青海省东部地区喜马拉雅旱獭种群遗传结构
|
摘要
本研究利用11个微卫星标记对采自青海省东部地区的13个喜马拉雅旱獭(Marmota himalayana)种群149个个体进行基因分型,并运用种群遗传学方法对其遗传多样性和遗传结构进行分析。结果显示,11个微卫星标记位点共计检测到97个等位基因,各种群的平均观测杂合度和期望杂合度范围分别为0.58～0.82和0.60～0.79,种群遗传多样性水平相对较高;遗传结构分析表明,青海省东部地区的喜马拉雅旱獭种群具有显著的遗传结构,13个地理种群形成了3个遗传聚类群,且3个遗传聚类群与湟水河和黄河上游干流所划分的地理单元完全一致,因此我们认为湟水河和黄河上游干流是阻碍该地区喜马拉雅旱獭种群进行迁移扩散和基因交流的天然屏障。同时,STRUCTURE分析结果还显示3个遗传聚类群间仍有明显的基因流,AMOVA分析也显示3个聚类群间变异百分比为6.60%,仅略高于聚类群内种群间的变异(4.51%),而远低于种群内变异水平(88.90%),表明3个聚类群间的分化程度并不是很深。这说明喜马拉雅旱獭可能通过桥梁或在枯水期等穿越河流进行基因交流。以上结果为该地区的旱獭种群监控和鼠疫防控提供科学的理论基础。
In this study,149 Himalayan marmot individuals from 13 populations were sampled from eastern Qinghai and genotyped at 11 microsatellite loci. Then the genetic diversity and genetic structure of these populations were analyzed using different population genetics methods. As the results showed,a total of 97 alleles were detected at all 11 SSR loci. The average observed heterozygosity and expected heterozygosity for each population ranged from 0. 58 and 0. 60 to 0. 82 and0. 79,representing a relatively high level of genetic diversity. The genetic structure analyses demonstrated that the marmot populations in eastern Qinghai exhibited a strong genetic structure,where 13 geographical populations were allocated into 3 genetic clusters. Surprisingly,such three gene-tic clusters are in perfect accordance with the geographical units divided by the trunk stream of the Huangshui River and the head trunk stream of the Yellow River. Therefore,we conclude that these two rivers act as natural barriers to the dispersal and gene-flow between the marmot populations in different units. Meanwhile,as suggested by the STRUCTURE analysis,there was still obvious gene-flow between the three genetic clusters,and the AMOVA analysis also showed that the percentage of the variance between genetic clusters was 6. 60%,slightly higher than that between different populations within clusters( 4. 51%) and far lower than that within populations( 88. 90%),indicating a low degree of differentiation between the genetic clusters. All such results implied that the Himalayan marmots may cross over the rivers by some bridges or in low water periods to disperse and exchange. These results can provide scientific information for the monitoring and management of marmot populations and even plague control in this region.
In this study,149 Himalayan marmot individuals from 13 populations were sampled from eastern Qinghai and genotyped at 11 microsatellite loci. Then the genetic diversity and genetic structure of these populations were analyzed using different population genetics methods. As the results showed,a total of 97 alleles were detected at all 11 SSR loci. The average observed heterozygosity and expected heterozygosity for each population ranged from 0. 58 and 0. 60 to 0. 82 and0. 79,representing a relatively high level of genetic diversity. The genetic structure analyses demonstrated that the marmot populations in eastern Qinghai exhibited a strong genetic structure,where 13 geographical populations were allocated into 3 genetic clusters. Surprisingly,such three gene-tic clusters are in perfect accordance with the geographical units divided by the trunk stream of the Huangshui River and the head trunk stream of the Yellow River. Therefore,we conclude that these two rivers act as natural barriers to the dispersal and gene-flow between the marmot populations in different units. Meanwhile,as suggested by the STRUCTURE analysis,there was still obvious gene-flow between the three genetic clusters,and the AMOVA analysis also showed that the percentage of the variance between genetic clusters was 6. 60%,slightly higher than that between different populations within clusters( 4. 51%) and far lower than that within populations( 88. 90%),indicating a low degree of differentiation between the genetic clusters. All such results implied that the Himalayan marmots may cross over the rivers by some bridges or in low water periods to disperse and exchange. These results can provide scientific information for the monitoring and management of marmot populations and even plague control in this region.
引文
Chen Y,Wang Z,Zhang G,Fan W,Tao Y,He X,Zhao S,Huang B,Fan J,Shuji K,Liu E.2012.Genetic characterization of four wild species of Chinese marmots using microsatellite markers.Biologia,67(5):1013-1017.
