Banks, S. C. et al. How does ecological disturbance influence genetic diversity?. Trends Ecol. Evol. 28, 670–679 (2013).
Coltman, D. W., Pilkington, J. G., Smith, J. A. & Pemberton, J. M. Parasite-mediated selection against inbred soay sheep in a free living island population. Evolution 53, 1259–1267 (1999).
Hedrick, P. W. & Fredrickson, R. Genetic rescue guidelines with examples from Mexican wolves and Florida panthers. Cons. Genet. 11, 615–626 (2010).
Frankham, R. Genetics and extinction. Biol. Cons. 126, 131–140 (2005).
Markert, J. A. et al. Population genetic diversity and fitness in multiple environments. BMC. Evol Biol. 10, 205 (2010).
Willoughby, J. R. et al. The reduction of genetic diversity in threatened vertebrates and new recommendations regarding IUCN conservation rankings. Biol. Cons. 191, 495–503 (2015).
Gray, T. N. E. et al. Rucervus eldii. The IUCN red list of threatened species. e.T4265A22166803 (2015). https://dx.doi.org/10.2305/IUCN.UK.2015-2.RLTS.T4265A22166803.en. Downloaded on 19 January 2020.
Grubb, P. Artiodactyla. In Mammal Species of the World (eds Wilson, D. E. & Reeder, D. M.) 637–722 (Johns Hopkins University Press, Baltimore, 2005).
Salter, R. E. & Sayer, J. A. The brow-antlered deer in Myanmar—Its distribution and status. Oryx. 20, 241–245 (1986).
McShea, W. J., Leimgruber, P., Aung, M., Monfort, S. L. & Wemmer, C. Range collapse of a tropical cervid (Cervus eldi) and the extent of remaining habitat in central Myanmar. Anim. Conserv. 2, 173–183 (1999).
Zhang, Q., Zeng, Z., Ji, Y., Zhang, D. & Song, Y. Microsatellite variation in China’s Hainan Eld’s deer (Cervus eldi hainanus) and implications for their conservation. Cons. Genet. 9, 507–514 (2008).
Zhang, Q., Zeng, Z., Sun, L. & Song, Y. The origin and phylogenetics of Hainan Eld’s deer and implications for Eld’ s deer conservation. Acta. Ther. Sin. 29, 365–371 (2009).
Ranjitsinh, M. K. Keibul Lamjao Sanctuary and the Brow-antlered deer—1972 with notes on a visit in 1975. J. Bom. Nat. His. Soc. 72, 243–255 (1975).
Hussain, S. A. & Badola, R. Conservation Ecology of Sangai and Its Wetland Habitat. Study Report Vol. I (Wildlife Institute of India, Dehra Dun, 2013).
McShea, W. J., Aung, M., Songer, M. & Connette, G. M. The challenges of protecting an endangered species in the developing world: A case history of Eld’s Deer conservation in Myanmar. Case Stud. Environ. 2, 1–9 (2018).
Ginsburg, L., Ingavat, R. & Sen, S. A Middle Pleistocene (Loagian) cave fauna in Northern Thailand. Comptes Rendus de l’Académie des Sciences Paris. 294, 295–297 (1982).
Tougard, C. Y., Chaimanee, V., Sutheethron, S. & Triamwichanon, Jaeger, J. J. Extension of the geographic distribution of the giant panda (Ailuropoda) and reasons for its progressive disappearance in Southeast Asia during the Latest Middle Pleistocene. C. R. Acad. Sci. Paris. 323, 973–979 (1996).
Corbett, G. B. & Hill, J. E. The Mammals of the Indomalay Region: A Systematic Review. Natural History Museum Publications (Oxford University Press, Oxford, 1992).
Woodruff, D. S. & Turner, L. M. The Indochinese-Sundaic zoogeographic transition: A description and analysis of terrestrial mammal species distributions. J. Biogeo. 36, 803–821 (2009).
Hassanin, A. & Ropiquet, A. Molecular phylogeny of the tribe Bovini (Bovidae, Bovinae) and the taxonomic status of the kouprey, Bos sauveli Urbain, 1937. Mol. Phylo. Evol. 33, 896–907 (2004).
