Genetics / DNA
Faust, L.J., S.D. Thompson, J.M. Earnhardt (2006). Is reversing the decline of Asian elephants in North American zoos possible? An individual-based modeling approach. Zoo Biology 25(3): 201-218. ISSN: 0733-3188.
NAL Call Number: QL77.5.Z6
Descriptors: Elephas maximus, zoo animals, population dynamics, population structure, simulation models, stochastic processes, mortality, fecundity, animal reproduction, animal husbandry, North America, captive elephants, population decline, demographic models, individual based stochastic models.
Fernando, P., T.N. Vidya, J. Payne, M. Stuewe, G. Davison, R.J. Alfred, P. Andau, E. Bosi, A. Kilbourn, and D.J. Melnick (2003). DNA analysis indicates that Asian elephants are native to Borneo and are therefore a high priority for conservation. PLoS Biology 1(1): E6.
NAL Call Number: QH301.P56
Abstract: The origin of Borneo's elephants is controversial. Two competing hypotheses argue that they are either indigenous, tracing back to the Pleistocene, or were introduced, descending from elephants imported in the 16th-18th centuries. Taxonomically, they have either been classified as a unique subspecies or placed under the Indian or Sumatran subspecies. 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. 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, interbreeding Borneo elephants with those from other populations would be contraindicated in ex situ conservation, and their genetic distinctiveness makes them one of the highest priority populations for Asian elephant conservation.
Descriptors: conservation of natural resources methods, alleles, Borneo, DNA chemistry, mitochondrial DNA chemistry, molecular evolution, gene frequency, population genetics, genotype, geography, haplotypes, microsatellite repeats, statistical models, molecular sequence data, phylogeny, polymerase chain reaction, DNA sequence analysis, species specificity, variation genetics.
Rautian, G.S. and I.A. Dubrovo (2003). Data on DNA give evidence for parallel development in mammoths and elephants. Deinsea 9: 381-394. ISSN: 0923-9308.
Descriptors: Elephas maximus, Loxodonta africana, Mammuthus primigenius, Elephantidae, Mammut americanus, Mammutidae, nucleic acids, molecular genetics, DNA, parallel evolution, genetic data, phylogeny.
Roca, A.L. and S.J. O'Brien (2005). Genomic inferences from Afrotheria and the evolution of elephants. Current Opinion in Genetics and Development 15(6): 652-659.
NAL Call Number: QH426.C88
Abstract: Recent genetic studies have established that African forest and savanna elephants are distinct species with dissociated cytonuclear genomic patterns, and have identified Asian elephants from Borneo and Sumatra as conservation priorities. Representative of Afrotheria, a superordinal clade encompassing six eutherian orders, the African savanna elephant was among the first mammals chosen for whole-genome sequencing to provide a comparative understanding of the human genome. Elephants have large and complex brains and display advanced levels of social structure, communication, learning and intelligence. The elephant genome sequence might prove useful for comparative genomic studies of these advanced traits, which have appeared independently in only three mammalian orders: primates, cetaceans and proboscideans.
Descriptors: evolution, genetics, DNA, African elephants, Asian elephants, genomic patterns.
Thitaram, C., N. Thongtip, C. Somgird, B. Colenbrander, D.C.J. van Boxtel, F. van Steenbeek, and J.A. Lenstra (2008). Evaluation and selection of microsatellite markers for an identification and parentage test of Asian elephants (Elephas maximus). Conservation Genetics 9(4): 921-925. ISSN: 1566-0621.
Abstract: Numbers of the Asian elephants (Elephas maximus) population are declining due to poaching, human-elephant conflicts, capture of wild calves for tourism and export and habitat destruction, which also may cause inbreeding in fragmented populations. In order to contribute to a reversal of this trend, we have developed an identification and parentage test by evaluation and selection of markers from 43 microsatellite loci that have been previously described for Asian or African elephants. Testing these markers on a panel of 169 Asian elephants comprising the 23 mother-offspring, 13 father-offspring and 13 parents-offspring pairs yielded 26 polymorphic markers. However, only 14 of these were found to be suitable for an analysis of molecular diversity, 12 of which will be implemented for an identification and parentage test to control the capture of wild calves in Thailand and neighboring countries. Reproduced with Permission from CAB Abstracts.
Descriptors: Asian elephant, Elephas maximus, genetic markers, genetic polymorphism, microsatellites, parentage.
Vidya, T.N., P. Fernando, D.J. Melnick, and R. Sukumar (2005). Population differentiation within and among Asian elephant (Elephas maximus) populations in southern India. Heredity 94(1): 71-80.
NAL Call Number: 443.8 H42
Abstract: Southern India, one of the last strongholds of the endangered Asian elephant (Elephas maximus), harbours about one-fifth of the global population. We present here the first population genetic study of free-ranging Asian elephants, examining within- and among-population differentiation by analysing mitochondrial DNA (mtDNA) and nuclear microsatellite DNA differentiation across the Nilgiris-Eastern Ghats, Anamalai, and Periyar elephant reserves of southern India. Low mtDNA diversity and 'normal' microsatellite diversity were observed. Surprisingly, the Nilgiri population, which is the world's single largest Asian elephant population, had only one mtDNA haplotype and lower microsatellite diversity than the two other smaller populations examined. There was almost no mtDNA or microsatellite differentiation among localities within the Nilgiris, an area of about 15,000 km2. This suggests extensive gene flow in the past, which is compatible with the home ranges of several hundred square kilometres of elephants in southern India. Conversely, the Nilgiri population is genetically distinct at both mitochondrial and microsatellite markers from the two more southerly populations, Anamalai and Periyar, which in turn are not genetically differentiated from each other. The more southerly populations are separated from the Nilgiris by only a 40-km-wide stretch across a gap in the Western Ghats mountain range. These results variably indicate the importance of population bottlenecks, social organization, and biogeographic barriers in shaping the distribution of genetic variation among Asian elephant populations in southern India.