Corander J,Marttinen P,Sirén J,Tang J.2008.Enhanced Bayesian modelling in BAPS software for learning genetic structures of populations.BMC Bioinformatics,9(1):539.
Da Silva A,Luikart G,Yoccoz N,Cohas A,Allaine D.2006.Genetic diversity-fitness correlation revealed by microsatellite analyses in European alpine marmots(Marmota marmota).Conservation Genetics,7(3):371-382.
Earl D A.2012.STRUCTURE HARVESTER:a website and program for visualizing STRUCTURE output and implementing the Evanno method.Conservation Genetics Resources,4(2):359-361.
Excoffier L,Lischer H E.2010.Arlequin suite ver 3.5:a new series of programs to perform population genetics analyses under Linux and Windows.Molecular Ecology Resources,10(3):564-567.
Gage K L,Kosoy M Y.2005.Natural history of plague:perspectives from more than a century of research.Annu Rev Entomol,50:505-528.
Ge Y L,Lin G H,Ci H X,Zhang T Z,Tang L Z,Su J P.2009.Genetic diversity and differentiation of Ochotona curzoniae based on ISSRand Cyt b gene.Chinese Journal of Zoology,44(4):34-40.(in Chinese)
He X,Wang Z D,Tao Y Q,Fan W,Zhang G W,Huang B Q,Chen YL,Liu E Q.2012.Genetic polymorphism of Marmota himalayana populations in Qinghai Province using microsatellite markers.Chinese Veterinary Science,42(06):627-631.(in Chinese)
Jakobsson M,Rosenberg N A.2007.CLUMPP:a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure.Bioinformatics,23(14):1801-1806.
Jombart T,Devillard S,Balloux F.2010.Discriminant analysis of principal components:a new method for the analysis of genetically structured populations.BMC Genetics,11(1):94.
Kruckenhauser L,Pinsker W,Haring E,Arnold W.1999.Marmot phylogeny revisited:molecular evidence for a diphyletic origin of sociality.Journal of Zoological Systematics and Evolutionary Research,37(1):49-56.
Kruckenhauser L,Bryant A A,Griffin S C,Amish S J,Pinsker W.2009.Patterns of within and between-colony microsatellite variation in the endangered Vancouver Island marmot(Marmota vancouverensis):implications for conservation.Conservation Genetics,10(6):1759-1772.
Li Y,Wang Z,Tao Y,Fan W,Li M,Huang B,Zhao S,Fan J,Liu E.2012.Characteristics of Himalayan marmots and their response to an atherogenic diet.Experimental Animals,61(4):461-466.
Liu C X,Su J P,Zhang T Z,Lin G H.2013.The effect of Qingzang-Tibet Plateau geographical barrier on plateau pika population differentiation.Sichuan Journal of Zoology,32(5):651-657.(in Chinese)
Liu W,Zhang Y,Wang X,Zhao J Z,Xu Q M,Zhou L.2009.Food selection pattern for plateau pika in winter.Acta Theriologica Sinica,29(1):12-19.(in Chinese)
Liu Y,Yang Y K,Cai Q F,Ma H Z,Shi J F.2006.June to July runoff reconstruction for Huangshui River from tree ring width for the last248 years.Journal of Arid Land Resources and Environment,20(6):69-73.(in Chinese)
Luo X Z,Hai R.2010.An overview of the epidemiological characteristics of Marmota himalayana plague on Qinghai-Tibet Plateau.Chin J Vector Biol and Control,21(4):394-398.(in Chinese)
Mc Kean T,Mendenhall W.1996.Comparison of the responses to hypoxia,ischaemia and ischaemic preconditioning in wild marmot and laboratory rabbit hearts.Journal of Experimental Biology,199(3):693-697.
Menne S,Cote P J.2007.The woodchuck as an animal model for pathogenesis and therapy of chronic hepatitis B virus infection.World Journal of Gastroenterology,13(1):104.
Nikol’skii A,Rumiantsev V Y.2012.Center of species diversity of Eurasian marmots(Marmota,Rodentia)in an epi-platformal orogeny area.Doklady Biological Sciences,445(1):261-264.
Perry R D,Fetherston J D.1997.Yersinia pestis-etiologic agent of plague.Clinical Microbiology Reviews,10(1):35-66.
Pritchard J K,Stephens M,Donnelly P.2000.Inference of population structure using multilocus genotype data.Genetics,155(2):945-959.