Meijaard, E. Solving mammalian riddles. A reconstruction of the Tertiary and Quaternary distribution of mammals and their palaeoenvironments in island South-East Asia. PhD Thesis, The Australian National University, Canberra (2004).
Ropiquet, A. & Hassanin, A. Molecular evidence for the polyphyly of the genus Hemitragus (Mammalia, Bovidae). Mol. Phylo. Evol. 36, 154–168 (2005).
Bird, M. I., Taylor, D. & Hunt, C. Palaeoenvironments of insular Southeast Asia during the Last Glacial Period: A Savanna corridor in Sundaland?. Quat. Sci. Rev. 24, 2228–2242 (2005).
Geist, V. Deer of the World: Their Evolution, Behaviour, and Ecology (Stackpole Books, Mechanicsburg, 1998).
Ellerman, J. R. & Morrison-Scott, T. C. S. Checklist of Palaearctic and Indian Mammals, 1758 to 1947 (British Museum Natural History, London, 1951).
Gilbert, C., Ropiquet, A. & Hassanin, A. Mitochondrial and nuclear phylogenies of Cervidae (Mammalia, Ruminantia): Systematics, morphology, and biogeography. Mol. Phylo. Evol. 40, 101–117 (2006).
Hassanin, A. et al. Pattern and timing of diversification of cetartiodactyla (mammalia, laurasiatheria), as revealed by a comprehensive analysis of mitochondrial genomes. C. R. Biol. 335, 32–50 (2012).
Pitra, C., Fickel, J., Meijaard, E. & Groves, C. P. Evolution and phylogeny of old world deer. Mol. Phyl. Evol. 33, 880–895 (2004).
Balakrishnan, C. N., Monfort, S. L., Gaur, A., Singh, L. & Sorenson, M. D. Phylogeography and conservation genetics of Eld’s deer (Cervus eldi). Mol. Ecol. 12, 1–10 (2003).
Thomas, O. The nomenclature and the geographical forms of the panolia deer (Rucervus eldi) and its relatives. J. Bom. Nat. His. Soci. 23, 363–367 (1918).
Angom, S., Kumar, A., Gupta, S. K. & Hussain, S. A. Analysis of mtDNA control region of an isolated population of Eld’s deer (Rucervus eldii) reveals its vulnerability to inbreeding. Mito. DNA. Part B. 2, 277–280 (2017).
Xia, X., Xie, Z., Salemi, M., Chen, L. & Wang, Y. An index of substitution saturation and its application. Mol. Phylo. Evol. 26, 1–7 (2002).
Lande, R. Risks of population extinction from demographic and environmental stochasticity and random catastrophes. Am. Nat. 142, 911–927 (1993).
Hughes, A. R., Inouye, B. D., Johnson, M. T. J., Underwood, N. & Vellend, M. Ecological consequences of genetic diversity. Ecol. Lett. 11, 609–623 (2008).
Haq, B. U., Hardenbol, J. & Vail, P. R. The chronology of fluctuating sea level since the Triassic. Sci. 235, 1156–1165 (1987).
Suraprasit, K., Jongautchariyakul, S., Yamee, C., Pothichaiya, C. & Bocherens, H. New fossil and isotope evidence for the Pleistocene zoogeographic transition and hypothesized savanna corridor in peninsular Thailand. Quat. Sci. Rev. 221, 105861 (2019).
Suraprasit, K. et al. The middle Pleistocene vertebrate fauna from Khok Sung (Nakhon Ratchasima, Thailand): Biochronological and paleobiogeographical implications. Zoo Keys. 613, 1–157 (2016).
Nautiyal, C. M. & Chauhan, M. S. Late Holocene vegetation and climate change in Loktak Lake region, Manipur, based on pollen and chemical evidence. Palaeob. 58, 21–28 (2009).
Tripathi, S., Singh, Y. R., Nautiyal, C. M. & Thakur, B. Vegetation history, monsoonal fluctuations and anthropogenic impact during the last 2330 years from Loktak Lake (Ramsar site), Manipur, Northeast India: A pollen-based study. Palynology 42, 406–419 (2017).
Leonard, J. A. et al. Phylogeography of vertebrates on the Sunda Shelf: A multi-species comparison. J. Biogeogr. 42, 871–879 (2015).
