Range-wide mtDNA phylogeography yields insights into the origins of Asian elephants

Vidya, T. N. C.; Sukumar, Raman; Melnick, Don J.

doi:10.1098/rspb.2008.1494

Cited by 60 publications

(68 citation statements)

References 42 publications

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“…We extracted DNA from nine elephantid teeth from Kahramanmaraş and sequenced 579 bp mitochondrial DNA, including 574 bp of the fragment analysed in Vidya, Sukumar and Melnick (2009), comprising the C-terminal of cyt-b, t-RNA Thr , t-RNA Pro and the hypervariable left (Olivier 1978, Choudhury et al 2008, the location of Kahramanmaraş, and the relative proportion of mtDNA haplotypes based on data published in Vidya, Sukumar and Melnick (2009). (B) A Bayesian phylogenetic tree produced in MrBayes of haplotypes analysed in Vidya, Sukumar and Melnick (2009), but restricted to the 570 base pairs sequenced for this study.…”

Section: Methodsmentioning

confidence: 99%

“…Here we demonstrate the phylogenetic position of the elephant teeth (determinate and indeterminate) in relation to the known mitochondrial phylogeography of modern Asian elephant populations (Vidya, Sukumar and Melnick 2009). Further, by estimating mtDNA coalescence times we discuss the position of the Turkish remains in the broader historical context of E. maximus.…”

Section: Introductionmentioning

confidence: 99%

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Genetic Insight into an Extinct Population of Asian Elephants (Elephas maximus) in the Near East

Albayrak¹,

Lister²

2018

Open Quaternary

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The current range of the Asian elephant is fragmented and restricted to southern Asia. Its historical range was far wider and extended from Anatolia and the Levant to Central China. The fossil record from these peripheral populations is scant and we know little of their relationship to modern Asian elephants. To gain a first insight to the genetic affinity of an E. maximus population that once inhabited Turkey we sequenced ca. 570 bp mtDNA from four individuals dating to ~3500 cal. BP. We show that these elephants carried a rare haplotype previously only observed in one modern elephant from Thailand. These results clarify the taxonomic identity of specimens with indeterminate morphologies and show that this ancient population groups within extant genetic variation. By placing the age of the common ancestor of this haplotype in the interval 3.7-58.7 kya (mean = 23.5 kya) we show that range-wide connectivity occurred at some time or times since the start of MIS 3, ~57 kya, probably reflecting range and population expansion during a favourable climatic episode. The genetic data do not distinguish natural versus anthropogenic origin of the Near Eastern Bronze Age population, but together with archaeological and paleoclimatic data they allow the possibility of a natural westward expansion around that time.

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Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Genetic Insight into an Extinct Population of Asian Elephants (Elephas maximus) in the Near East

Albayrak¹,

Lister²

2018

Open Quaternary

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“…

In Vidya et al [1], the last paragraph on page 896 (continuing to page 897; Results section) provided the rate of sequence divergence incorrectly as the mutation rate, which was used for the calculation of mean times of expansion and effective population sizes. We provide the correct values in the two paragraphs below.

…”

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confidence: 99%

Range-wide mtDNA phylogeography yields insights into the origins of Asian elephants

Vidya¹,

Sukumar²,

Melnick³

2010

Proc. R. Soc. B.

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In Vidya et al. [1], the last paragraph on page 896 (continuing to page 897; Results section) provided the rate of sequence divergence incorrectly as the mutation rate, which was used for the calculation of mean times of expansion and effective population sizes. We provide the correct values in the two paragraphs below. However, these changes do not make any difference to the inferences drawn or to the conclusions of the paper. The last paragraph on page 896 should read as follows:Analysis of mismatch distributions showed that observed data were explained by the fitted models, with the combined data of the two clades indicating demographic stability, and the a and b clades indicating population expansion (see electronic supplementary material, S8). The HKY-corrected distance between clades was 0.025 and the rate of sequence divergence in the mtDNA segment was estimated to be 1.6 and 1.2 per cent per Myr based on the mean divergence times, between the Asian and African elephants, of 6.6 and 8.8 Myr ago, respectively. This was considerably lower than the rate (3.5%) calculated by Fleischer et al.[2], partly owing to the different time estimate used and partly owing to the smaller HKY-corrected distance between clades in our larger sample. Based on the values of t (¼2mt generations; m is the mutation rate over the entire sequence analysed and t is the time to expansion of a population with initial effective number of females ¼ N 0 to a final size N 1 ) from the mismatch distributions, a generation time of 27 years estimated (as the average age of reproducing females) from field data in southern India (C. Arivazhagan, T. N. C. Vidya, R. Sukumar 2001Sukumar -2003, and rates of sequence divergence of 1.6 per cent (divergence time between clades of 1.6 Myr) and 1.2 per cent (divergence time between clades of 2.1 Myr) per Myr, respectively, the mean times of expansion of the a clade were approximately 255 700 and 340 900 yr ago and mean times of expansion of the b clade were 766 100 and 1 021 400 yr ago. N 0 was very low in both clades but confidence limits were large and upper limits of N 0 were 4380 in the a clade and 9615 in the b clade based on a 1.6 Myr divergence between clades and 5841 in the a clade and 12 820 in the b clade based on a 2.1 Myr divergence. N 0 and N 1 (¼u 1 /2 m; estimation of mutation parameter u 1 thought to be biased upwards [3]) were both approximately 47 000 (based on a 1.6 Myr divergence) or 63 000 (based on a 2.1 Myr divergence) based on the combined data of both clades, although the two clades seemed too different demographically to be combined.The last but one paragraph on page 900 (Discussion) should read as follows:An alternative hypothesis to allopatric fragmentation of Elephas hysudricus populations giving rise to the two mtDNA clades is that of lineage retention within a single population. We find that the historical effective population size during the last population bottleneck of less than 50 females in each clade with upper limits of a few to several thousand females in each c...

