e966 |
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output file from Eigensoft (pca output file) | Tabular data | UNKNOWN | 2.81 kB | 2018-08-07 | MD5 checksum: 780d88d8b073bdd36c954bfd84a70b4a |
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Plots generated from STRUCTURE results | Image | PNG | 18.21 kB | 2018-08-07 | MD5 checksum: c26ef9e791760e680ca6c485e2cdfe16 |
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 |
November 11, 2022 | Manuscript Link updated : 10.1093/gigascience/giy106 |
November 15, 2022 | Data type for File K5.indfile updated |