Molecular genetics of the Asian elephant (Elephas maximus) in Taman Negara National Park, Peninsular Malaysia for conservation management purposes

Abstract

Conservation of Asian elephant (Elephas maximus) lies within the full understanding of ecology, behaviour aspects and complete genetic assessment. Lacking a comprehensive genetic evaluation at individual and population level for Asian elephant’s limits decisions on conservation and management in Peninsular Malaysia. Thus, this comprehensive genetic assessment study was carried out on wild elephants in Taman Negara National Parks (TNNP) to guide long term population management. This study has four main objectives: i) to validate different dung decay rate in obtaining high yield of DNA, ii) to genotype, evaluate genetic diversity and population structure by using 15 pairs of microsatellite markers, iii) to evaluate haplotype distribution and phylogenetic pattern using a pair of mitochondrial DNA (mtDNA) D-loop region and iv) to determine of sex ratio and age group structure of elephants in TNNP by using three pairs of molecular sexing markers SRY1,AMELY2 and PLP1. A non-invasive sampling was carried out at 31 sampling sites in TNNP starting from October 2016 until December 2017. Laboratory analyses were involved DNA extraction of faecal samples; amplification of polymerase chain reaction; fragment and sequencing data analysis; statistical interpretations for genotypes, genetic relatedness and genetic variation. A total of 217 elephant individuals were identified from microsatellite genotype analysis. The cumulative probability of identity (PID) and probability of identity siblings (PISib) were 2.79 X10-07 and 8.59X10-04 respectively. Similarly, polymorphic information content (PIC) was averaged at 0.9158 and ranged from 0.86 to 0.96. This PIC index value shows all the tested microsatellite DNA markers have high diversity. The larger PIC index with more than 0.5 indicates that the microsatellite locus has high genetic variability. The value of inbreeding coefficient index (FIS) was -0.08 indicating no signs of inbreeding among populations. Elephant populations in TNNP were stable because all the microsatellite loci conform to Hardy Weinberg equilibrium as observed heterozygosity were higher than the expected heterozygosity. No null alleles detected in this study. Total of 6 haplotypes with haplotype diversity (Hd) of 0.2016 were observed from mtDNA D-loop region. The genetic distance among elephant population were 0.022. Molecular sexing techniques have identified 86 male elephants and 131 female elephants in the TNNP. Total of 124 adult elephants were identified while 15 neonates and 78 subadults were classified. This study has successfully generated comprehensive information on the genetic structure, profile and population status of E. maximus in TNNP. This novel dataset can be used in the conservation and management of Asian elephants by Department of Wildlife and National Parks (DWNP) in accordance with the National Elephant Conservation Action Plan.