Using genetic methods and an integrative multi-stakeholder approach to understand small fragmented Asian elephant populations in Cambodia

The Asian elephant (Elephas maximus) is classified as globally endangered, with geographically isolated populations scattered across socio-ecological landscapes in 13 countries. Historical and current anthropogenic threats have caused local extirpations and population declines. These include illegal hunting, illegal and legal live capture, habitat loss and fragmentation, and negative human-elephant interactions (NHEIs). Asian elephants are often adaptable and can utilise a wide range of natural and human-modified habitats. However, further disruptions to their movements could lead to population fragmentation, impact long-term viability and lead to an escalation in NHEIs. Obtaining detailed population data can be extremely challenging for this often elusive, wide-ranging, highly mobile species. Genetic approaches are now increasingly used to provide valuable population parameter data that are often difficult or impossible to collect using other methods. This thesis used conservation genetics methods to evaluate the population dynamics of elephants in eastern Cambodia, as well as a multifaceted approach to gather ecological data and expert knowledge on elephant status at the national level. Results indicated that the quantity and quality of genetic data from degraded samples can be improved by combining microsatellite and SNP marker datasets (Chapter two). Using this approach, results indicate that the Phnom Prich and Srepok Wildlife Sanctuaries support Cambodia’s largest elephant population. However, anecdotal reports suggest recent population fragmentation has likely occurred due to the cumulative impacts of various anthropogenic factors (i.e., linear infrastructure and exploratory mining concessions). Small effective population size, skewed sex ratios and low number of juveniles were evident for each of the probable fragmented populations, thus raising concerns regarding population viability (Chapter two). Population and diversity analyses were expanded to include additional genetic data for elephants in the adjacent Keo Seima Wildlife Sanctuary (Chapter three). Despite evidence of a recent population contraction, there were no signs of genetic differences between the three geographic groups. Global comparisons found that the wider population still retained moderately high levels of nuclear and mitochondrial (mtDNA) diversity, with haplotypes found in both alpha and beta mitochondrial clades (Chapter three). These findings highlight the conservation value of all three populations, yet also emphasise the need to restrict future land-use alterations and anthropogenic disturbances to facilitate continuous gene flow exchange among populations to safeguard existing diversity levels and prevent genetic drift. Results from Chapter four found that genetic marker performance, genotyping call rates and accuracy of genotype assignments were all higher for SNP markers compared to microsatellite markers. These results combined with lower costs and the relative ease of performing SNP genotyping in-country highlight the benefits of this universally transferable SNP panel in future Asian elephant genotyping studies. In Chapter five, an integrative multi-stakeholder approach identified 18 PAs supporting varying-sized populations, yet range reduction and population fragmentation were evident. Habitat loss, fragmentation, snaring, and disturbances all likely pose a threat to the survival of several small, isolated populations. Moreover, the perceived efficacy of current management efforts to mitigate these threats was variable. The increased distribution of NHEIs across the country also poses a concern for the wellbeing of elephants and people using shared spaces. Overall findings from this thesis research can assist with identifying landscape-level priorities so that real-time adaptive strategies can be developed to benefit both elephants and people in shared spaces.