# Genetic Diversity and Population Structure of Tufted Deer (Elaphodus cephalophus) in Chongqing, China

## TL;DR

Researchers studied the genetic diversity and population structure of tufted deer in China, finding that Simian Mountain has the most genetic diversity while Jinfo Mountain is isolated, requiring conservation strategies to protect the species.

## Contribution

The study provides new insights into the genetic structure and historical demographic patterns of tufted deer populations in Chongqing, China.

## Key findings

- Simian Mountain has the highest genetic diversity and serves as a genetic hub for tufted deer.
- Jinfo Mountain population is highly isolated with low genetic diversity and significant differentiation from other populations.
- The population likely expanded during the Pleistocene, but some groups remain separated.

## Abstract

The tufted deer (Elaphodus cephalophus) is a rare and endangered animal that lives only in China and Myanmar, and protecting it requires understanding how healthy and connected its populations are. This study looked at three groups of tufted deer living in different mountains in China to see how genetically diverse they are and the extent of gene flow among them. By analyzing specific parts of their DNA, researchers found that one area, Simian Mountain, has the most genetic diversity, making it very important for the species’ survival and as a source of genetic exchange. The study also revealed that one group, Jinfo Mountain, is more isolated, likely due to its unique terrain, which could hinder its ability to mingle with other groups. Evidence suggests that the overall population underwent a significant expansion during the Pleistocene epoch, but some groups remain separated. These findings highlight the importance of conserving and managing these deer populations carefully, especially by protecting key areas like Simian Mountain and establishing ecological corridors, particularly to enhance connectivity between the Jinfo and Simian Mountain populations. The results will help scientists and conservationists develop effective strategies to safeguard the tufted deer and ensure the future of this unique species.

The tufted deer (Elaphodus cephalophus), a Near-Threatened (NT) species endemic to China and Myanmar, requires robust genetic data for effective conservation. However, the genetic landscape of key populations, such as those in Chongqing, remains poorly understood. This study aimed to comprehensively evaluate the genetic diversity, population structure, gene flow, and demographic history of tufted deer across this critical region. We analyzed mitochondrial DNA (mtDNA) from 46 non-invasively collected fecal samples from three distinct populations: Jinfo Mountain (JF, n = 13), Simian Mountain (SM, n = 21), and the Northeastern Mountainous region (NEM, n = 12). Genetic variation was assessed using the cytochrome b (Cyt b) and D-loop regions, with analyses including Fst, gene flow (Nm), neutrality tests, and Bayesian Skyline Plots (BSP). Our results revealed the highest genetic diversity in the SM population, establishing it as a genetic hub. In contrast, the JF population exhibited the lowest diversity and significant genetic differentiation (>0.23) from the SM and NEM populations, indicating profound isolation. Gene flow was substantial between SM and NEM but severely restricted for the JF population. Demographic analyses, including BSP, indicated a long history of demographic stability followed by a significant expansion beginning in the Middle to Late Pleistocene. We conclude that the SM/NEM metapopulation serves as the genetic core for the species in this region, while the highly isolated JF population constitutes a distinct and vulnerable Management Unit (MU). This historical demographic expansion is likely linked to climatic and environmental changes during the Pleistocene, rather than recent anthropogenic factors. These findings underscore the urgent need for a dual conservation strategy: targeted management for the isolated JF population and the establishment of ecological corridors to connect the Jinfo Mountain and Simian Mountain populations, ensuring the long-term persistence of this unique species.