基于线粒体Cty b基因的西藏马鹿种群遗传多样性研究
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- 英文论文题名：Population genetic diversity in Tibet red deer(Cervus elaphus wallichi)revealed by mitochondrial Cty b gene analysis
- 论文作者：刘艳华 ; 张明海
- 英文论文作者：Liu Yanhua ; Zhang Minghai ; College of Wildlife Resources ; Northeast Forestry University
- 年：2016
- 作者机构：东北林业大学野生动物资源学院;
- 论文关键词：西藏马鹿 ; 粪便DNA ; Cty b ; 遗传多样性 ; 西藏
- 英文论文关键词：Tibet red deer(Cervus elaphus wallichi) ; fecal DNA ; Cty b ; genetic diversity ; Tibet
- 会议召开时间：2016-06-01
- 会议录名称：“十二五” 鹿科学研究进展
- 语种：中文
- 分类号：S825
- 学会代码：ZXMY
- 学会名称：中国畜牧业协会
- 页数：9
- 文件大小：456k
- 原文格式：O
摘要
西藏马鹿(Cervus elaphus wallichi)为我国特有物种,仅分布在西藏东南部的桑日县,目前关于西藏马鹿的研究报道很少。因此,深入了解西藏马鹿各地理单元内种群的遗传变异,可以制定保护管理策略提供依据,进而使其种群得到有效的保护和管理。对54个不同西藏马鹿个体(来自3个不同地点)的线粒体DNA Ctyb基因进行了测定和群体分析,获得了731bp的片段,并检测到24个变异位点,占分析长度的3.28%,且这24个变异位点皆为碱基置换,并未出现碱基插入或缺失的现象,并定义了14种单倍型,核苷酸多样性平均值为0.027 81,种群总体遗传多样性较高。从Tajima's D和Fu and Li's D值的估算结果来看,这3个马鹿种群相对于中性进化的歧异度并没有明显的偏离(P>0.1),没有明显的证据显示这3个西藏马鹿种群间存在很强的平衡选择。分子变异分析表明3个群体间基因流(5.36>Nm>1.87)均大于1,说明这3个马鹿种群间存在着丰富的基因流,并建议将3个地区的西藏马鹿作为一个管理单元进行保护和管理。
The Tibet red deer,Cervus elaphus wallichi,is a middling and primitive living member of the Cervidae family Tibet red deer were once wildly distributed in Tibet,Sikkim,Nepal and Bhutan.However,in the last century their range and number was drastically reduced because of overhunting In 1992,the World Wildlife Fund(WWF) announced that Tibet red deer in the wild had become extinct.Subsequently,there were very few reports of Tibet red deer in the wild.In July 2005,we investigated the distribution of Tibet red deer and discovered a population of red deer in southeast Tibet.From the body size,morphometrie traits and hair color,we thought it was likely to be Tibet red deer.We collected 123 fecal samples from the red deer distribution area and analyzed the cytochrome b gene sequences from the mitochondrial DNA(mtDNA) of the samples.We used BLAST(mega blast)at NCBI to identify sequences with the highest similarities(> 97%) and the lowest differences(<3%) to the published Cyt b sequence,AY044861,of the Tibet red deer(Cervus elaphus wallichi).105 samples were identified as having high sequence similarity to the red deer(Cervus elaphus wallichi)sequence.We carried out genotype analysis using eleven microsatellites to identify individuals in the 105 fecal samples and obtained 54 different genotypes.Forensic medicine criteria and the results of data analysis allow the identification of different individuals according to genotypes.On the basis of forensic medicine criteria,when the genotype is in full accord with a probability of 10,then we may assume that the genotype represents either one individual or identical twins.Tibet red deer is an endemic species in China.Systematic and detailed ecological research on Tibet red deer is almost nonexistent.To further understand its ecological characteristics and to effectively manage its protection,basic research is urgently required.In this study,we investigated the genetic diversity and gene flow in three Tibet red deer populations by analyzing 731 base pairs of the mtDNA Cyt b gene fragment in 54 individuals sampled from Zengqi,Woka and Baidui.Twenty- four variable sites and fourteen haplotypes were identified.The red deer exhibited high mtDNA diversity with both haplotype diversity(h =0.897 ± 0.014) and nucleotide diversity(77 = 2.781 ±0.02465).The estimates of Tajima's D and Fu and Li's D did not deviate significantly from the neutral selection hypothesis(P > 0.1) for all three populations of deer,showing no evidence of strong selective sweeps or balancing selection.An analysis of molecular variance(AMOVA) showed abundant gene flow(5.36 > Nm > 1.87) among the three populations.Therefore,we suggest that the three populations can be regarded as one unit for conservation and management.
