喜马拉雅旱獭线粒体DNA控制区遗传多样性及系统发育
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摘要
喜马拉雅旱獭是青藏高原的优势种,数量多、分布广,全面了解其遗传背景对该地区旱獭资源的保护与合理利用具有重要的意义。本研究以青藏高原云南、西藏和青海三省区共13个地理种群计258只旱獭为研究对象,PCR扩增获得线粒体DNA控制区基因部分序列(887 bp),并运用种群遗传学方法进行遗传多样性分析。结果显示:258份样品共发现了84个变异位点(9.40%),定义了68种单倍型,其单倍型多样性(h)平均值为0.968±0.003、核苷酸多样性(π)平均值为0.017 25±0.016 37,种群总体遗传多样性较高。AMOVA方差分析显示13个地理种群间存在着明显的遗传分化(Fst=0.620 67,P<0.001),种群间基因交流多数较低(Nm<1)。基于单倍型构建的系统发育树中13个地理种群的喜马拉雅旱獭聚为两支,其中来自青藏高原西南地区(西藏安多、青海格尔木、青海囊谦、云南迪庆)的18个单倍型聚成一个大的分支(A支),其余50个单倍型聚为一个大的分支(B支),在NETWORK网络图中也可见到相似网络拓扑结构。研究结果显示青藏高原喜马拉雅旱獭种群以唐古拉山脉为界分为两个大的种群,说明地理隔离是影响喜马拉雅旱獭种群动态变化的主要因素。
The Himalayan marmot(Marmota himalayana) is an exceedingly common species widely-distributed across vast areas of the Qinghai-Tibet Plateau. In order to improve conservation and management strategies of this species, we must understand its genetic structure and genetic diversity at the population level. In this study, 258 Marmota himalayana individuals were collected from 13 geographic populations. The genetic diversity and genetic structures of these populations were analyzed according to the sequence variation of the mitochondrial D-loop sequence. All 258 samples were successfully sequenced for 887 bp of the mitochondrial D-loop sequence. We found 84 sites(9.40%) to be polymorphic and genetic diversity was high overall(mean haplotype diversity 0.968±0.003, mean nucleotide diversity 0.017 25±0.016 37). The results of AMOVA analysis showed obvious genetic differentiation(Fst=0.620 67, P<0.001) and relatively low gene flow among different populations(Nm<1). A neighbor-joining phylogenetic tree produced two main branches; the first branch(A) included 18 haplotypes from the southwestern Qinghai-Tibet Plateau(including Tibet Anduo, Qinghai Golmud, Qinghai Nangqian, and Yunnan Diqing), and the second branch(B) included the other 50 haplotypes from the northeastern Qinghai-Tibet Plateau. A similar topology was also found using network diagram methods. Populations of the Himalayan marmot on the Qinghai-Tibet Plateau are separable into two groups, with the Tanggula Mountains serving as a geographic barrier between them. Therefore, geographical isolation via this mountain range appears to be the primary factor enforcing genetic structure of Himalayan marmot populations.
The Himalayan marmot(Marmota himalayana) is an exceedingly common species widely-distributed across vast areas of the Qinghai-Tibet Plateau. In order to improve conservation and management strategies of this species, we must understand its genetic structure and genetic diversity at the population level. In this study, 258 Marmota himalayana individuals were collected from 13 geographic populations. The genetic diversity and genetic structures of these populations were analyzed according to the sequence variation of the mitochondrial D-loop sequence. All 258 samples were successfully sequenced for 887 bp of the mitochondrial D-loop sequence. We found 84 sites(9.40%) to be polymorphic and genetic diversity was high overall(mean haplotype diversity 0.968±0.003, mean nucleotide diversity 0.017 25±0.016 37). The results of AMOVA analysis showed obvious genetic differentiation(Fst=0.620 67, P<0.001) and relatively low gene flow among different populations(Nm<1). A neighbor-joining phylogenetic tree produced two main branches; the first branch(A) included 18 haplotypes from the southwestern Qinghai-Tibet Plateau(including Tibet Anduo, Qinghai Golmud, Qinghai Nangqian, and Yunnan Diqing), and the second branch(B) included the other 50 haplotypes from the northeastern Qinghai-Tibet Plateau. A similar topology was also found using network diagram methods. Populations of the Himalayan marmot on the Qinghai-Tibet Plateau are separable into two groups, with the Tanggula Mountains serving as a geographic barrier between them. Therefore, geographical isolation via this mountain range appears to be the primary factor enforcing genetic structure of Himalayan marmot populations.
