Prithiviraj Fernando; T. N. C Vidya; John Payne; Michael Stuewe; Geoffrey Davison; Raymond J Alfred; Patrick Andau; Edwin Bosi; Annelisa Kilbourn; Don J Melnick

“ Thus, if elephants were introduced to Borneo, the source population could have been India, Sumatra, or peninsular Malaysia, and as a feral population, Borneo's elephants would have low conservation importance. ”

“ If shown to be a unique indigenous population, this would extend the natural species range of the Asian elephant by 1300 km, and therefore Borneo elephants would have much greater conservation importance than if they were a feral population. We compared DNA of Borneo elephants to that of elephants from across the range of the Asian elephant, using a fragment of mitochondrial DNA, including part of the hypervariable d-loop, and five autosomal microsatellite loci. ”

“ While Borneo's elephants appear to be genetically depauperate, through a long history of isolation and inbreeding, they may have purged deleterious recessive alleles from their genome and decreased their genetic load, thus becoming less susceptible to inbreeding depression. ”

“ Borneo was significantly more likely to be the source than any other population for all five genotypes, since each of the assignment likelihoods to Borneo fell outside the upper end of the corresponding distribution of assignment likelihoods to the other populations. ”

“ If Borneo's elephants are of indigenous origin, this would push the natural range of Asian elephants 1300 km to the east, and as a unique population at an extreme of the species' range, Borneo elephants' in situ conservation would be a priority and ex situ cross-breeding with other populations would be contraindicated. ”

“ We find that Borneo's elephants are genetically distinct, with molecular divergence indicative of a Pleistocene colonisation of Borneo and subsequent isolation. We reject the hypothesis that Borneo's elephants were introduced. The genetic divergence of Borneo elephants warrants their recognition as a separate evolutionary significant unit. ”

“ Thus, genotypes in an introduced population would retain a high likelihood of assignment to the source population, enabling its identification from among a number of candidate populations. Therefore, the assignment tests strongly suggest that the Borneo elephants were not derived from another population in the recent past. ”

“ Thus, the Borneo haplotype fits a pattern of distribution and relatedness to other ‘Sundaland' haplotypes that is congruent with an ancient colonisation of the Sunda region by β clade and subsequent allopatric divergence of populations on its larger landmasses.
Microsatellite data also support the indigenous hypothesis. If the Borneo population originated from animals introduced in the 16th–18th centuries, it would have reached its mid-20th-century size of approximately 2,000 individuals ( [17] ) in fewer than 30 generations, assuming an Asian elephant generation time of 15–20 years ( [18] ) . ”

“ Sequences were aligned and edited using SEQUENCHER version 3.1.1 (GeneCodes Corporation, Ann Arbor, Michigan, United States) . Sequences were deposited in GenBank (accession numbers AY245538 and AY245802 to AY245827) . Phylogenetic analyses were conducted using PAUP* version 4.0 ( [27] ) . ”

“ Figures and Tables Table 1 "Comparison of Measures of Genetic Variation at Individual Loci in Borneo with Those of the Other Populations"File:Pbio.0000006.t001 Table 2 "Measures of Genetic Variation Using Five Loci, in Asian Elephant Populations from across the Range"File:Pbio.0000006.t002 Table 3 "FST Values in Pairwise Comparison of Borneo with Other Populations"File:Pbio.0000006.t003Conflicts of Interest. The authors have declared that no conflicts of interest exist.Author Contributions. This project is part of an ongoing multicentre collaboration on elephant conservation. ”