The Genetic Diversity of Tibetan Red Deer Populations Determined using Mitochondrial and Microsatellite Markers. | [International Journal of Agriculture and Biology • 2017]

Author(s):

1. Liu Yan Hua: College of Wildlife Resources, Northeast Forestry University, China

2. Zhang Minghai: College of Wildlife Resources, Northeast Forestry University, China

Abstract:

The Tibetan red deer (Cervus elaphus wallichi) is an indigenous Chinese species, mainly inhabiting Sangri County, located in the southeast segment of the Tibetan Autonomous Region. Currently, scientific data on the Tibetan red deer are sparse. Knowledge of the genetic diversity of geographically separate populations could help in formulating strategies to protect this species. In this study, we collected 123 fecal samples from three different regions. These contained 105 samples identified as red deer feces from which 54 genotypes were obtained and analyzed, including 21 Zengqi, 15 Woka and 18 Baidui populations. We performed genetic analysis using mitochondrial and microsatellite markers. The mtDNA CytB genes from 54 individual Tibetan red deer were sequenced and 731 bp fragments were obtained. We defined 14 haplotypes with a haplotype diversity (H) of 0.897. The nucleotide diversity (p) between populations was 2.781. Microsatellite typing analysis showed that the average allele number, mean expected heterozygosity and mean observed heterozygosity were 4.385, 0.721 and 0.641, respectively. Our findings suggest that these Tibetan red deer populations have relatively high genetic diversity. As indicated by Tajima's D and Fu and Li's D values, these three populations had not significantly deviated from a neutral evolutionary path (p > 0.1), nor was any evidence found to suggest a strong equilibrium selection. AMOVA revealed that the inter-gene flow of these three populations was greater than 1 (5.14 > Nm > 1.67), suggesting that abundant gene flow exists between them. No obvious genetic differentiation was observed. Thus, we propose to protect and control the Tibetan red deer in these three regions as a single management unit.

Page(s): 1286-1292

DOI: 10.17957/IJAB/15.0453

Published: Journal: International Journal of Agriculture and Biology, Volume: 19, Issue: 5, Year: 2017

Keywords:

Keywords are not available for this article.

References:

[1] Avise , J.C.,J. Arnold , R.M.,Ball , E. Bermingham, T.,Lamb , J.E.,Niegel , C.A.A.,Reeb and N.C.,Saunders, 1987.Intraspecific phylogeography: the mitochondrial DNA bridge between population genetics and systematics,Annu. Rev. Ecol. Syst. 18 489 -522

[2] Alpers , D.L.,B.J. Van Vuuren,P.Arctander,T.J.Robinson, 2004.Population genetics of the roan antelope (Hippotragus equinus) with suggestions for conservation,Mol. Ecol 13 1771 -1784

[3] Bailey , F., 1911.Notes on game animals from near Gyantse and in the Chumbi valley,J. Bombay Nat. Hist. Soc 20 1028 -1032

[4] Bauert , M.R.,M.Kälin,M.Baltisberger,E.P.Jdwards, 1998.No genetic variation within isolated relict populations of Saxifraga cernua in the Alps using RAPD markers,Mol. Ecol 7 1519 -1527

[5] Broders , H.G., S.P.,Mahoney and W.A.,Montevecchi, 1999.Population genetic structure and the effect of founder events on the genetic variability of moose, Alces alces,Mol. Ecol 8 1309 -1315

[6] Bishop,M.D. , S.M.,Kappes and J.W.,Keele, 1994.A genetic linkage map for cattle,Genetics 136 619 -639

[7] Cote , S.D.,F.Dallas,F.Marshall, 2002.Microsatellite DNA evidence for genetic drift and philopatry in Svalbard reindeer,Mol. Ecol 11 1923 -1930

[8] Caughley , G., 1970.Cervus elaphus in southern Tibet,J. Mammal 51 611 -614

[9] Christian , J.,W.Schroeder,R.Oswald,K.Ralph, 2004.Mitochondrial DNA phylogeography of red deer (Cervus elaphus),Mol. Phylogenet 31 1064 -1083