Naish, D. Eld’s deer: Endangered, persisting in fragmented populations, and morphologically weird… but it wasn’t always so. Scientific American Blog Network. https://blogs.scientificamerican.com/tetrapod-zoology/elds-deer-endangered-fragmented-weird/. Accessed on 20 April, 2020 (2015).
National Studbook of Sangai (Rucervus eldii eldii), Wildlife Institute of India, Dehradun and Central Zoo Authority (2018) New Delhi. TR. No. 2018/07. https://wii.gov.in/research_report2018.
Angom, S., Tuboi, C., Ghazi, M. G. U., Badola, R. & Hussain, S. A. Demographic and genetic structure of a severely fragmented population of the endangered hog deer (Axis porcinus) in the Indo Burma biodiversity hotspot. PLoS ONE 15, e0210382 (2020).
Hartl, D. L. & Clark, A. G. Organisation of genetic variation. In Principles of Population Genetics (eds Hartl, D. L. & Clark, A. G.) 74–110 (Sinauer Associates, Sunderland, 1997).
Sharma, C. & Chauhan, M. S. Vegetation and climate since Last Glacial Maxima in Darjeeling (Mirik Lake), Eastern Himalaya. in Proc. 29th Int. Geol. Congr. Part B, 279.e288 (1994).
Tripathi, S., Thakur, B., Nautiyal, C. M. & Bera, S. K. Floristic and climatic reconstruction in the Indo-Burma region for the last 13,000 cal. yr: A palynological interpretation from the endangered wetlands of Assam, northeast India. The Holocene. 30, 1–17 (2019).
Mehrotra, N., Shah, S. K. & Bhattacharyya, A. Review of palaeoclimate records from Northeast India based on pollen proxy data of Late Pleistocene-Holocene. Quat. Inter. 325, 41–54 (2014).
Singh, N. R. Fluvial regime of the Manipur river basin and Loktak Lake with study of backflow. M. Tech thesis. Indian Institute of Technology (2006).
Excoffier, L., Foll, M. & Petit, R. J. Genetic consequences of range expansions. Annu. Rev. Ecol. Evol. Syst. 40, 481–501 (2009).
Slatkin, M. & Excoffier, L. Serial founder effects during range expansion: A spatial analog of genetic drift. Genetics 191, 171–181 (2012).
Frankham, R., Bradshaw, C. J. A. & Brook, B. W. Genetics in conservation management: revised recommendations for the 50/500 rules, Red List criteria and population viability analyses. Biol. Cons. 170, 56–63 (2014).
Hassanin, A., Ropiquet, A., Couloux, A. & Cruaud, C. Evolution of the mitochondrial genome in mammals living at high altitude: New insights from a study of the tribe Caprini (Bovidae, Antilopinae). J. Mol. Evol. 68, 293–310 (2009).
Moore, S. S., Barendse, W., Berger, K. T., Armitage, S. M. & Hetzel, D. J. S. Bovine and ovine DNA microsatellites from the EMBL and GenBank databases. Anim. Genet. 23, 463–467 (1992).
Gaur, A. et al. Development and characterisation of 10 novel microsatellite markers from chital deer (Cervus axis) and their cross-amplification in other related species. Mol. Ecol. Not. 3, 607–609 (2003).
Bishop, M. D. et al. A genetic linkage map for cattle. Genet. 136, 619–639 (1994).
Marshall, T. C., Slate, J., Kruuk, L. E. & Pemberton, J. M. Statistical confidence for likelihood-based paternity inference in natural populations. Mol. Ecol. 7, 639–655 (1998).
DeWoody, J. A., Honeycutt, R. L. & Skow, L. C. Microsatellite markers in white-tailed deer. J. Hered. 86, 317–319 (1995).
Jones, K. C., Levine, K. F. & Banks, J. D. DNA-based genetic markers in black-tailed and mule deer for forensic applications. California Dept Fish Game. 86, 115–126 (2000).
Vaiman, D., Osta, R., Mercier, D., Grohs, C. & Leveziel, H. Characterization of five new bovine dinucleotide repeats. Anim. Genet. 23, 537–541 (1992).