Rosenberg N A.2004.DISTRUCT:a program for the graphical display of population structure.Molecular Ecology Notes,4(1):137-138.
Shi S M,Liu F Y,Yan X B.2008.Habitat selection by Marmota himalayana in the eastern Qilian Mountains.Journal of Gansu Agricultural University,43(1):125-130.(in Chinese)
Steppan S J,Storz B L,Hoffmann R S.2004.Nuclear DNA phylogeny of the squirrels(Mammalia:Rodentia)and the evolution of arboreality from c-myc and RAG1.Mol Phylogenet Evol,30(3):703-719.
Wang L L,Xu J H,Qin Z,Wang Y S,Xu L X.2008.Genetic diversity of microsatellite loci in Marmota himalayana.Journal of Qufu Normal University,34(4):101-104.(in Chinese)
Xu J,Wang L,Xue H,Wang Y,Xu L.2009.Genetic structure of Himalayan marmot(Marmota himalayana)population alongside the Qinghai-Tibet Railway.Acta Ecologica Sinica,29(5):314-319.
Yan J,Chen H,Lin G,Li Q,Chen J,Qin W,Su J,Zhang T.2017.Genetic evidence for subspecies differentiation of the Himalayan marmot,Marmota himalayana,in the Qinghai-Tibet Plateau.PLo SONE,12(8),e0183375.
Zhang A N,Liu L,Zhang Y Z.2002.Dynamic observation of quantity of fleas on Marmota himalayana in certain area of eastern Qilian Mountain.Chin J Ctrl Endem Dis,17(6):369-371.(in Chinese)
Zheng Y,Zhang A P,Li Q,Wang X,Chen H J,Zhang X F,Wang ZY.2017.Epidemiological characteristics of human plague in Qinghai Province.Capital Journal of Public Health,11(2):50-52.(in Chinese)
马怀雷.2011.小尺度范围喜马拉雅旱獭家族之间个体迁移的研究.北京:中国疾病预防控制中心硕士学位论文.
马跃新,张国强,马俊杰,杨小平,张才德.1990.灰旱獭生态拾零.地方病通报,5:88.
王琳琳,徐金会,秦桢,王玉山,徐来祥.2008.三个微卫星标记在喜马拉雅旱獭种群中的遗传多态性.曲阜师范大学学报,34(4):101-104.
刘天仇.1993.雅鲁藏布江冰情.西藏大学学报,8(1):37-42.
刘伟,张毓,王溪,赵建中,许庆民,周立.2009.高原鼠兔冬季的食物选择.兽类学报,29(1):12-19.
刘禹,杨银科,蔡秋芳,马海洲,史江峰.2006.以树木年轮宽度资料重建湟水河过去248年来6-7月份河流径流量.干旱区资源与环境,20(6):69-73.
刘翠霞,苏建平,张同作,林恭华.2013.青藏高原的地理屏障在高原鼠兔种群分化中的作用.四川动物,32(5):651-657.
杨赉斐.1997.黄河上游冰情及其研究.西北水电,60:1-5.
张安宁,刘麟,张玉贞.2002.东祁连山某部喜马拉雅旱獭蚤类数量观察.中国地方病防治杂志,17(6):369-371.
尚国宝,魏荣杰,杨永海,张爱萍,赵忠志,吴海莲,吴海生,陈刚,吴树生,唐新元,田富彰,王虎,王祖郧.2015.青海地区喜马拉雅旱獭鼠疫风险评估研究.中国卫生统计,32(4):661-665.
侍世梅,刘发央,严学兵.2008.东祁连山喜马拉雅旱獭生境的选择.甘肃农业大学学报,43(1):125-130.
郑谊,张爱萍,李千,王雪,陈洪舰,张雪飞,王祖郧.2017.青海省人间鼠疫流行病学分析.首都公共卫生,11(2):50-52.
贺学,王忠东,陶元清,范薇,张光伟,黄炳俏,陈玉龙,刘恩岐.2012.青海省喜马拉雅旱獭种群的遗传多态性分析.中国兽医科学,42(06):627-631.
骆孝志,海荣.2010.青藏高原喜马拉雅旱獭鼠疫流行特征研究概况.中国媒介生物学及控制杂志,21(4):394-398.
葛艳丽,林恭华,慈海鑫,张同作,唐利洲,苏建平.2009.基于ISSR标记和线粒体Cyt b基因分析高原鼠兔的遗传多样性及其遗传分化.动物学杂志,44(4):34-40.
