Mitochondrial DNA analyses revealed low genetic diversity in the endangered Indian wild ass Equus hemionus khur

References

• Aleksandr M, George C, Yan R, Thomas LM, Richa A, Alejandro AS. 2008. Database indexing for production MegaBLAST search. Bioinformatics. 24:1757–1764.
   PubMed Web of Science ®Google Scholar
• Allendorf FW, Hohenlohe PA, Luikart G. 2010. Genomics and the future of conservation genetics. Nat Rev Genet. 11:697–709.
   PubMed Web of Science ®Google Scholar
• Beja-Pereira A, Oliveira R, Alves PC, Schwartz MK, Luikart G. 2009. Advancing ecological understandings through technological transformations in noninvasive genetics. Mol Ecol Resour. 9:1279–1301.
   PubMed Web of Science ®Google Scholar
• Darriba D, Doallo R, Posada D. 2012. JModelTest 2: more models, new heuristics and parallel computing. Nat Methods. 9:772. doi:10.1038/nmeth.2109.
   PubMed Web of Science ®Google Scholar
• Der Sarkissian C, Ermini LC, Schubert M, Yang MA, Librado P, Fumagalli M, Jónsson H, Bar-Gal GK, Albrechtsen A, Vieira FG, et al. 2015. Evolutionary genomics and conservation of the endangered Przewalski’s horse. Curr Biol. 25:2577–2583.
   PubMed Web of Science ®Google Scholar
• Drummond AJ, Rambaut A, Shapiro B, Pybus OG. 2005. Bayesian coalescent inference of past population dynamics from molecular sequences. Mol Biol Evol. 22:1185–1192.
   PubMed Web of Science ®Google Scholar
• Drummond AJ, Suchard MA, Xie D, Rambaut A. 2012. Bayesian phylogenetics with BEAUti and the BEAST 1.7. Mol Biol Evol. 29:1969–1973.
   PubMed Web of Science ®Google Scholar
• Gee EP. 1963. The Indian wild ass: a survey. J Bomb Nat Hist Soc. 60:517–529.
   Google Scholar
• Goyal SP, Sinha B, Shah N, Panwar HS. 1999. Sardar Sarovar Project – a conservation threat to the Indian wild ass (Equus hemionus khur). Biol Cons. 88:277–284.
   Web of Science ®Google Scholar
• Groves CP. 1974. Horses, asses and Zebras in the wild. Hollywood, Florida, USA: Ralph Curtis Books. p. 192.
   Google Scholar
• Groves CP, Mazák V. 1967. On some taxonomic problems of Asiatic wild asses; with the description of a new subspecies (Perissodactyla; Equidae). Z Saugetierkunde. 32:321–355.
   Google Scholar
• Grubb P, editor. 2005. Order Perissodactyla. Baltimore (MD): The Johns Hopkins University Press.
   Google Scholar
• Guindon S, Gascuel O. 2003. A simple, fast and accurate method to estimate large phylogenies by maximum-likelihood. Syst Biol. 52:696–704.
   PubMed Web of Science ®Google Scholar
• Kenoyer JM. 1998. Ancient cities of the Indus Valley Civilization. Oxford: Oxford University Press. p. 38.
   Google Scholar
• Kimura B, Marshall FB, Chen S, Rosenbom S, Moehlman PD, Tuross N, Sabin RC, Peters J, Barich B, Yohannes H, et al. 2011. Ancient DNA from Nubian and Somali wild ass provides insights into donkey ancestry and domestication. Proc Biol Sci. 278:50–57.
   PubMed Web of Science ®Google Scholar
• MacFadden BJ. 2005. Evolution: fossil horses-evidence for evolution. Science (New York, NY). 307:1728–1730.
   Google Scholar
• McCue ME, Bannasch DL, Petersen JL, Gurr J, Bailey E, Binns MM, Distl O, Guerin G, Hasegawa T, Hill EW, et al. 2008. A high density SNP array for the domestic horse and extant Perissodactyla: utility for association mapping, genetic diversity, and phylogeny studies. PLoS Genet. 8:e1002451.
