Bornean Elephant Research Articles

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 km2, 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 km2). During high flood levels, available habitat is reduced to only 61 km2. 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.

Sabah Wildlife Department and 10 years of research: Towards a better conservation of Sabah's wildlife

In this paper, we present an update on the current wildlife research undertaken by the Sabah Wildlife Department (SWD) and its partners. For the last ten years, SWD has been extremely active in developing research programmes on all Sabah's flagship species including the Bornean orangutan, the proboscis monkey, the Sumatran rhinoceros, the Bornean elephant, the Bornean banteng, the Malayan sun bear, and the Sunda clouded leopard. This has been facilitated by: (1) the setting up of their own field research centre located in the Lower Kinabatangan Wildlife Sanctuary, the Danau Girang Field Centre, in collaboration with Cardiff University; (2) the development of strong collaborations with different overseas institutions such as Leibniz Institute for Zoo and Wildlife Research, University of Indiana, Kyoto University, Oxford WildCRU, EcoHealth Alliance, Houston Zoo, and many others; and (3) the collaboration with several NGOs such as HUTAN-Kinabatangan Orangutan Conservation Programme, Borneo Conservation Trust (BCT), WWF-Malaysia, Borneo Rhino Alliance (BORA), UK Appeal, and many others. Recently, some of the research carried out by SWD and partners has received funding from the palm oil industry through the Malaysian Palm Oil Council, Sime Darby Foundation, and others. The main aim of the research carried out by SWD and partners is to contribute to the conservation and management of the species and ecosystems, which are under their responsibility.

The Evolution of Human Cooperation

Cooperation was prominent among the suite of behaviors that marked the emergence of behaviorally modern humans in Africa. Both Homo neanderthalensis and the recently discovered Homo floresiensis survived well into the Late Pleistocene and hunted large game, the latter targeting the pygmy elephants that had evolved on the island environment of Flores, off the coast of Indonesia. Price-fixing by cartels and other baleful economic effects of collusion motivated Adam Smith to advocate a competitive economic system under which such forms of antisocial collusion would unravel. Culture is an evolutionary force in its own right, not simply an effect of the interaction of genes and natural environments. Human reliance on the meat of large hunted animals and other high-quality, large package-size, and hence high-variance foods meant that our livelihoods were risky, skill-intensive, and characterized by increasing returns to scale. The distinctive human capacity for institution building and cultural transmission of learned behavior allowed social preferences to proliferate.

Investigation of individual and group variability in estrous cycle characteristics in female Asian elephants (Elephas maximus) at the Oregon Zoo

Evaluating ovarian cycle activity through longitudinal progestagen monitoring is important for optimizing breeding management of captive elephants and understanding impact of life events (births, deaths, and transfers) on reproductive function. This study summarized serum progestagen profiles for eight Asian mainland elephants (Elephas maximus indicus) and one Bornean elephant (E. maximus borneensis) at the Oregon Zoo over a 20-yr interval, and represents the longest longitudinal dataset evaluated to date. Estrous cycle characteristics were more varied than previously reported for this species, with an overall duration of 12 to 19 wk, luteal phase duration of 4 to 15 wk, and follicular phase duration of 2 to 12 wk. In general, there was more cycle variability across than within individual elephants. Compared with other elephants in the group, the Borneo female exhibited consistently longer cycle lengths, higher progestagen concentrations, and greater cycle variability; however, it is not known if this represents a subspecies or an individual difference. Cycle durations did not appear to change over time or with age, and the first pubertal cycle was similar to subsequent cycles. Variability in duration of the follicular phase was greater than that of the luteal phase. In addition, there was a significant negative relationship between luteal and follicular phase durations, suggesting a possible regulatory role of the follicular phase in maintaining a relatively consistent cycle duration within individuals. Overall, we found these elephants to be highly resilient in that major life events (births, deaths, and changes in herd structure) had minimal effect on cycle dynamics over time. In conclusion, the higher range in cycle phase characteristics is likely because of the larger number of elephants studied and longer duration of longitudinal monitoring, and may be more representative of the captive population as a whole. Furthermore, identification of significant interanimal variability suggests that understanding the complexities of herd reproductive characteristics could facilitate development of more effective institution-specific breeding management strategies.

