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In the Kinabatangan floodplain, Sabah, Malaysian Borneo, oil palm and settlements have reduced and fragmented lowland tropical forests, home to around 200 endangered Bornean elephants ( Elephas maximus borneensis ). In this region, elephants range within forests, oil palm and community areas. The degree to which elephants are using these areas remains unclear. We used GPS telemetry data from 2010 to 2020 for 14 collared elephants to map their entire known ranges and highly used areas (hot spots) across four land use categories and estimate time spent within these. The use of land use types across elephants varied significantly. Typically, females had strong fidelity to forests, yet many of these forests are threatened with conversion. For the three males, and several females, they heavily used oil palm estates, and this may be due to decreased landscape permeability or foraging opportunities. At the pooled level, the entire range and hot spot extents, constituted 37% and 34% for protected areas, respectively, 8% and 11% for unprotected forests, 53% and 51% for oil palm estates, and 2% for community areas. Protecting all forested habitats and effectively managing areas outside of protected areas is necessary for the long-term survival of this population.

Home range is defined as the extent and location of the area covered annually by a wild animal in its natural habitat. Studies of African and Indian elephants in landscapes of largely open habitats have indicated that the sizes of the home range are determined not only by the food supplies and seasonal changes, but also by numerous other factors including availability of water sources, habitat loss and the existence of man-made barriers. The home range size for the Bornean elephant had never been investigated before. The first satellite tracking program to investigate the movement of wild Bornean elephants in Sabah was initiated in 2005. Five adult female elephants were immobilized and neck collars were fitted with tracking devices. The sizes of their home range and movement patterns were determined using location data gathered from a satellite tracking system and analyzed by using the Minimum Convex Polygon and Harmonic Mean methods. Home range size was estimated to be 250 to 400 km(2) in a non-fragmented forest and 600 km(2) in a fragmented forest. The ranging behavior was influenced by the size of the natural forest habitat and the availability of permanent water sources. The movement pattern was influenced by human disturbance and the need to move from one feeding site to another. Home range and movement rate were influenced by the degree of habitat fragmentation. Once habitat was cleared or converted, the availability of food plants and water sources were reduced, forcing the elephants to travel to adjacent forest areas. Therefore movement rate in fragmented forest was higher than in the non-fragmented forest. Finally, in fragmented habitat human and elephant conflict occurrences were likely to be higher, due to increased movement bringing elephants into contact more often with humans.

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.

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.

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.

Sabah, on the northeastern corner of Borneo, is concurrently Malaysia’s largest producer of oil palm (Elaeis guineensis) and home to the endangered Bornean elephants (Elephas maximus borneensis; elephants). Concomitantly, Sabah has been experiencing increasing and unsustainable human–elephant conflicts (HECs), which have not been thoroughly investigated from a human dimensions standpoint. To address this void, in March 2019, we conducted semistructured interviews with 37 villagers located in the Sabah districts of Lahad Datu, Tawau, and Telupid to investigate villager cognitions regarding elephants, behaviors toward elephants, the formal and informal village institutions employed to mediate HECs, and the future viability of human–elephant coexistence. Respondents highlighted emotions of fear, anger, and frustration over crop and property damage that villagers were unable to effectively mitigate employing traditional institutions and strategies. Although negative emotions were somewhat tempered by the cultural significance of elephants, respondents indicated that coexistence with elephants remains challenging and is likely only viable under certain conditions: domestication of elephants, if elephants no longer destroyed crops, and/or if elephants were provided separate forested habitat away from humans. Our results demonstrated that elephant conservation in Sabah is viewed as a “not in my backyard” claim, which can hint at the presence of environmental injustice. We further examined Sabah HECs using an environmental justice framework and concluded that HEC as an environmental justice problem requires traditional fixes to be merged with more extensive, sustainable solutions that improve stakeholder agency.

Plant recovery rates after herbivory are thought to be a key factor driving recursion by herbivores to sites and plants to optimise resource-use but have not been investigated as an explanation for recursion in large herbivores. We investigated the relationship between plant recovery and recursion by elephants (Elephas maximus borneensis) in the Lower Kinabatangan Wildlife Sanctuary, Sabah. We identified 182 recently eaten food plants, from 30 species, along 14 × 50 m transects and measured their recovery growth each month over nine months or until they were re-browsed by elephants. The monthly growth in leaf and branch or shoot length for each plant was used to calculate the time required (months) for each species to recover to its pre-eaten length. Elephant returned to all but two transects with 10 eaten plants, a further 26 plants died leaving 146 plants that could be re-eaten. Recursion occurred to 58% of all plants and 12 of the 30 species. Seventy-seven percent of the re-eaten plants were grasses. Recovery times to all plants varied from two to twenty months depending on the species. Recursion to all grasses coincided with plant recovery whereas recursion to most browsed plants occurred four to twelve months before they had recovered to their previous length. The small sample size of many browsed plants that received recursion and uneven plant species distribution across transects limits our ability to generalise for most browsed species but a prominent pattern in plant-scale recursion did emerge. Plant recovery time was a good predictor of time to recursion but varied as a function of growth form (grass, ginger, palm, liana and woody) and differences between sites. Time to plant recursion coincided with plant recovery time for the elephant's preferred food, grasses, and perhaps also gingers, but not the other browsed species. Elephants are bulk feeders so it is likely that they time their returns to bulk feed on these grass species when quantities have recovered sufficiently to meet their intake requirements. The implications for habitat and elephant management are discussed.