Brezinsky, L., Kemp, S. J. & Teale, A. J. ILSTS005: A polymorphic bovine microsatellite. Anim. Genet. 24, 75–76 (1993).
Zhang, Q., Ji, Y. J., Zeng, Z. G., Song, Y. L. & Zhang, D. X. Polymorphic microsatellite DNA markers for the vulnerable Hainan Eld’s deer (Cervus eldi hainanus) in China. Act. Zoo. Sin. 51, 530–534 (2005).
Buchanan, F. C. & Crawford, A. M. Ovine dinucleotide repeat polymorphism at the MAF70 locus. Anim. Genet. 23, 185 (1992).
Poetsch, M., Seefeldt, S., Maschke, M. & Lignitz, E. Analysis of microsatellite polymorphism in red deer, roe deer, and fallow deer possible employment in forensic applications. Foren. Sci. Int. 6, 1–8 (2001).
Thompson, J. D., Higgins, D. G. & Gibson, T. J. CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucl. Aci. Res. 22, 4673–4680 (1994).
Kumar, S., Stecher, G., Li, M., Knyaz, C. & Tamura, K. MEGA X: Molecular evolutionary genetics analysis across computing platforms. Mol. Biol. Evol. 35, 1547–1549 (2018).
Librado, P. & Rozas, J. DnaSPv5: A software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25, 1451–1452 (2009).
Leigh, J. W. & Bryant, D. PopART: Full-feature software for haplotype network construction. Methods Ecol. Evol. 6, 1110–1116 (2015).
Cheng, L., Connor, T. R., Sirén, J., Aanensen, D. M. & Corander, J. Hierarchical and spatially explicit clustering of DNA sequences with BAPS software. Mol. Biol. Evol. 30, 1224–1228 (2013).
Corander, J., Marttinen, P., Siren, J. & Tang, J. Enhanced Bayesian modelling in BAPS software for learning genetic structures of populations. BMC. Bioinf. 9, 539 (2008).
Ronquist, F. et al. MrBayes 3.2: Efficient Bayesian phylogenetic inference and model choice across a large model space. Syst. Biol. 61, 539–542 (2012).
Akaike, H. A new look at the statistical model identification. IEEE Trans. Autom. Control. 19, 716-723 (1974).
Darriba, D., Taboada, G. L., Doallo, R. & Posada, D. jModelTest 2: More models, new heuristics and parallel computing. Nat. Meth. 9, 772 (2012).
Posada, D. jModelTest: Phylogenetic model averaging. Mol. Biol. Evol. 25, 1253–1256 (2008).
Grant, J. R. & Stothard, P. The CG View Server: A comparative genomics tool for circular genomes. Nucl. Aci. Res. 36, 181–184 (2008).
Xia, X. & Xie, Z. DAMBE: Software package for data analysis in molecular biology and evolution. J. Hered. 92, 371–373 (2001).
Drummond, A. J., Suchard, M. A., Xie, D. & Rambaut, A. Bayesian phylogenetics with BEAUti and the BEAST 1.7. Mol. Biol. Evol. 29, 1969–1973 (2012).
Lanfear, R., Calcott, B., Ho, S. Y. & Guindon, S. PartitionFinder: Combined selection of partitioning schemes and substitution models for phylogenetic analyses. Mol. Biol. Evol. 29, 1695–1701 (2012).
Bibi, F. A multi-calibrated mitochondrial phylogeny of extant Bovidae (artiodactyla, ruminantia) and the importance of the fossil record to systematics. BMC. Evol. Biol. 13, 166 (2013).
Dong, W., Pan, Y. & Liu, J. The earliest Muntiacus (Artiodactyla, Mammalia) from the Late Miocene of Yuanmou, southwestern, China. C. R. Palevol. 3, 379–386 (2004).
Hulce, D., Li, X., Snyder-Leiby, T. & Liu, C. S. J. GeneMarker® genotyping software: Tools to increase the statistical power of DNA fragment analysis. J. Biomol. Tech. 22, S35–S36 (2011).
Valiere, N. GIMLET: A computer program for analysing genetic individual identification data. Mol. Ecol. Not. 2, 377–379 (2002).