Home Range and Ranging Behaviour of Bornean Elephant (Elephas maximus borneensis) Females

BackgroundHome 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.Methodology/Principal FindingsThe 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 km2 in a non-fragmented forest and 600 km2 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.Conclusions/SignificanceHome 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.

Density and Population Estimation of the Bornean Elephants (Elephas maximus borneensis) in Sabah

Problem statement: In Asia, four elephant subspecies have been identified, Elephas maximus maximus from Sri Lanka, Elephas maximus summatranus from Sumatra, Elephas maximus borneensis (based on recent DNA analysis) from Borneo and Elephas maximus indicus, from mainland Asia. The Bornean elephant has a limited distribution and is found only in the northeastern part of the island, (Malaysian Sabah and Indonesian Kalimantan). Previous estimations for the population in Sabah have ranged between 500-2000 elephants. These estimations have been carried out through a non-systematic approach, either via interview or from direct sightings or extrapolating population count data from limited sites. In order to prepare the conservation plan for this species in Sabah, there is a need to establish reliable information on their density and population size. The main objective of this study was to determine the elephant density and population size in five main elephant managed ranges in Sabah. Approach: In this study, relative distribution and spatial density of the Bornean elephant was developed and established, using a systematic line transect survey and a long term monitoring of dung decay rates. We conducted the elephant population census in Sabah between July 2007 and December 2008. Using a line-transect dung-count methodology, we surveyed 216 line transects; with a total distance of 186.12 km, in five main elephant managed ranges. Namely (i) Tabin Wildlife Reserve, (ii) Lower Kinabatangan, (iii) Central Forest, (iv) North Kinabatangan and (v) Ulu Kalumpang. Results: We presented the elephant density estimate using long term monitoring of dung decay rates. In each range, the elephant’s density varied depending on the size of the suitable habitat. The size of the suitable habitat was derived from WWF’s study report (WWF-Malaysia, 2008). Densities were analyzed following line-transect analysis guidelines and were computed using the software Distance v6.0. Conclusion: Our survey indicated that approximately 2,040 (95% CI: 1,184-3,652) elephants remain in the five main ranges in Sabah, with the largest population being in the unprotected central forests. Elephant density was highest in ranges where habitat has been removed and elephants are concentrated in remaining forest areas. These results provide new baseline data for the elephant population in Sabah.

The Importance of Maintaining a Proper Database on Forest Restoration Program for Orangutans in Borneo

Problem statement: The lowland forest of Sabah is the most important h abitat for orangutans and pygmy elephants. This is shown in the WWF-Malaysia's elephant tracking programme in which satellite-based Global Position System (GP S) collar devices are used to monitor their movement and the range of their habitats, as well a s an aerial survey on orangutan's nest is performed to determine the spatial distribution pattern. We o bserved the activities of both species and we found that these species stay inside lowland forests with on flat ground or with gentle slopes, below 500 m elevation, which is mostly covered by natural fores t. The density of orangutan's population was estimated to be higher in a certain location in nat ural lowland forests where the soils are more ferti le. A suitable long term habitat for both species is loca ted in the lowland dipterocarp forests. However, mo st of the pristine habitats in the lowland area have b een converted into other land use activities such a s a large scale plantation. This is due to the fact tha t most of the lowland forests are facing a continuo us degradation process that will decrease its commerci al value when it comes to generating revenue to the state government. As a result, the efforts to resto re the forest are very vital. Approach: This study described the technical and biological aspects in t he forest restoration planning, prioritizing, implementation and monitoring process, integrated with the data on habitat utilization by orangutan in lowland degraded dipterocarp forest. Key habitats f or orangutans were identified, forest condition wer e mapped and field works are carried out using a plot sampling technique to identify the diversity and density of the forest (current and potential), in o rder to support the forest restoration planning. A proper database on forest restoration and tree main tenance planning had been developed to enable the monitoring process. Results: This study outlined some of the findings that incl ude the main challenges that were faced in the forest restoration programme in North Ulu Segama (NUS), which could be used as lessons and guideline in the future. Conclusion: A long term monitoring programme is important in order to have a successful forest restoration progr amme as well as to have the opportunity to study th e impact of this restoration on the behavior of orang utan as a result of their adaptation to the new for est structure.

