Genomic Population Structure of the Sunda Pangolin ( Manis javanica ) in Thailand: Implications for Conservation and Wildlife Forensics

Pangolins are the most heavily trafficked mammal globally, yet the population structure and genetic diversity remain poorly understood for many of the eight species. In Thailand, the Sunda pangolin ( Manis javanica ) is subject to illegal hunting and has a fragmented distribution among protected areas; however, relatively little is known about its genetic variation, due in part to the elusive nature of the species, which presents significant challenges for sampling and population genetic research. This study analyses whole genome sequences from 30 georeferenced samples across Thailand to examine population structure and genetic diversity, in order to inform conservation management and underpin the development of wildlife forensic tools. We identified four distinct genetic populations within Thailand, corresponding to the Western, Khao Yai, Mid-south, and Southernmost regions, with moderate genetic differentiation ( F _ST = 0.06-0.14) between populations. The Western population showed elevated inbreeding levels ( F _ROH = 18.50%) compared to other populations ( F _ROH < 12.5%), while the Southernmost population maintained the highest genetic diversity. Geographic barriers, including the Chao Phraya River and Nakhon Si Thammarat Mountain range, coincided with strong population structure. Our findings establish a foundational genomic baseline for Sunda pangolin conservation in Thailand, identifying distinct genetic management units. The population-specific genetic signatures provide a framework for developing wildlife forensic tools to trace the geographic origin of confiscated pangolins within Thailand. These insights are crucial for implementing targeted conservation strategies and combating illegal wildlife trade of this Critically Endangered species.