[10] David , P., 1998.Heterozygosity-fitness correlations: new perspectives on old problems, 80 531 -537

[11] Dolan , J.,L.Killmar, 1825.A rare and little-known cervid with remarks on three additional Asiatic elaphines,Zool. Garten 58 84 -96

[12] Excoffier , L.,P.E.Smouse,J.M.Quattro, 1992.Analysis of molecular variance inferred from metric distances among DNA haplotypes: Applications to human mitochondrial DNA restriction data,Genetics 131 479 -491

[13] Ernest , H.B.,M.C.T. Penedo , B.P.,May , M.,Syvanen and W.M.,Boyce, 2000.Molecular tracking of mountain lions in the Yosemite Valley region in California: genetic analysis using microsatellites and faecal DNA,Mol. Ecol 9 433 -441

[14] Flerov , K.K., 1960.2: Musk Deer and Deer. The Academy of Sciences of the USSR (The Israel Program for Scientific Translation, 1 -

[15] Feng , Z.,G.Cai,C.Zheng, 1986., -

[16] Frankham , R.,J.D.Ballou,D.A.Briscoe, 2002., 78 -104

[17] Frankham , R., 1995.Conservation genetics,Annu. Rev. Genet 29 305 -327

[18] Goodman , S.J.,H.B.Tamate,R.Wilson, 2001.Bottlenecks, drift and differentiation: the population structure and demographic history of sika deer (Cervus nippon) in the Japanese archipelago,Mol. Ecol 11 1357 -1370

[19] Hughes , A.R.,B.D.Inouye,M.T.J.Johnson,N.Underwood,M.Vellend, 2008.Ecological consequences of genetic diversity,Ecol. Lett. 11 609 -623

[20] Hartl , G.B.,F.Zachos,K.Nadlinger, 2003.Genetic diversity in European red deer (Cervus elaphus L.): anthropogenic influences natural populations,Mamm. Biol 326 S27 -S42

[21] Hartl , G.B.,F.Zachos,K.Nadlinger,M.Ratkiewicz,F.Klein,G.Lang, 2005.Allozyme and mitochondrial DNA analysis of French red deer (Cervus elaphus) populations: genetic structure and its implications for management and conservation,Mamm. Biol 70 24 -34

[22] Huelsenbeck , J.P.,F.Ronquist, 2001.Bayesian inference of phylogeny,Bioinformatics 17 754 -755

[23] Hedrick , P.W.,R.C.Lacy,F.W.Allendorf, 1995.Direction in conservation biology: comment on Caughley,Conserv. Biol 10 1312 -1320

[24] Hmwe , S.,E.Zachos,J.Sale, 2006.Genetic variability and differentiation in red deer (Cervus elaphus) from Scotland and England, 270 479 -487

[25] Jones , K.C.,K.F.Levine,J.D.Banks, 2002.Characterization of 11 polymorphic tetranucleotide microsatellites for forensic applications in California Elk (Cervus elaphus canadensis),Mol. Ecol. Notes 2 425 -427

[26] Jones , K.C.,K.F.Levine,J.D.Banks, 2000.DNA-based genetic markers in black-tailed and mule deer for forensic applications, 86 115 -126

[27] Koban , E.,M.Denizci,O.Aslan,D.Aktoprakligil,S.Aksu,M.Bower,B.K.Balcioglu,A.Ozdemir,Bahadir,R.Bilgin,B.Erdag,H.Bagisand,S.Arat, 2011.High microsatellite and mitochondrial diversity in Anatolian native horse breeds shows Anatolia as a genetic conduit between Europe and Asia,Anim. Genet 43 401 -409

[28] Kuehn , R.,W.Schroeder,F.Pirchner, 2003.Genetic diversity, gene flow and drift in Bavarian red deer populations (Cervus elaphus),Conserv. Genet 4 157 -166