引文
Bandelt H J,Forster P,R?hl A.1999.Median-joining networks for inferring intraspecific phylogenies.Molecular Biology & Evolution,16(1):37-48.
Bullerwell C E,Gray M W.2004.Evolution of the mitochondrial genome protist connections to animals,fungi and plants.Current Opinion in Microbiology,7(5):528-534.
Cai Z Y,Zhang T G,Ci H X,Tang L Z,Lian X M,Liu J Q,Su J P.2007.Mitochondrial phylogeography and genetic diversity of plateau zokor (Myospalax baileyi).Acta Therologica Sinica,27(2):130-137.(in Chinese)
Chang Y B,Yang Q S,Wen Z X,Xia L,Lv X,Cheng J L,Andrey A L,Hou J H,Ge D Y.2016.Population genetic structure and demographic history of Ochotona cansus (Lagomorpha,Ochotonidae).Acta Therologica Sinica,36(4):373-387.(in Chinese)
Chen Q M,Ye Y C,Xia Y M.1992.Comparative studies on the cerebral cortex structure and the blood gaseous.Acta Therologica Sinica,12(1):25-30.(in Chinese)
Chen X,Shen Y Y,Zhang Y P.2012.Review of mtDNA in molecular evolution studies.Zoological Research,33(6):566-573.(in Chinese)
Excoffier L,Laval G,Schneider S.2005.Arlequin (version 3.0):an integrated software package for population genetics data analysis.Evolutionary Bioinformatics Online,1:47-50.
Fu Y X.1997.Statistical tests of neutrality of mutations against population growth,hitchhiking and background selection.Genetics,147(2):915-925.
Harpending H C.1994.Signature of ancient population growth in a low-resolution mitochondrial DNA mismatch distribution.Human Biology,66(4):591–600.
Hirota T,Hirohata T,Mashima H,Mashima H,Satoh T,Obara Y.2004.Population structure of the large Japanese field mouse,Apodemus speciosus (Rodentia:Muridae),in suburban landscape,based on mitochondrial D-loop sequences.Molecular Ecology,13(11):3275-3282.
Huang H,Yang Y,Liu J,Zhang Z H,Tian Y J,Wang B J,Hao Y H,Yang D L.2006.Prokaryotic expression,purification and renaturation of CRDH1 and CRDH2 of Chinese marmata asialoglycoprotein receptor.Journal Medical Molecular Biology,3(4):255-259.(in Chinese)
Imsiridou A,Triantafyllidis A,Baxevanis A D,Triantaphyllidis C.2009.Genetic characterization of common carp (Cyprinus carpio) populations from Greece using mitochondrial DNA sequences.Biologia,64(4):781-785.
Li A Y,Wang B J,Tian Y J,Jiang M,Bao J J,Hao Y H,Yu Z Q,Lu M J,Yang D L.2006.Cloning and sequence analysis of Chinese Marmot interleukin-10.Journal Medical Molecular Biology,3(5):344-346.(in Chinese)
Li Z C,Xia L,Yang Q S,Liang M Y.2005.Population genetic structure of the yarkand hare (Lepus yarkandensis).Acta Therologica Sinica,25(3):224-228.(in Chinese)
Librado P,Rozas J.2009.DnaSP v5:a software for comprehensive analysis of DNA polymorphism data.Bioinformatics,25(11):1451-1452.
Lu Y,Wang B,Huang H,Tian Y J,Dong J H,Lu M J,Yang D L.2008.The interferon-alpha gene family of Marmota himalayana,a Chinese marmot species with susceptibility to woodchuck hepatitis virus infection.Developmental & Comparative Immunology,32(4):445-457.
Ma Y,Wang H.2010.Epidemiologic characteristics of natural foci of plague in Qinghai Province from 1999 to 2009.Chinese Journal Endemiology,29(6):42-44.(in Chinese)
Ma Z J,Zhong J C,Han J L,Xu J T,Bai W L,Li J Y,Cairang D Z,Jin X Y,Zhang J.2010.Genetic diversity and demographic history of wild yak (Bos grunniens mutus) inferred from mtDNA D-loop sequences.African Journal of Biotechnology,9(46):7805-7810.
Millar C L,Libby W J.1991.Strategies for conserving clinal,ccotypic ,and disjunct population diversity in widespread species.In:Fald D A,Holsinger K E eds.Genetics and Conservation of Rare Plants.New York:Oxford University Press,149-170.
