Analysis of Genetic Diversity and Population Structure in Three Forest Musk Deer Captive Populations with Different Origins

Abstract

Musk deer (Moschidae), whose secretion is an expensive and irreplaceable component of traditional medicine, have become endangered in the wild due to habitat fragmentation and over-exploitation. In recent years, China has had success in the artificial breeding of forest musk deer, thus relieving the pressure on wild populations. However, many farmed populations are experiencing degradation, and little genetic information is available for conservation management. In this study, we selected 274 individuals from three typical captive populations (originated from the Ta-pa Mountains (Tp), the midrange of the Qinling Mountains (Ql) and the Western Sichuan Plateau (WS), respectively) to evaluate the genetic variations. A total of more than 3.15 billion high-quality clean reads and 4.37 million high-quality SNPs were generated by RAD sequencing. Based on the analysis, we found that captive forest musk deer populations exhibit a relatively low level of genetic diversity. Ql displayed a higher level of genetic diversity than the Tp and WS populations. Tp and WS had experienced population bottlenecks in the past as inferred from the values of Tajima’s D. There were high levels of heterozygote deficiency caused by inbreeding within the three populations. Population structure analysis suggested that the three populations have evolved independently, and a moderate amount of genetic differentiation has developed, although there was a low level of gene flow between the Ql and Tp populations. Furthermore, the average quantities of musk secreted by musk deer in the Tp and WS populations were significantly higher than that in the Ql population. The present genetic information should be considered in management plans for the conservation and utilization of musk deer from captive breeding.

Comparative analysis of gut microbial composition and potential functions in captive forest and alpine musk deer

“…Recent studies have demonstrated that gut microbial structure abnormalities are associated with mental disorders, intestinal, metabolic, and other diseases (Dinleyici et al 2018;Qin et al 2012;Fung et al 2017;Valles-Colomer et al 2019). Moreover, various intrinsic and extrinsic factors such as host genetics (Fan et al 2021), genetic background (Korach-Rechtman et al 2019), diet (Wang et al 2019), age (O'Toole et al 2015;Guo et al 2020a), seasonal change (Peddada 2017), and habitat environment (Barelli et al 2020;Xiong et al 2021) greatly affect gut microbial community structure.…”

“…In the late 1950s, China performed artificial FMD and AMD breeding, generating the largest captive population of musk deer species. This breeding relieved the resource pressure on wild populations and provided, to an extent, the traditional and natural musk resources (Huang et al 2013;Fan et al 2019). Artificial breeding of musk deer can also reintroduce provenance.…”

Marked Seasonal Variation in Structure and Function of Gut Microbiota in Forest and Alpine Musk Deer

“…The International Union for Conservation of Nature (IUCN) Red List (Wang and Harris, 2015;Harris, 2016) and red list of China's vertebrates (Jiang et al, 2016) have listed both the species as endangered (EN) and critically endangered (CR), respectively. The captivity breeding of the FMD and AMD began in China in the 1960s to curb the rapid decline of the musk deer population by reducing the pressure on hunting wild musk deer to some extent (Fan et al, 2019). Captive individuals can also serve as a rewilding resource for reintroduction, which is beneficial for effective conservation and population recovery of wild musk deer.…”

Restoring faith in conservation action: Maintaining wild genetic diversity through the Tasmanian devil insurance program

“…Both the IP and Maria Island have high H S compared with the wild at both genome-wide and functional SNPs. However, these populations do exhibit evidence of inbreeding, which may be explained in part by sampling of related individuals but could also be impacted by unequal reproductive success and population sub-structuring ( Tables 1 and S2 ; Figure 3 ; O'Connell et al., 2019 ; Fan et al., 2019 ; Jamieson, 2011 ). Haplotype frequencies at the immune genes are similar across the IP, Maria Island, and the wild as evidenced by neither location clustering independently of the wild sites ( Figures 4 and S3–S9 ).…”