The Tibet red deer,Cervus elaphus wallichi,is a middling and primitive living member of the Cervidae family Tibet red deer were once wildly distributed in Tibet,Sikkim,Nepal and Bhutan.However,in the last century their range and number was drastically reduced because of overhunting In 1992,the World Wildlife Fund(WWF) announced that Tibet red deer in the wild had become extinct.Subsequently,there were very few reports of Tibet red deer in the wild.In July 2005,we investigated the distribution of Tibet red deer and discovered a population of red deer in southeast Tibet.From the body size,morphometrie traits and hair color,we thought it was likely to be Tibet red deer.We collected 123 fecal samples from the red deer distribution area and analyzed the cytochrome b gene sequences from the mitochondrial DNA(mtDNA) of the samples.We used BLAST(mega blast)at NCBI to identify sequences with the highest similarities(> 97%) and the lowest differences(<3%) to the published Cyt b sequence,AY044861,of the Tibet red deer(Cervus elaphus wallichi).105 samples were identified as having high sequence similarity to the red deer(Cervus elaphus wallichi)sequence.We carried out genotype analysis using eleven microsatellites to identify individuals in the 105 fecal samples and obtained 54 different genotypes.Forensic medicine criteria and the results of data analysis allow the identification of different individuals according to genotypes.On the basis of forensic medicine criteria,when the genotype is in full accord with a probability of 10,then we may assume that the genotype represents either one individual or identical twins.Tibet red deer is an endemic species in China.Systematic and detailed ecological research on Tibet red deer is almost nonexistent.To further understand its ecological characteristics and to effectively manage its protection,basic research is urgently required.In this study,we investigated the genetic diversity and gene flow in three Tibet red deer populations by analyzing 731 base pairs of the mtDNA Cyt b gene fragment in 54 individuals sampled from Zengqi,Woka and Baidui.Twenty- four variable sites and fourteen haplotypes were identified.The red deer exhibited high mtDNA diversity with both haplotype diversity(h =0.897 ± 0.014) and nucleotide diversity(77 = 2.781 ±0.02465).The estimates of Tajima's D and Fu and Li's D did not deviate significantly from the neutral selection hypothesis(P > 0.1) for all three populations of deer,showing no evidence of strong selective sweeps or balancing selection.An analysis of molecular variance(AMOVA) showed abundant gene flow(5.36 > Nm > 1.87) among the three populations.Therefore,we suggest that the three populations can be regarded as one unit for conservation and management.
引文
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[29]Liu H,Yang G,Wei F W,Li M,Hu J C.Sequence variability of the mitochondrial DNA control region and population genetic structure of sika deers(Cervus nippon)in China[J].Acta Zool Sinica,2003,49(1):53-60.
[2]Chen S B.Management and conservation for Tibet red deer[J].Central South Forest Inventory and Planning,1999,(3):40-42.
[3]Zhang Y P,Shi L M.Mitochondrial DNA polymorphisms in animals:a review[J].Zoological Research,1992,13(3):289-298.
[4]Cao L R,Wang X M,Rao G,Wan Q H,Fang S G.The phylogenetic relationship among goat,sheep and bharal based on mitochondrial cytochrome b gene sequences[J].Acta Theriologica Sinica,2004,24(2):109-114.
[5]Chen Y J,Zhang Y P,Zou X M,Dong F Y,Wang J J.Molecular Phylogeny of Canidae using mitochondrial cytochrome b DNA sequences[J].Journal of Genetics and enomics,2000,27(1):7-11.
[6]Wei M,Hou P,Huang Z H,Liu N F.Effects of environmental factors on the population genetic structure in alectoris magna[J].Acta EcologicaSinica,2002,22(4):528-534.
[7]Ludt C J,Schroeder W,Rottmann O,Kuehn R.Mitochondrial DNA phylogeography of red deer(Cervus elaphus).[J]Molecular Phylogenetics and Evolution,2004,31(3):1064-1083.