Carbon payments as a safeguard for threatened tropical mammals

AbstractOne reason for the rapid loss of species‐rich tropical forests is the high opportunity costs of forest protection. In Kalimantan (Indonesian Borneo), the expansion of high‐revenue oil palm (Elaeis guineensis) plantations currently threatens 3.3 million ha of forest. We estimate that payments for Reduced Emissions from Deforestation and forest Degradation (REDD) could offset the costs of stopping this deforestation at carbon prices of US$10–33 per tonne of CO2, or $2–16 per tonne if forest conservation targets only cost‐efficient areas. Forty globally threatened mammals are found within these planned plantations, including the Bornean orangutan (Pongo pygmaeus) and Borneo pygmy elephant (Elephas maximus borneensis). Cost‐efficient areas for emissions reductions also contain higher‐than‐average numbers of threatened mammals, indicating that there may be synergies between mitigating climate change and conserving biodiversity. While many policy and implementation issues need clarification, our economic assessment suggests that REDD could offer a financially realistic lifeline for Kalimantan's threatened mammals if it is included in future climate agreements.

Status of the so-called African pygmy elephant ( Loxodonta pumilio ( Noack 1906)): phylogeny of cytochrome b and mitochondrial control region sequences

Among the African elephants, it has been unanimously acknowledged that the forest elephants ( cyclotis form) are peculiar, so that they have been elevated to the specific rank. The development of molecular analyses of extant Loxodonta has only focused on two forms yet: the savannah form ( africana) and the forest form ( cyclotis), disregarding the so-called pygmy elephants ( pumilio or fransseni) the systematic status of which has been debated since their discovery. Therefore, we have sampled nine dwarfed-labelled specimens in collection and eight specimens of typical forest elephants that we compared to three savannah elephants and two Asian elephants. Because of the degraded nature of the nuclear DNA content in bone samples of old specimens, we assayed mitochondrial markers; 1961 bp of the mitochondrial genome were sequenced (over a continuous range spanning the cytochrome b gene, tRNA Thr, tRNA Pro, hypervariable region 1 and central conserved region of the control region). Pumilio and cyclotis are not sister-taxa: the phylogenetic analyses rather account for the inclusion of the so-called pygmy elephants within a monophyletic group of forest elephants sensu lato. The internal structure of this clade reveals to depend on isolation and remoteness between populations, characteristics that may have been extensively influenced by climatic variations during the Quaternary period. We conclude that the specific taxon Loxodonta pumilio (or Loxodonta fransseni) should be abandoned. To cite this article: R. Debruyne et al., C. R. Biologies 326 (2003).

Are there Pygmy Elephants?

Are there Pygmy Elephants?