[29] Kumar , S.,K.Tamura,I.B.Jakobsen,M.Nei,MolecularEvolutionary Genetics Analysis Software. Temple, 2001., -

[30] Ludlow , F., 1959.The shou or 'Sikkim stag,' J. Bombay Nat. Hist. Soc. 56 626 -628

[31] Liu , H., G.,Yang , F.W.,Wei , M.,Li and J.C.,Hu, 2003.Sequence variability of the mitochondrial DNA control region and population genetic structure of sika deers (Cervus nippon) in China,Acta Zool 49 53 -60

[32] Ludt , C.J.,W.Schroeder,O.Rottmann,R.Kuehn, 2004.Motochondrial DNA phylogeography of red deer (Cervus elaphus),Mol. Phylogenet Evol 31 1064 -1083

[33] Meredith , E.P.,J.A.Rodzen,K.F.Levine, 2005.Charecterization of an additional 14 microsatellite loci in California Elk (Cervus elaphus) for use in forensic and population applications,Conserv. Genet 6 151 -153

[34] Moore , S.S.,W.Berger,K.T.Berger, 1992.Bovine and ovine DNA microsatellites from the EMBL and GenBank databases,Anim. Genet 23 463 -367

[35] Marshall , T.C.,J. Slate , L.E.B.,Kruuk and J.M.,Pemberton, 1998.Statistical confidence for likelihood-based paternity inference in natural populations,Mol. Ecol 7 639 -655

[36] Ohtaishi , N., 1995.Red deer-the most prosperous deer,Chikusan Kenkyu (Livestock Res.) 49 132 -139

[37] Polziehn , R.O.,J.Hamr,F.F.Mallory,C.Strobeck, 2000.Micriosatellite analysis of North American wapiti (Cervus elaphus) populations,Mol. Ecol 9 1561 -1576

[38] Posada , D.,K.A.Crandall, 1998.Model test: Testing the model of DNA substitution,Bioinformatics 14 817 -818

[39] Røed , K.H., 1998.Microsatellite variation in Scandinavian Cervidae using primers derived from Bovidae, 129 19 -25

[40] Rozas , J.,R.Rozas, 1999.Dnasp version 3: An integrated program for molecular population genetics and molecular evolution analysis,Bioinformatics 15 174 -175

[41] Ronquist , F.,J.P.Huelsenbeck, 2003.MRBAYES 3: Bayesian phylogenetic inference under mixed models,Bioinformatics 19 1572 -1574

[42] Sheng , H.L. and N.,Ohtaishi,H.L.,Ammsterdam, 1993.The status of deer in China, 1 -11

[43] Swofford , D.L., 2002.Phylogenetic Analysis Using Parsimony, Version 4, -

[44] Schneider , S.,D.Roessli,L.Excoffier, 2000.A Software for Genetic Data Analysis, -

[45] Thornback , J.,MammaliaIUCN, 1978.Red Data Book, 1 -

[46] Thompson , J.D.,T.J.Gibson,F.Plewniak,F.Jeanmougin,D.G.Higgins, 1997.The Clustal X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools,Nucleic Acids Res 24 4876 -4882

[47] Valiere , N., 2015.a computer program for analyzing genetic individual identification data,Mol. Ecol 2 377 -379

[48] Wu , H.,Q.H.Wan,S.G.Fang, 2004.Two genetically distinct units of the Chinese sika deer (Cervus nippon): analysis of mitochondrial DNA variation,Biol 119 183 -190

[49] Wehausen , J.D.R.R.,H.Ramey,C.W.Epps, 2004.PCR amplification from bighorn sheep feces: the importance of DNA extraction method,J. Hered. 95 503 -509

[50] Yachi , S.,M.Loreau, 1999.Biodiversity and ecosystem productivity in a fluctuatingenvironment:theinsurancehypothesis, 94 1463 -1468

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