   Web of Science ®Google Scholar
• Moehlman PD, editor. 2002. Equids: zebras, asses and horses. Status survey and conservation. Gland, Switzerland: IUCN.
   Google Scholar
• Oakenfull EA, Lim H, Ryder O. 2000. A survey of equid mitochondrial DNA: implications for the evolution, genetic diversity and conservation of Equus. Conserv Genet. 1:341–355.
   Google Scholar
• Possehl Gregory L. 1996. Mehrgarh. In: Fagan B, editor. Oxford companion to archaeology. Oxford: Oxford University Press.
   Google Scholar
• Rambaut A, Drummond AJ. 2007. Tracer Version 1.4. Available from: http://tree.bio.ed.ac.uk/software/tracer/.
   Google Scholar
• Ronquist F, Teslenko M, vander Mark P, Ayres DL, Darling A, Höhna S, Larget B, Liu L, Suchard MA, Huelsenbeck JP. 2012. MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Syst Biol. 61:539–542.
   PubMed Web of Science ®Google Scholar
• Renan S, Greenbaum G, Shahar N, Templeton A, Bouskila A, Bar-David S. 2015. Stochastic modeling of shifts in allele frequencies reveals a strongly polygynous mating system in the re-introduced Asiatic wild ass. Mol Ecol. 24:1433–1446.
   PubMed Web of Science ®Google Scholar
• Rosenbom S, Costa V, Chen S, Khalatbari L, Yusefi G, Abdukadir A, Yangzom C, Kebede F, Teclai R, Yohannes H, et al. 2015. Reassessing the evolutionary history of ass-like equids: insight from pattern of genetic variation in contemporary extant populations. Mol Phylogenet E. 85:88–96.
   PubMed Web of Science ®Google Scholar
• Ryder OA, Chemnick LG. 1990. Chromosomal and molecular evolution in Asiatic wild asses. Genetica. 83:67–72.
   PubMed Web of Science ®Google Scholar
• Schaller GB. 1998. Wild life of the Tibetan Steppe. Chicago (IL): University of Chicago Press.
   Google Scholar
• Shah N. 2002. Status and action plan for the Kiang (Equuskiang). In: Moehlman PD, editor. Status survey and conservation action plan–equids: zebras, asses and horses, gland. Switzerland: IUCN.
   Google Scholar
• Shah NV. 1999. Mammals. In: Singh HS, Patel BH, Parvez R, Soni VC, Shah N, Tatu K, Patel D, editors. Ecological study of wild ass sanctuary little Rann of Kutch. Gandhinagar, Gujurat, India: GEER Foundation.
   Google Scholar
• Shah NV, Qureshi Q. 2007. Social organization and determinants of spatial distribution of khur (Equus hemionus khur). Explor Biol Resourc Mongolia. 10:189–2000.
   Google Scholar
• Singh HB. 2000. Status of Indian wild ass (Equus hemionus khur) in the little Rann of Kutch. Zoos Print. 15:253–256.
   Google Scholar
• Srivastav A, Nigam P. 2010. National studbook of Indian Wild Ass (Equus hemionus khur). New Delhi: Wild life Institute of India, Dehradun and Central Zoo Authority.
   Google Scholar
• Steiner CC, Mitelberg A, Tursi R, Ryder OA. 2012. Molecular phylogeny of extant equids and effects of ancestral polymorphism in resolving species-level phylogenies. Mol Phylogenet Evol. 65:573–581.
   PubMed Web of Science ®Google Scholar
• Steiner CC, Ryder OA. 2011. Molecular phylogeny and evolution of the Perissodactyla. Zool J Linn Soc. 163:1289–1303.
   Web of Science ®Google Scholar
• Vilstrup JT, Seguin-Orlando A, Stiller M, Ginolhac A, Raghavan M, Nielsen SC, Weinstock J, Froese D, Vasiliev SK, Ovodov ND, et al. 2013. Mitochondrial phylogenomics of modern and ancient equids. PLoS One. 8:e55950.
   PubMed Web of Science ®Google Scholar
• Zhang Z, Schwartz S, Wagner L, Miller W. 2000. A greedy algorithm for aligning DNA sequences. J Comput Biol. 7:203–214.
   PubMed Web of Science ®Google Scholar