Mipam T D,Wen Y L,Fu C X,Li S R,Zhao H W,Ai Y,Li L,Zhang L,Zou D Q.2012.Maternal phylogeny of newly-found yak population in China.International Journal of Molecular Sciences,13(9):11455-11470.
Mora M S,Lessa E P,Cutrera A P,Kittlein M J,Vassallo A.2007.Phylogeographical structure in the subterranean tuco-tuco Ctenomys talarum (Rodentia:Ctenomyidae):contrasting the demographic consequences of regional and habitat-specific histories.Molecular Ecology,16(16):3453-3465.
Nei M.1987.Molecular Evolutionary Genetics.New York:Columbia University Press.
Nicolas V,Bryja J,Akpatou B,Konecny A,Lecompte E,Colyn M,Lalis A,Couloux A,Denys C,Granjon L.2008.Comparative phylogeography of two sibling species of forest-dwelling rodent (Praomys rostratus and P.tullbergi) in West Africa:different reactions to past forest fragmentation.Molecular Ecology,17(23):5118-5134.
Niu Y D,Li M Wei F W,Feng Z J.2001.Reliability of mtDNA as molecular marker and its perspective.Hereditas,23(6):593-598.(in Chinese)
Saccone C,Gissi C,Lanave C,Larizza A,Pesole G,Reyes A.2000.Evolution of the mitochondrial generic system:an over view.Gene,261(1):153-159.
Slatkin M,Barton N H.1989.A comparison of three indirect methods for estimating average levels of gene flow.Evolution,43:1349-1368.
Su B,Fu Y X,Wang Y X,Jin L,Chakraborty R.2001.Genetic diversity and population history of the red p and a as inferred from mitochondrial DNA sequence variations.Mol Biol Evol,18(6):70-76.
Tajima F.1989.Statistical method for testing the neutral mutation hypothesis by DNA polymorphism.Genetics,123(3):585-595.
Tajima F.1996.The amount of DNA polymorphism maintained in a finite population when the neutral mutation rate varies among sites.Genetics,143(3):1457-1465.
Tamura K,Stecher G,Peterson D,Filipski A,Kumar S.2013.MEGA 6:molecular evolutionary genetics analysis version 6.0.Molecular Biology Evolution,30(12):2725-2729.
Thompson J D,Gibson T J,Plewniak F,Jeanmougin F,Higgins D G.1997.The Clustal X windows interface:flexible strategies for multiple sequence alignment aided by quality analysis tools.Nucleic Acid Research,25(24):4876-4882.
Wright S.1949.The gentical structure of populations.Annals of Eugenics,15(1):323-354.
Xu J H,Wang L L,Xue H L,Wang Y S,Xu L X.2009.Microsatellite variation and genetic diversity in Marmota himalayana.Chinese Journal of Zoology,44(2):34-40.(in Chinese)
Xu W,Jameson D,Tang B,Higgs P G.2006.The relationship between the rate of molecular evolution and the rate of genome rearrangement in animal mitochondrial genomes.Journal Molecular Evolution,63(3):375-392.
Zhang T J,Li H F,Chen K W,Chang H,Tang Q P,Zhang J X.2007.Analysis on the genetic polymorphism and systematic evolution in domestic ducks by mitochondrial DNA D-loop region.Acta Veterinaria et Zootechnica Sinica,38(11):1168-1175.(in Chinese)
Zhou H,Li D Q,Zhang Y G,Yi X R,Liu Y.2006.Study on mitochondrial DNA genetic diversity of Tibetan antelope.Hereditas,28(3):299-305.(in Chinese)
牛屹东,李明,魏辅文,冯祚建.2001.线粒体DNA用作分子标记的可靠性和研究前景.遗传,23(6):593-598.
马英,王虎.2010.1990-2009年青海省鼠疫流行病学分析,中国地方病学杂志,29(6):42-44
李安意,王宝菊,田拥军,江敏,鲍俊杰,郝友华,喻植群,陆蒙吉,杨东亮.2006.中国早獭IL-10分子的克隆和序列分折.医学分子生物学杂志,3(5):344-346.
李增超,夏霖,杨奇森,梁孟元.2005.塔里木兔种群遗传结构的初步探讨.兽类学报,25(3):224-228.
张汤杰,李慧芳,陈宽维,常洪,汤青萍,张晶鑫.2007.利用线粒体D-loop区分析家鸭品种遗传多态性与系统进化.畜牧兽医学报,38(11):1168-1175.
