Non-Invasive Genotyping of Sumatran Elephants: Implications for Conservation

Abstract

Reliable baseline information necessary for the monitoring and conservation of Sumatran elephants is scarce. We here combine non-invasive molecular genetics methods and capture-recapture modeling to estimate elephant population size, distribution, sex ratio, and age structure for the Bukit Tigapuluh landscape in Sumatra, Indonesia. Two separate subpopulations were found, for which we estimated a population size of 99 (95% CI = [86, 125], PCCL = 38.59%) and 44 elephants (95% CI = [37, 56], PCCL = 43.18%), respectively. Low elephant densities are likely the result of patchy habitat usage and anthropogenically increased mortality, the latter assumption being supported by strong skews in both sex ratio and age structure as well as direct evidence of elephant killing. Still, the Bukit Tigapuluh landscape currently holds the largest known population of elephants in central Sumatra, representing one of the most important areas for their conservation in Indonesia. Conservation of both the elephant population and their habitat in this region should thus be of high priority. We identified several threats to the population, including (i) the risk of inbreeding and subsequent loss of genetic diversity, (ii) illegal elephant killing, and (iii) the lack of protected habitat. In order to overcome these challenges we suggest: (i) the implementation of a meta-population management program, (ii) monitoring and safeguarding elephants and improving law enforcement, and (iii) providing sufficient safe habitat to mitigate human-elephant-conflict (HEC) and ensure elephant survival.

Genetic Tools for the Conservation of Wild Asian Elephants

“…Alternative methods such as dung count (Hedges et al, 2005) and noninvasive genetic method (Ahlering et al, 2011;Hedges, Johnson, Ahlering, Tyson, & Eggert, 2013;Gray, Vidya, Potdar, Bharti, & Sovanna, 2014;Moßbrucker et al, 2015) have been applied to obtain data of wild elephant populations in such habitats. One of the advantages of noninvasive genetic method over the dung count method is that the genetic method provides genetic information of the populations that could not be obtained from field data collection alone.…”

“…Multilocus microsatellite genotyping together with mark-recapture analyses allows researchers to reliably estimate population size (Hedges et al, 2013;Gray et al, 2014;Moßbrucker et al, 2015). Cross specific microsatellite primers developed for the African elephant (Loxodonta africana) have also been commonly applied to the Asian elephant populations (Vidya et al, 2007;Flagstad, Pradhan, Kvernstuen, & Wegge, 2012;Moßbrucker et al, 2015). Note that null allele should be under concerned when cross specific primers are used.…”

“…Individual sex can be determined by amplification of sex determination regions on sex chromosomes Gupta, Thangaraj, & Singh, 2006;Vidya et al, 2007;Munshi-South et al, 2008;Ahlering et al, 2011;Chakraborty, Boominathan, Desai, & Vidya, 2014), thus the population sex ratio can be estimated Vidya et al, 2007;Ahlering et al, 2011;Flagstad et al, 2012;Chakraborty et al, 2014;Moßbrucker et al, 2015).…”

“…It is a suitable DNA marker to refer genetics of maternal lineage and to study a population in evolutionary aspects such as evolutionary phylogeny and phylogeography (Fleischer, Perry, Muralidharan, Stevens, & Wemmer, 2001;Fernando et al, 2003;Vidya, Sukumar, & Melnick, 2009). DNA primers for amplification of the mitochondrial DNA fragment of the Asian elephant have been designed and used to study mitochondrial haplotype distribution of wild populations across their range (Fleischer et al, 2001;Vidya et al, 2009), and in particular populations in Sri Lanka (Fernando, Pfrender, Encalada, & Lande, 2000), India (Vidya, Fernando, Melnick, & Sukumar, 2005b), Vietnam (Vidya et al, 2007), Laos (Ahlering et al, 2011), peninsular Malaysia (Elliza, Shukor, Othman, & Md-Zain, 2015), Sumatra (Moßbrucker et al, 2015), and Borneo (Goossens et al, 2016). The primer pair designed by has been used in most of the studies, thus the variation of mitochondrial DNA of different populations could be directly compared.…”

“…Major threats to wild Asian elephants worldwide are habitat loss and fragmentation (Santiapillai & Jackson, 1990), illegal poaching, and conflicts with human (Sukumar, 1992(Sukumar, , 2003(Sukumar, , 2006. These threats resulted in population decline, skewed sex ratio (Ramakrishnan, Santosh, Ramakrishnan, & Sukumar, 1998;Vidya, Kumar, Arivazhagan, & Sukumar, 2003;Moßbrucker et al, 2015), and disruption of social organization (Vidya, Varma, Dang, Thanh, & Sukumar, 2007). Intensive studies on biology, ecology, behavior and genetic diversity of wild Asian elephants have been carried out in India and Sri Lanka, though such information in other countries is still limited.…”