Descriptors: mitochondrial DNA genetics, population genetics, microsatellite repeats, variation genetics, cell nucleus genetics, elephant classification, molecular evolution, geography, haplotypes, India, phylogeny, genetic polymorphism.
Vidya, T.N.C. and R. Sukumar (2005). Social organization of the Asian elephant (Elephas maximus) in southern India inferred from microsatellite DNA. Journal of Ethology 23(2): 205-210. ISSN: 0289-0771.
NAL Call Number: QL750.J68
Descriptors: Asian elephant, social organization, dung, extracted DNA, families, males, matriarchal groups, dispersal, microsatellite, India.
Vidya, T.N.C., R. Sukumar, and D.J. Melnick (2009). Range wide mtDNA phylogeography yields insights into the origins of Asian elephants. Proceedings of the Royal Society of London Series B, Biological Sciences 276(1658): 893-902. ISSN: 0962-8452.
Abstract: Recent phylogeographic studies of the endangered Asian elephant (Elephas maximus) reveal two highly divergent mitochondrial DNA (mtDNA) lineages, an elucidation of which is central to understanding the species's evolution. Previous explanations for the divergent clades include introgression of mtDNA haplotypes between ancestral species, allopatric divergence of the clades between Sri Lanka or the Sunda region and the mainland, historical trade of elephants, and retention of divergent lineages due to large population sizes. However, these studies lacked data from India and Myanmar, which host approximately 70 per cent of all extant Asian elephants. In this paper, we analyse mtDNA sequence data from 534 Asian elephants across the species's range to explain the current distribution of the two divergent clades. Based on phylogenetic reconstructions, estimates of times of origin of clades, probable ancestral areas of origin inferred from dispersal-vicariance analyses and the available fossil record, we believe both clades originated from Elephas hysudricus. This probably occurred allopatrically in different glacial refugia, the alpha clade in the Myanmar region and the beta clade possibly in southern India-Sri Lanka, 1.6-2.1 Myr ago. Results from nested clade and dispersal-vicariance analyses indicate a subsequent isolation and independent diversification of the beta clade in both Sri Lanka and the Sunda region, followed by northward expansion of the clade. We also find more recent population expansions in both clades based on mismatch distributions. We therefore suggest a contraction-expansion scenario during severe climatic oscillations of the Quaternary, with range expansions from different refugia during warmer interglacials leading to the varying geographical overlaps of the two mtDNA clades. We also demonstrate that trade in Asian elephants has not substantially altered the species's mtDNA population genetic structure. Reproduced with Permission from CAB Abstracts.
Descriptors: Asian elephant, Elephas maximus, endangered species, mitochondrial DNA, nucleotide sequences, population genetics.
Vidya, T.N.C., Surendra Varma, N.X. Dang, T.v. Thanh, and R. Sukumar (2007). Minimum population size, genetic diversity, and social structure of the Asian elephant in Cat Tien National Park and its adjoining areas, Vietnam, based on molecular genetic analyses. Conservation Genetics 8(6): 1471-1478. ISSN: 1566-0621.
Abstract: Vietnam's elephant population that has suffered severe declines during the past three decades is now believed to number 60-80 individuals in the wild. Cat Tien National Park is thought to be one of the key areas for the recovery of Vietnam's elephants. We carried out a molecular genetic study of elephants in Cat Tien National Park and its adjoining areas with the objectives of estimating minimum population size, assessing genetic diversity, and obtaining insights into social organization. We obtained a minimum population size of 11 elephants based on a combination of unique nuclear microsatellite genotypes and mitochondrial haplotypes. While mitochondrial diversity based on a 600-base pair segment was high in this small sample of individuals, the six microsatellite loci examined showed low diversity and the signature of a recent population bottleneck. Along with nuclear genetic depauperation of Cat Tien's elephants, we also report disruption of normal social organization, with different matrilines having coalesced into a single social group because of anthropogenic disturbance. The results emphasize the critical condition of this elephant population and the need for urgent conservation measures if this population is to be saved. Reproduced with Permission from CAB Abstracts.
Descriptors: Asian elephant, Elephas maximus, endangered species, genetic diversity, population genetics.
Vidya, T., P. Fernando, D. Melnick, and R. Sukumar (2005). Population genetic structure and conservation of Asian elephants (Elephas maximus) across India. Animal Conservation 8(4): 377-388. ISSN: 1367-9430.
NAL Call Number: QH75.A1
Descriptors: Asian elephant, Elephas maximus, conservation measures, population genetics, genetic structure, nuclear microsatellite, mtDNA marker study, phylogeny variation, social organization, India, mitochondrial DNA, allele frequencies, haplotypes.
Vidya, T. and R. Sukumar (2005). Amplification success and feasibility of using microsatellite loci amplified from dung to population genetic studies of the Asian elephant (Elephas maximus). Current Science (Bangalore) 88(3): 489-492. ISSN: 0011-3891.
NAL Call Number: 475 SCI23
Descriptors: Asian elephant, Elephas maximus, population genetics, nucleic acids, feces, molecular genetics, microsatellite DNA, India, fecal microsatellite DNA samples, dung samples, population genetics analysis, evaluation.