Peakall, R. & Smouse, P. E. GenAlEx 6.5: Genetic analysis in Excel. Population genetic software for teaching and research-an update. Bioinformatics 28, 2537–2539 (2012).
Kalinowski, S. T., Taper, M. L. & Marshall, T. C. Revising how the computer program CERVUS accommodates genotyping error increases success in paternity assignment. Mol. Ecol. 16, 099–1106 (2007).
Pritchard, J. K., Stephens, M. & Donnelly, P. Inference of population structure using multilocus genotype data. Genet. 155, 945–959 (2000).
Evanno, G., Regnaut, S. & Goudet, J. Detecting the number of clusters of individuals using the software STRUCTURE: A simulation study. Mol. Ecol. 14, 2611–2620 (2005).
Earl, D. A. & von Holdt, B. M. STRUCTURE HARVESTER: A website and program for visualising STRUCTURE output and implementing the Evanno method. Cons. Genet. Res. 4, 359–361 (2012).
Rosenberg, N. A. DISTRUCT: A program for the graphical display of population structure. Mol. Ecol. Not. 4, 137–138 (2004).
Archer, F. I., Adams, P. E. & Schneiders, B. B. strataG: An r package for manipulating, summarising and analysing population genetic data. Mol. Ecol. Res. 17, 5–11 (2017).
Piry, S., Luikart, G. & Cornuet, J. M. BOTTLENECK: A program for detecting recent effective population size reductions from allele data frequencies. J. Hered. 90, 502–503 (1999).
Cornuet, J. M. & Luikart, G. Description and power analysis of two tests for detecting recent population bottlenecks from allele frequency data. Genet. 144, 2001–2014 (1996).
Luikart, G., Allendorf, F. W., Cornuet, J. M. & Sherwin, W. B. Distortion of allele frequency distributions provides a test for recent population bottlenecks. J. Hered. 89, 238–247 (1998).
Peel, D., Waples, R. S., Macbeth, G. M., Do, C. & Ovenden, J. R. Accounting for missing data in the estimation of contemporary genetic effective population size (Ne). Mol. Ecol. Res. 13, 243–253 (2013).
Waples, R. S. A bias correction for estimates of effective population size based on linkage disequilibrium at unlinked gene loci. Cons. Genet. 7, 167–184 (2006).
Waples, R. S. & Do, C. Linkage disequilibrium estimates of contemporary Ne using highly variable genetic markers: A largely untapped resource for applied conservation and evolution. Evol. Appl. 3, 244–262 (2010).
Do, C. et al. NeEstimator v2: Re-implementation of software for the estimation of contemporary effective population size from genetic data. Mol. Ecol. Res. 14, 209–214 (2014).
Nikolic, N. & Chevalet, C. Detecting past changes in effective population size. Evol. Appl. 7, 663–681 (2014).
Chevalet, C. & Nikolic, N. The distribution of coalescence times and distances between microsatellite alleles with changing effective population size. Theor. Popul. Biol. 77, 152–163 (2010).
Dallas, J. F. Estimation of microsatellite mutation rates in recombinant inbred strains of mouse. Mam. Gen. 3, 452–456 (1992).
Weber, J. L. & Wong, C. C. Mutation of human short tandem repeats. Hum. Mol. Genet. 2, 1123–1128 (1993).
Brinkmann, B., Klintschar, M., Neuhuber, F., Huhne, J. & Rolf, B. Mutation rate in human microsatellites: Influence of the structure and length of the tandem repeat. Am. J. Hum. Genet. 62, 1408–1415 (1998).
Sajantila, A., Lukka, M. & Syvänen, A. Experimentally observed germline mutations at human micro- and minisatellite loci. Eur. J. Hum. Genet. 7, 263–266 (1999).
Ellegren, H. Microsatellite mutations in the germline: Implications for evolutionary inference. Trends. Genet. 16, 551–558 (2000).
Hrbek, T., de Brito, R. A., Wang, B., Pletscher, L. S. & Cheverud, J. M. Genetic characterisation of a new set of recombinant inbred lines (LGXSM) formed from the intercross of SM/J and LG/J inbred mouse strains. Mam. Gen. 17, 417–429 (2006).
Source: Ecology - nature.com