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“…A total of eight mitochondrial haplotypes were detected across the populations in India, though the haplotype diversity in each region was very low with only 1-3 haplotypes found (Vidya et al, 2005b). Surprisingly, only one mitochondrial haplotype was fixed in Nilgiris (Vidya, Fernando, Melnick, & Sukumar, 2005a, Vidya et al, 2005b, Vidya et al, 2009 which is the world's largest population of at least 9,000 free-ranging elephants. Fixed haplotype could possibly be due to elephant social structure in which maternally related groups formed clans over decades or centuries, or due to past bottlenecks (Vidya et al, 2005b).…”

Section: Population Fragmentation In Human-dominated Areasmentioning

confidence: 99%

“…It is a suitable DNA marker to refer genetics of maternal lineage and to study a population in evolutionary aspects such as evolutionary phylogeny and phylogeography (Fleischer, Perry, Muralidharan, Stevens, & Wemmer, 2001;Fernando et al, 2003;Vidya, Sukumar, & Melnick, 2009). DNA primers for amplification of the mitochondrial DNA fragment of the Asian elephant have been designed and used to study mitochondrial haplotype distribution of wild populations across their range (Fleischer et al, 2001;Vidya et al, 2009), and in particular populations in Sri Lanka (Fernando, Pfrender, Encalada, & Lande, 2000), India (Vidya, Fernando, Melnick, & Sukumar, 2005b), Vietnam (Vidya et al, 2007), Laos (Ahlering et al, 2011), peninsular Malaysia (Elliza, Shukor, Othman, & Md-Zain, 2015), Sumatra (Moßbrucker et al, 2015), and Borneo (Goossens et al, 2016). The primer pair designed by has been used in most of the studies, thus the variation of mitochondrial DNA of different populations could be directly compared.…”

Section: Mitochondrial Dnamentioning

confidence: 99%

Genetic Tools for the Conservation of Wild Asian Elephants

Kongrit

2017

IJB

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The distribution of the Asian elephant (Elephas maximus) has been limited to the remaining discontinuous forests, mainly in the South and Southeast Asia. A global number of wild Asian elephants have been declining due to habitat loss, forest fragmentation, and anthropogenic disturbance. Acquiring information of wild populations is important for effective conservation and management plan. This article reviews the applications of noninvasive genetic method as a tool for studying wild Asian elephants. Noninvasive genetic method has been introduced to the field of wildlife conservation for more than two decades. The method provides reliable information of a population and facilitates investigation of genetic effects on small and fragmented populations. Various DNA markers for the Asian elephant, those include mitochondrial DNA, microsatellite DNA, and sex determination markers, have been developed and used to study wild elephant populations across the distribution range. Most of the studies revealed the issues of low genetic diversity in the small populations and interruption of gene flow among the fragmented populations. Tracking of ivory poaching has not yet been done in the Asian elephant. It could be carried out if a reference genetic database of the natural populations is available. Noninvasive genetic method has been proved to be a promising tool for conservation of the wild Asian elephants. Transboundary collaboration would give hope for a successful long-term conservation of this charismatic species in their natural habitats.

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Range-wide mtDNA phylogeography yields insights into the origins of Asian elephants

Cited by 60 publications

References 42 publications

Genetic Insight into an Extinct Population of Asian Elephants (Elephas maximus) in the Near East

Genetic Insight into an Extinct Population of Asian Elephants (Elephas maximus) in the Near East

Range-wide mtDNA phylogeography yields insights into the origins of Asian elephants

Genetic Tools for the Conservation of Wild Asian Elephants

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