Habitat fragmentation and genetic diversity in natural populations of the Bornean elephant: Implications for conservation

Abstract

The Bornean elephant population in Sabah, with only 2,000 individuals, is currently mainly restricted to a limited number of forest reserves. The main threats to the species" survival are population fragmentation and isolation of the existing herds. To support and help monitor future conservation and management measures, we assessed the genetic diversity and population structure of Bornean elephants using mitochondrial DNA, microsatellites and single nucleotide polymorphisms. Our results confirmed a previously reported lack of mitochondrial control region diversity, characterized by a single widespread haplotype. However, we found low but significant degree of genetic differentiation among populations and marked variation in genetic diversity with the other two types of markers among Bornean elephants. Microsatellite data showed that Bornean elephants from the Lower Kinabatangan and North Kinabatangan ranges are differentiated and perhaps isolated from the main elephant populations located in the Central Forest and Tabin Wildlife Reserve. The pairwise F ST values between these sites ranged from 0.08 to 0.14 (p < 0.001). Data from these markers also indicate that the Bornean elephant populations from Lower Kinabatangan Wildlife Sanctuary and North Kinabatangan (Deramakot Forest Reserve) possess higher levels of genetic variation compared to the elephant populations from other areas. Our results suggest that (i) Bornean elephants probably derive from a very small female population, (ii) they rarely disperse across current human-dominated landscapes that separate forest fragments, and (iii) forest fragments are predominantly comprised of populations that are already undergoing genetic drift. To maintain the current levels of genetic diversity in fragmented habitats, conservation of the Bornean elephants should aim at securing connectivity between spatially distinct populations. Study sites and samplingElephants in Sabah are distributed in five main ranges: i) Lower Kinabatangan, ii) North Kinabatangan (Deramakot, Tangkulap and Segaliud Forest Reserves), iii) Central Forest (Ulu Segama, Malua, Kuamut, Gunung Rara, and Kalabakan Forest Reserves, Danum Valley and Maliau Basin Conservation Areas), iv) Tabin Wildlife Reserve, and v) Ulu Kalumpang (Alfred et al., 2010; Elephant Action Plan, Sabah Wildlife Department, 2012-2016. All ranges (but Ulu Kalumpang, due to its inaccessibility) were covered and systematically searched for elephant feces between October 2005 and November 2007 (Figure 1). Samples were mainly collected along logging roads where elephants consume grass and travel. The same procedure was conducted for three ranges (Central Sabah, Tabin and North Kinabatangan). For the Lower Kinabatangan population, samples were collected along the main river, in riparian feeding areas where individuals were encountered, allowing collection of fresh samples. Samples were collected during field expeditions of 5-7 days, giving a short time period during which samples were collected from every location. Fresh elephant du...

Genetic Tools for the Conservation of Wild Asian Elephants

“…The habitat of the Bornean elephants those are distributed only in Borneo Island and considered as an evolutionarily significant unit (Fernando et al, 2003), was highly fragmented due to land conversion to palm oil plantations and human settlement. Genetic analysis of the Bornean elephants revealed low genetic diversity compared to that of other mainland Asian elephant populations (Goossens et al, 2016) such as populations in Laos (Ahlering et al, 2011) and Cambodia (Gray et al, 2014). Only one mitochondrial haplotype was found in the studied populations (Fernando et al, 2003;Goossens et al, 2016).…”

“…Genetic analysis of the Bornean elephants revealed low genetic diversity compared to that of other mainland Asian elephant populations (Goossens et al, 2016) such as populations in Laos (Ahlering et al, 2011) and Cambodia (Gray et al, 2014). Only one mitochondrial haplotype was found in the studied populations (Fernando et al, 2003;Goossens et al, 2016). A low but significant level of genetic differentiation was detected, possibly due to the existence of gene flow between populations within the region or recent fragmentation (Goossens et al, 2016).…”

“…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.…”

“…Recently, the single nucleotide polymorphisms (SNPs) maker has been applied for evaluation and comparison of genetic diversity in the two populations of Bornean elephants (Goossens et al, 2016). The SNP loci used in the study were polymorphic and showed similar patterns of genetic diversity as those obtained from the microsatellite loci.…”

“…Combining different types of DNA markers allows researchers to investigate a population in fine-scale, such as relatedness among individuals within and between groups, social structure and genetic structure of the populations (Vidya et al, 2005b;Vidya et al, 2007;Goossens et al, 2016).…”