Vertebrate extinction in Mediterranean islets: an example from Cyprus

B/OGEOGRAPHIA — vol. XVIII — 1995 (Pubblicato il 31 ottobre 1996) Le piccole Isole Circumsarde e il loro significato Biogeografico Vertebrate extinction in Mediterranean islets: an example from Cyprus E. HADJISTERKOTIS” and B. MASALAM‘ qqOfi’zqcer of tlae Game zzml Fauna Service, Mzfiirtry of Interior; Nzrorzkz, Cyprus. ”°qI7zrz‘z'tzIte of General P/Jyrziology mm’ Biological C/Jemzirtry, Faculty of Bz'0logz'czzl Sciences, U72z'verrz'z‘y of Sczsrarz; Szzsrarz; Italy Key words: Vertebrate, extintion, mediterranean islets, Cyprus. SUMMARY Cyprus is the third island in the Mediterranean \vith an area of 9.251 Kmz. Is a 15 million year old island of oceanic origin which has never been connected to the mainland. In this study we attempt to tally all the extinctions that took place on the island of Cyprus and compare the emerging pattern with that of other islands. All the endemic animals recorded from the Pleistocene Fauna, the Pygmy hippopotamus P/Ja/zoz.trz'0s /7zz'IIzIl‘m', the Pygmy elephant Elzzp/Mr cypria/ax, the Cyprus genet Gezzetta /7/er/rtoizler, and the Ancient Cypriot shrew Crociclzzm rzzzzueole/zr [mu/c_vpI'1‘a, are extinct. These animals represent 60% of the endemic mammalian species aver recorded in Cyprus and 20% of the endemic subspecies. From the Archaeological Fauna nine taxa of animals were reported, which (with the exception of the Cyprus mouflon Oz;/: gmelz'm' op/Jz'0Iz) are not present today. From the avifauna two species and seven subspecies (12% of the total number of breeding taxa) were noted as endemic. Two of the latter, the Dipper C/‘uclz/r rinclz/5 oly/up/qcur is extinct and the Raven Coruzzr camx cjvprizzr is in danger of extinction. This pattern of extinction of indigenous spe— cies was also observed on other islands and is a consequence of small isolated island populations. INTRODUCTION A characteristic of modern extinctions of birds and mammals is that they are concentrated on islands (Diamond, 1984). For birds, 171 species and sub- species have become extinct since 1600, and over 90 percent of these extinc- tions have occurred on islands. For mammals out of 115 documented historic extinctions, 36 percent of these have occurred on islands. This pattern is in part due to the nature of island populations. They are small and isolated; thus they cannot recover from local extirpation following environmental perturba- tions or long—term climatic changes by immigration from other areas (MacArthur and \Wilson, 1967; Leigh, 1981). A growing body of evidence for birds and mammals indicates that over the last few thousand years, the most important agent of direct change in the envi- ronments is human disturbance and alteration of habitats (Diamond, 1984). Most extinct species in recorded history are attributed to some aspects of human interference, such as: habitat destruction; human hunting; effects of introduced taxa particularly predators, and trophic cascades (i.e., secondary extinctions caused by previous extinctions; Diamond and Case, 1986). Usually the period immediately following the initial settlement of islands is correlated 691

Did Komodo dragons evolve to eat pygmy elephants?

Did Komodo dragons evolve to eat pygmy elephants?

The pygmy elephant: a myth and a mystery

The paper reviews aspects of the long held debate concerning the existence of the pgymy elephant and notes the author's own observations in the Bayanga Forest in southwestern Central African Republic during a survey in early 1986. The author suggests the persistence of the pygmy elephant myth may be the result of two factors: the tusk development of the forest elephant is more rapid than the savannah or bush elephant, and the belief that such a species exists. However, it appears that two races of elephants do exist in much of the forest areas, but that the two are the forest L. cyclotis and the bush L. africana. This sympatry suggests that there is broader zone of overlap between the ecological conditions favoured by each of the races than generally assumed.

Indo-Australian insular elephants.

Various Pleistocene dwarfed elephants known from the islands of Celebes, Flores and Timor in the eastern part of the Malay Archipelago are described and their relationships considered. It is evident that these pygmy forms arose independently on each of the islands as a result of isolation and genetic drift favouring small size as in the better-known cases of the Mediterranean and Santa Barbara Channel Islands dwarf species. The dispersal possibilities of elephants are discussed; the conclusion must be drawn that geographic spacing has been the prime factor in species formation. Idle or fruitless speculations about ecological or other non-morphological species criteria have been omitted; the taxonomy of proboscideans as far as needed in the present context is however elucidated. It is pointed out that wherever we find pygmy elephants we have also giant rodents; in these presumably small isolated populations giganticism in small rodents appears to have been as advantageous to the animals as is dwarfing in elephants. As neither the exact date of colonization nor that of the eventual extinction (brought about by man or otherwise) is known, we have no means of knowing how many generations were involved; it is, however, likely that evolutionary velocity has been higher under these conditions than is usual.