Corander J,Marttinen P,Sirén J,Tang J.2008.Enhanced Bayesian modelling in BAPS software for learning genetic structures of populations.BMC Bioinformatics,9(1):539.
Da Silva A,Luikart G,Yoccoz N,Cohas A,Allaine D.2006.Genetic diversity-fitness correlation revealed by microsatellite analyses in European alpine marmots(Marmota marmota).Conservation Genetics,7(3):371-382.
Earl D A.2012.STRUCTURE HARVESTER:a website and program for visualizing STRUCTURE output and implementing the Evanno method.Conservation Genetics Resources,4(2):359-361.
Excoffier L,Lischer H E.2010.Arlequin suite ver 3.5:a new series of programs to perform population genetics analyses under Linux and Windows.Molecular Ecology Resources,10(3):564-567.
Gage K L,Kosoy M Y.2005.Natural history of plague:perspectives from more than a century of research.Annu Rev Entomol,50:505-528.
Ge Y L,Lin G H,Ci H X,Zhang T Z,Tang L Z,Su J P.2009.Genetic diversity and differentiation of Ochotona curzoniae based on ISSRand Cyt b gene.Chinese Journal of Zoology,44(4):34-40.(in Chinese)
He X,Wang Z D,Tao Y Q,Fan W,Zhang G W,Huang B Q,Chen YL,Liu E Q.2012.Genetic polymorphism of Marmota himalayana populations in Qinghai Province using microsatellite markers.Chinese Veterinary Science,42(06):627-631.(in Chinese)
Jakobsson M,Rosenberg N A.2007.CLUMPP:a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure.Bioinformatics,23(14):1801-1806.
Jombart T,Devillard S,Balloux F.2010.Discriminant analysis of principal components:a new method for the analysis of genetically structured populations.BMC Genetics,11(1):94.
Kruckenhauser L,Pinsker W,Haring E,Arnold W.1999.Marmot phylogeny revisited:molecular evidence for a diphyletic origin of sociality.Journal of Zoological Systematics and Evolutionary Research,37(1):49-56.
Kruckenhauser L,Bryant A A,Griffin S C,Amish S J,Pinsker W.2009.Patterns of within and between-colony microsatellite variation in the endangered Vancouver Island marmot(Marmota vancouverensis):implications for conservation.Conservation Genetics,10(6):1759-1772.
Li Y,Wang Z,Tao Y,Fan W,Li M,Huang B,Zhao S,Fan J,Liu E.2012.Characteristics of Himalayan marmots and their response to an atherogenic diet.Experimental Animals,61(4):461-466.
Liu C X,Su J P,Zhang T Z,Lin G H.2013.The effect of Qingzang-Tibet Plateau geographical barrier on plateau pika population differentiation.Sichuan Journal of Zoology,32(5):651-657.(in Chinese)
Liu W,Zhang Y,Wang X,Zhao J Z,Xu Q M,Zhou L.2009.Food selection pattern for plateau pika in winter.Acta Theriologica Sinica,29(1):12-19.(in Chinese)
Liu Y,Yang Y K,Cai Q F,Ma H Z,Shi J F.2006.June to July runoff reconstruction for Huangshui River from tree ring width for the last248 years.Journal of Arid Land Resources and Environment,20(6):69-73.(in Chinese)
Luo X Z,Hai R.2010.An overview of the epidemiological characteristics of Marmota himalayana plague on Qinghai-Tibet Plateau.Chin J Vector Biol and Control,21(4):394-398.(in Chinese)
Mc Kean T,Mendenhall W.1996.Comparison of the responses to hypoxia,ischaemia and ischaemic preconditioning in wild marmot and laboratory rabbit hearts.Journal of Experimental Biology,199(3):693-697.
Menne S,Cote P J.2007.The woodchuck as an animal model for pathogenesis and therapy of chronic hepatitis B virus infection.World Journal of Gastroenterology,13(1):104.
Nikol’skii A,Rumiantsev V Y.2012.Center of species diversity of Eurasian marmots(Marmota,Rodentia)in an epi-platformal orogeny area.Doklady Biological Sciences,445(1):261-264.
Perry R D,Fetherston J D.1997.Yersinia pestis-etiologic agent of plague.Clinical Microbiology Reviews,10(1):35-66.
Pritchard J K,Stephens M,Donnelly P.2000.Inference of population structure using multilocus genotype data.Genetics,155(2):945-959.