[8]Kuehn R,Schroeder W,Pirchner F,Rottmann O.Genetic diversity,gene flow and drift in Bavarian red deer populations(Cervus elaphus).[J]Conservation Genetics,2003,4(2):157-166.
[9]Pierson C A,Ede A J,Crawford A M.Ovine microsatellites at the OarHH30,OarHH51,OarVH54,OarCP88,OarCP93,OarCP134 loci[J].AnimalGenetics,1994,25(4):294-295.
[10]Red K H,Midthjell L Microsatellites in reindeer,Rangifer tarandus,and their use in other Cervids[J].Molecular Ecology,1998,7(12):1771-1776.
[11]Talbot J,Haigh J,Plante Y.A parentage evaluation test in North American Elk(Wapiti)using microsatellites of ovine and bovine origin.[J]AnimalGenetics,1996,27(2):117-119.
[12]Wilson G A,Strobeck C,Wu L,Coffin J W.Characterization of microsatellite loci in caribou Rangifer tarandus,and their use in other artiodactyls[J].Molecular Ecology,1997,6(7):697-699.
[13]Thompson J D,Gibson T J,Plewniak F,Jeanmougin F,Higgins D G.The ClustalX windows interface:flexible strategies for multiple sequence alignment aided by quality analysis tools[J].Nucleic Acids Research,1997,25(24):4 876-4 882.
[14]Rozas J,Rozas R.DnaSP version3:an integrated program for molecular population genetics and molecular evolution analysis[J].Bioinformatics,1999,15(2):174-175.
[15]Kumar S,Tamura K,Jakobsen I B,Nei M.MEGA2:molecular evolutionary genetics analysis software[J].Bioinformatics,2001,17(12):1244-1245.
[16]Swofford D L.PAUP;phylogenetic analysis using parsimony,version 4[M].Sunderland:Sinauer Associates,2002.
[17]Ronquist F,Huelsenbeck J P.MRBAYES 3:Bayesian phylogenetic inference under mixed models[J].Bioinformatics,2003,19(12):1572-1574.
[18]Posada D,Crandall K A.Modeltest;testing the model of DNA substitution[J].Bioinformatics,1998,14(9):817-818.
[19]Excoffier L,Smouse P E,Quattro J M.Analysis of molecular variance inferred from metric distance among DNA haplotypes:application to human mitochondrial DNA restriction data[J].Genetics,1992,131(2):479-491.
[20]Janec ka J E,Jackson R,Zhang YQ,Li D Q,Munkhtsog B,Buckley-Beaso V,Murphy W J.Population monitoring of snow leopards using noninvasive collection of scat samples;a pilot study[J].Anima Conservation,2008,11(5):401-411.
[21]Neigel J E,Avise J C.Application of a random walk model to geographic distributions of animal mitochondrial DNA variation[J].Geneties,1993,135(4):1209-1220.
[22]Quinn T W,Wilson A C.Sequence evolution in and around the mitochondrial control region in birds[J].Journal of Molecular Evolution,1993,37(4):417-425.
[23]Frankham R,Ballou J D,Briscoe D A.Introduction to conservation genetics[M].Cambridge:Cambridge University Press,2002.
[24]David P.Heterozygosity-fitness correlations:new perspectives on old problems[J].Heredity,1998,80(5):531-537.
[25]Hedrick P W,Lacy R C,Allendorf F W,Soule M E.Direction in conservation biology:comment on Caughley[J].Conservation Biology,1995,10(5):1312-1320.
[26]Frankham R.Conservation genetics[J].Annual Review of Genetics,1995,29:305-327.
[27]Alpers D L,van Vuuren B J,Arctander P,Robinson T J.Population genetics of the roan antelope(Hippotragus equinus)with suggestions for conservation[J].Molecular Ecology,2004,13(7):1 771-1 784.
[28]Hmwe S S,Zachos F E,Sale J B,Rose H R,Haiti G B.Genetic variability and differentiation in red deer(Cervus elaphus)from Scotland and England[J].Journal of Zoology,2006,270(3):479-487.
[29]Liu H,Yang G,Wei F W,Li M,Hu J C.Sequence variability of the mitochondrial DNA control region and population genetic structure of sika deers(Cervus nippon)in China[J].Acta Zool Sinica,2003,49(1):53-60.