Genetic analyses favour an ancient and natural origin of elephants on Borneo.

The origin of the elephant on the island of Borneo remains elusive. Research has suggested two alternative hypotheses: the Bornean elephant stems either from a recent introduction in the 17th century or from an ancient colonization several hundreds of thousands years ago. Lack of elephant fossils has been interpreted as evidence for a very recent introduction, whereas mtDNA divergence from other Asian elephants has been argued to favor an ancient colonization. We investigated the demographic history of Bornean elephants using full-likelihood and approximate Bayesian computation analyses. Our results are at odds with both the recent and ancient colonization hypotheses, and favour a third intermediate scenario. We find that genetic data favour a scenario in which Bornean elephants experienced a bottleneck during the last glacial period, possibly as a consequence of the colonization of Borneo, and from which it has slowly recovered since. Altogether the data support a natural colonization of Bornean elephants at a time when large terrestrial mammals could colonise from the Sunda shelf when sea levels were much lower. Our results are important not only in understanding the unique history of the colonization of Borneo by elephants, but also for their long-term conservation.

Two different high throughput sequencing approaches identify thousands of de novo genomic markers for the genetically depleted Bornean elephant.

High throughput sequencing technologies are being applied to an increasing number of model species with a high-quality reference genome. The application and analyses of whole-genome sequence data in non-model species with no prior genomic information are currently under way. Recent sequencing technologies provide new opportunities for gathering genomic data in natural populations, laying the empirical foundation for future research in the field of conservation and population genomics. Here we present the case study of the Bornean elephant, which is the most endangered subspecies of Asian elephant and exhibits very low genetic diversity. We used two different sequencing platforms, the Roche 454 FLX (shotgun) and Illumina, GAIIx (Restriction site associated DNA, RAD) to evaluate the feasibility of the two methodologies for the discovery of de novo markers (single nucleotide polymorphism, SNPs and microsatellites) using low coverage data. Approximately, 6,683 (shotgun) and 14,724 (RAD) SNPs were detected within our elephant sequence dataset. Genotyping of a representative sample of 194 SNPs resulted in a SNP validation rate of ~83 to 94% and 17% of the loci were polymorphic with a low diversity (H(o)=0.057). Different numbers of microsatellites were identified through shotgun (27,226) and RAD (868) techniques. Out of all di-, tri-, and tetra-microsatellite loci, 1,706 loci had sufficient flanking regions (shotgun) while only 7 were found with RAD. All microsatellites were monomorphic in the Bornean but polymorphic in another elephant subspecies. Despite using different sample sizes, and the well known differences in the two platforms used regarding sequence length and throughput, the two approaches showed high validation rate. The approaches used here for marker development in a threatened species demonstrate the utility of high throughput sequencing technologies as a starting point for the development of genomic tools in a non-model species and in particular for a species with low genetic diversity.

Quantity and configuration of available elephant habitat and related conservation concerns in the Lower Kinabatangan floodplain of Sabah, Malaysia.

The approximately 300 (298, 95% CI: 152-581) elephants in the Lower Kinabatangan Managed Elephant Range in Sabah, Malaysian Borneo are a priority sub-population for Borneo's total elephant population (2,040, 95% CI: 1,184-3,652). Habitat loss and human-elephant conflict are recognized as the major threats to Bornean elephant survival. In the Kinabatangan region, human settlements and agricultural development for oil palm drive an intense fragmentation process. Electric fences guard against elephant crop raiding but also remove access to suitable habitat patches. We conducted expert opinion-based least-cost analyses, to model the quantity and configuration of available suitable elephant habitat in the Lower Kinabatangan, and called this the Elephant Habitat Linkage. At 184 km(2), our estimate of available habitat is 54% smaller than the estimate used in the State's Elephant Action Plan for the Lower Kinabatangan Managed Elephant Range (400 km(2)). During high flood levels, available habitat is reduced to only 61 km(2). As a consequence, short-term elephant densities are likely to surge during floods to 4.83 km(-2) (95% CI: 2.46-9.41), among the highest estimated for forest-dwelling elephants in Asia or Africa. During severe floods, the configuration of remaining elephant habitat and the surge in elephant density may put two villages at elevated risk of human-elephant conflict. Lower Kinabatangan elephants are vulnerable to the natural disturbance regime of the river due to their limited dispersal options. Twenty bottlenecks less than one km wide throughout the Elephant Habitat Linkage, have the potential to further reduce access to suitable habitat. Rebuilding landscape connectivity to isolated habitat patches and to the North Kinabatangan Managed Elephant Range (less than 35 km inland) are conservation priorities that would increase the quantity of available habitat, and may work as a mechanism to allow population release, lower elephant density, reduce human-elephant conflict, and enable genetic mixing.