Rosenberg N A.2004.DISTRUCT:a program for the graphical display of population structure.Molecular Ecology Notes,4(1):137-138.
Shi S M,Liu F Y,Yan X B.2008.Habitat selection by Marmota himalayana in the eastern Qilian Mountains.Journal of Gansu Agricultural University,43(1):125-130.(in Chinese)
Steppan S J,Storz B L,Hoffmann R S.2004.Nuclear DNA phylogeny of the squirrels(Mammalia:Rodentia)and the evolution of arboreality from c-myc and RAG1.Mol Phylogenet Evol,30(3):703-719.
Wang L L,Xu J H,Qin Z,Wang Y S,Xu L X.2008.Genetic diversity of microsatellite loci in Marmota himalayana.Journal of Qufu Normal University,34(4):101-104.(in Chinese)
Xu J,Wang L,Xue H,Wang Y,Xu L.2009.Genetic structure of Himalayan marmot(Marmota himalayana)population alongside the Qinghai-Tibet Railway.Acta Ecologica Sinica,29(5):314-319.
Yan J,Chen H,Lin G,Li Q,Chen J,Qin W,Su J,Zhang T.2017.Genetic evidence for subspecies differentiation of the Himalayan marmot,Marmota himalayana,in the Qinghai-Tibet Plateau.PLo SONE,12(8),e0183375.
Zhang A N,Liu L,Zhang Y Z.2002.Dynamic observation of quantity of fleas on Marmota himalayana in certain area of eastern Qilian Mountain.Chin J Ctrl Endem Dis,17(6):369-371.(in Chinese)
Zheng Y,Zhang A P,Li Q,Wang X,Chen H J,Zhang X F,Wang ZY.2017.Epidemiological characteristics of human plague in Qinghai Province.Capital Journal of Public Health,11(2):50-52.(in Chinese)
马怀雷.2011.小尺度范围喜马拉雅旱獭家族之间个体迁移的研究.北京:中国疾病预防控制中心硕士学位论文.
马跃新,张国强,马俊杰,杨小平,张才德.1990.灰旱獭生态拾零.地方病通报,5:88.
王琳琳,徐金会,秦桢,王玉山,徐来祥.2008.三个微卫星标记在喜马拉雅旱獭种群中的遗传多态性.曲阜师范大学学报,34(4):101-104.
刘天仇.1993.雅鲁藏布江冰情.西藏大学学报,8(1):37-42.
刘伟,张毓,王溪,赵建中,许庆民,周立.2009.高原鼠兔冬季的食物选择.兽类学报,29(1):12-19.
刘禹,杨银科,蔡秋芳,马海洲,史江峰.2006.以树木年轮宽度资料重建湟水河过去248年来6-7月份河流径流量.干旱区资源与环境,20(6):69-73.
刘翠霞,苏建平,张同作,林恭华.2013.青藏高原的地理屏障在高原鼠兔种群分化中的作用.四川动物,32(5):651-657.
杨赉斐.1997.黄河上游冰情及其研究.西北水电,60:1-5.
张安宁,刘麟,张玉贞.2002.东祁连山某部喜马拉雅旱獭蚤类数量观察.中国地方病防治杂志,17(6):369-371.
尚国宝,魏荣杰,杨永海,张爱萍,赵忠志,吴海莲,吴海生,陈刚,吴树生,唐新元,田富彰,王虎,王祖郧.2015.青海地区喜马拉雅旱獭鼠疫风险评估研究.中国卫生统计,32(4):661-665.
侍世梅,刘发央,严学兵.2008.东祁连山喜马拉雅旱獭生境的选择.甘肃农业大学学报,43(1):125-130.
郑谊,张爱萍,李千,王雪,陈洪舰,张雪飞,王祖郧.2017.青海省人间鼠疫流行病学分析.首都公共卫生,11(2):50-52.
贺学,王忠东,陶元清,范薇,张光伟,黄炳俏,陈玉龙,刘恩岐.2012.青海省喜马拉雅旱獭种群的遗传多态性分析.中国兽医科学,42(06):627-631.
骆孝志,海荣.2010.青藏高原喜马拉雅旱獭鼠疫流行特征研究概况.中国媒介生物学及控制杂志,21(4):394-398.
葛艳丽,林恭华,慈海鑫,张同作,唐利洲,苏建平.2009.基于ISSR标记和线粒体Cyt b基因分析高原鼠兔的遗传多样性及其遗传分化.动物学杂志,44(4):34-40.