Genetic insights for enhancing conservation strategies in captive and wild Asian elephants through improved non-invasive DNA-based individual identification

Asian elephant is a key umbrella species that plays a crucial role in maintaining biodiversity and ecological balance. As an iconic symbol of Thailand, it also significantly contributes to the nation's tourism industry. However, human activities pose serious threats to their long-term survival and population health. To tackle these challenges and develop effective conservation strategies, extensive genetic reference data were collected to enhance both captive and wild elephant conservation, improve non-invasive DNA-based individual identification, and assess genetic diversity using 18 microsatellite markers. High genetic diversity was observed across all populations; however, high levels of inbreeding were evident in NEI, EKS, BCEP, and wild elephant populations, except for the MEP population, which recorded low inbreeding levels. Significant variation in the gene pool estimates was observed across different populations, with three maternal haplogroups (alpha, beta 1, and a tentative beta 3) identified. A reduced panel of six microsatellite markers proved highly efficient for individual identification. Additionally, non-invasive DNA samples were tested using 18 microsatellite loci for individual identification. Using only 7 out of the 18 microsatellite loci tested, individuals were successfully identified, demonstrating enough discriminatory power to distinguish between individuals. Among these, four loci (LaT08, LaT13, FH19, and FH67) were both effective and efficient for reliable individual identification in fecal samples. These findings offer valuable insights for optimizing conservation efforts, including the design of tailored strategies to protect Asian elephants in Thailand and ensure the long-term viability of their populations.