Supporting data for "Population genomics of wild Chinese rhesus macaques reveals a dynamic demographic history and local adaptation, with implications for biomedical research" =============================================================================================================================================================================== 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 Summary: -------- 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.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 offers new insights into their evolution and provides valuable baseline information for biomedical investigation. Files: ------- tree/all.fa.gz - alignments used for phylogenetic trees tree/81_bootstrap.newick - phylogenetic tree files pca/eigenvevalTW.csv - TW test result (pca output file) pca/PCA.eigenvec.csv - output file from Eigensoft (pca output file) structure/deltaK.png - Plots generated from STRUCTURE results structure/K5.indfile - STRUCTURE result for five populations fastsimcoal/5pop_MSFS.obs - Fastsimcoal output; site frequency spectrum (SFS) file fastsimcoal/5pop.est - Fastsimcoal output; estimation (.est) file fastsimcoal/5pop.tpl - Fastsimcoal output; template (.tpl) file fastsimcoal/replicate.50.txt - Fastsimcoal output; the results of 50 replicates fastsimcoal/bootstrap100.result.txt - Fastsimcoal output; the results of 100 bootstraps population.vcf.gz - population vcf file for all the 81 rhesus macaques PSMC.tar - pairwise sequential Markovian coalescent (PSMC) output fies vcftools/five_populations_fst.tar.gz - fst values for five populations (vcftools output file) vcftools/five_populations_pi.tar.gz - pi values for five populations (vcftools output files)