Institute of Wetland Research, Chinese Academy of Forestry, Beijing Key Laboratory of Wetland Services and Restoration, Beijing, 100091, China.
College of Ecology and Nature Conservation, Beijing Forestry University, Beijing, 100085, China.
BMC Genomics. 2022 Sep 23;23(1):668. doi: 10.1186/s12864-022-08896-9.
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.
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 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 θ (1.69 × 10).
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.
许多濒危物种存在于遗传上贫弱或近交的小种群中，因此促进了遗传分化，降低了种群的长期生存能力。由于麝香具有药用和商业价值，林麝（Moschus berezovskii）已被非法猎捕数百年，导致其种群数量显著减少。然而，目前尚不清楚地理隔离种群之间的基因交流和近交程度。本研究通过全基因组数据，重建了林麝的种群历史、评估了遗传多样性，并对来自四川省一个野生种群和陕西省两个易地保护中心的两个圈养种群的种群遗传结构进行了特征描述。
通过 GATK 进行 SNP 调用，共获得了 44008662 个 SNPs。主成分分析（PCA）、系统发育树（NJ 树）、祖先成分分析（ADMIXTURE）和 ABBA-BABA 检验将四川和陕西的林麝分为两个遗传群，但两个圈养种群之间没有明显的遗传分化。四川和陕西种群之间的平均成对 F 值在 0.05-0.07 之间，表明遗传分化程度较低。林麝在基因组水平上的平均杂合 SNPs 率为 0.14%（0.11%-0.15%），三个种群之间存在显著差异（卡方=1.22，p<0.05，Kruskal-Wallis 检验），其中四川种群最低（0.11%）。三个种群的核苷酸多样性存在显著差异（p<0.05，Kruskal-Wallis 检验），其中四川种群的遗传θ值最低（1.69×10）。
与其他濒危物种相比，林麝在基因组水平上的遗传多样性中等。四川和陕西种群之间的遗传分化可能不仅是历史生物地理因素的结果，还与当代人类干扰有关。本研究结果为林麝的保护和管理提供了科学依据，并可以将在基因组水平上提出的保护措施扩展应用于全球其他麝香鹿物种。
