文献类型：期刊文献

英文题名：Population genomics reveals moderate genetic differentiation between populations of endangered Forest Musk Deer located in Shaanxi and Sichuan

作者：Liu, Gang[1] Zhang, Bao-Feng[2] Chang, Jiang[3] Hu, Xiao-Long[4] Li, Chao[1] Xu, Tin-Tao[5] Liu, Shu-Qiang[2] Hu, De-Fu[2]

第一作者：刘刚

通信作者：Liu, G[1];Hu, DF[2]

机构：[1]Chinese Acad Forestry, Inst Wetland Res, Beijing Key Lab Wetland Serv & Restorat, Beijing 100091, Peoples R China;[2]Beijing Forestry Univ, Coll Ecol & Nat Conservat, Beijing 100085, Peoples R China;[3]Chinese Res Inst Environm Sci, State Key Lab Environm Criteria & Risk Assessment, Beijing 100012, Peoples R China;[4]Jiangxi Agr Univ, Coll Anim Sci & Technol, Nanchang 330022, Jiangxi, Peoples R China;[5]Jilin Univ, Coll Plant Sci, Changchun 130062, Peoples R China

年份：2022

卷号：23

期号：1

外文期刊名：BMC GENOMICS

收录：;Scopus(收录号：2-s2.0-85138370296);WOS:【SCI-EXPANDED(收录号:WOS:000857077600001)】；

基金：This work was supported by National Natural Science Foundation of China (No. 31872962 to D.F.H.), and the Biodiversity Survey, Monitoring and Assessment Project (2019-2023) of the Ministry of Ecology and Environment, China (No. 2019HB2096001006 to D.F.H.). The funders had no role designing the study, collecting samples and and analyzing data, as well as no involvement with the decision to publish, or preparation of the manuscript.

语种：英文

外文关键词：Forest Musk Deer; Population decline; Population genomics; Genetic diversity; Genetic differentiation; Gene flow

摘要：Background Many endangered species exist in small, genetically depauperate, or inbred populations, hence promoting genetic differentiation and reducing long-term population viability. Forest Musk Deer (Moschus berezovskii) has been subject to illegal hunting for hundreds of years due to the medical and commercial values of musk, resulting in a significant decline in population size. However, it is still unclear to what extent the genetic exchange and inbreeding levels are between geographically isolated populations. By using whole-genome data, we reconstructed the demographic history, evaluated genetic diversity, and characterized the population genetic structure of Forest Musk Deer from one wild population in Sichuan Province and two captive populations from two ex-situ centers in Shaanxi Province. Results SNP calling by GATK resulted in a total of 44,008,662 SNPs. Principal component analysis (PCA), phylogenetic tree (NJ tree), ancestral component analysis (ADMIXTURE) and the ABBA-BABA test separated Sichuan and Shaanxi Forest Musk Deer as two genetic clusters, but no obvious genetic differentiation was observed between the two captive populations. The average pairwise F-ST value between the populations in Sichuan and Shaanxi ranged from 0.05-0.07, suggesting a low to moderate genetic differentiation. The mean heterozygous SNPs rate was 0.14% (0.11%-0.15%) for Forest Musk Deer at the genomic scale, and varied significantly among three populations (Chi-square = 1.22, p < 0.05, Kruskal-Wallis Test), with the Sichuan population having the lowest (0.11%). The nucleotide diversity of three populations varied significantly (p < 0.05, Kruskal-Wallis Test), with the Sichuan population having the lowest genetic theta(pi) (1.69 x 10(-3)). Conclusions Genetic diversity of Forest Musk Deer was moderate at the genomic scale compared with other endangered species. Genetic differentiation between populations in Sichuan and Shaanxi may not only result from historical biogeographical factors but also be associated with contemporary human disturbances. Our findings provide scientific aid for the conservation and management of Forest Musk Deer. They can extend the proposed measures at the genomic level to apply to other musk deer species worldwide.