陈星,沈永义,张亚平.2012.线粒体DNA在分子进化研究中的应用.动物学研究,33(6):566-573.
陈钦铭,叶子聪,夏寅明.1992.对不同年龄喜马拉雅旱獭大脑皮质结构与血液气体测定的比较研究.兽类学报,12(1):25-30.
周惠,李迪强,张于光,易湘蓉,刘毅.2006.藏羚羊mtDNA D-loop区遗传多样性研究.遗传,28(3):299-305.
徐金会,王琳琳,薛慧良,王玉山,徐来祥.2009.喜马拉雅旱獭种群微卫星变异及遗传多样性.动物学杂志,44(2):34-40.
黄凰,杨燕,刘嘉,张振华,田拥军,王宝菊,郝友华,杨东亮.2006.中国旱獭去唾液酸糖蛋白受体H1和H2亚基糖基识别域的原核表达及复性.医学分子生物学杂志,3(4):255-259.
常勇斌,杨奇森,温知新,夏霖,吕雪,程继龙,Andrey A L,侯建华,葛德燕.2016.间颅鼠兔的种群遗传结构和历史演化动态.兽类学报,36(4):373-387.
蔡振媛,张同作,慈海鑫,唐利洲,连新明,刘建全,苏建平.2007.高原鼢鼠线粒体谱系地理学和遗传多样性.兽类学报,27(2):130-137.
Bullerwell C E,Gray M W.2004.Evolution of the mitochondrial genome protist connections to animals,fungi and plants.Current Opinion in Microbiology,7(5):528-534.
Cai Z Y,Zhang T G,Ci H X,Tang L Z,Lian X M,Liu J Q,Su J P.2007.Mitochondrial phylogeography and genetic diversity of plateau zokor (Myospalax baileyi).Acta Therologica Sinica,27(2):130-137.(in Chinese)
Chang Y B,Yang Q S,Wen Z X,Xia L,Lv X,Cheng J L,Andrey A L,Hou J H,Ge D Y.2016.Population genetic structure and demographic history of Ochotona cansus (Lagomorpha,Ochotonidae).Acta Therologica Sinica,36(4):373-387.(in Chinese)
Chen Q M,Ye Y C,Xia Y M.1992.Comparative studies on the cerebral cortex structure and the blood gaseous.Acta Therologica Sinica,12(1):25-30.(in Chinese)
Chen X,Shen Y Y,Zhang Y P.2012.Review of mtDNA in molecular evolution studies.Zoological Research,33(6):566-573.(in Chinese)
Excoffier L,Laval G,Schneider S.2005.Arlequin (version 3.0):an integrated software package for population genetics data analysis.Evolutionary Bioinformatics Online,1:47-50.
Fu Y X.1997.Statistical tests of neutrality of mutations against population growth,hitchhiking and background selection.Genetics,147(2):915-925.
Harpending H C.1994.Signature of ancient population growth in a low-resolution mitochondrial DNA mismatch distribution.Human Biology,66(4):591–600.
Hirota T,Hirohata T,Mashima H,Mashima H,Satoh T,Obara Y.2004.Population structure of the large Japanese field mouse,Apodemus speciosus (Rodentia:Muridae),in suburban landscape,based on mitochondrial D-loop sequences.Molecular Ecology,13(11):3275-3282.
Huang H,Yang Y,Liu J,Zhang Z H,Tian Y J,Wang B J,Hao Y H,Yang D L.2006.Prokaryotic expression,purification and renaturation of CRDH1 and CRDH2 of Chinese marmata asialoglycoprotein receptor.Journal Medical Molecular Biology,3(4):255-259.(in Chinese)
Imsiridou A,Triantafyllidis A,Baxevanis A D,Triantaphyllidis C.2009.Genetic characterization of common carp (Cyprinus carpio) populations from Greece using mitochondrial DNA sequences.Biologia,64(4):781-785.
Li A Y,Wang B J,Tian Y J,Jiang M,Bao J J,Hao Y H,Yu Z Q,Lu M J,Yang D L.2006.Cloning and sequence analysis of Chinese Marmot interleukin-10.Journal Medical Molecular Biology,3(5):344-346.(in Chinese)
Li Z C,Xia L,Yang Q S,Liang M Y.2005.Population genetic structure of the yarkand hare (Lepus yarkandensis).Acta Therologica Sinica,25(3):224-228.(in Chinese)
Librado P,Rozas J.2009.DnaSP v5:a software for comprehensive analysis of DNA polymorphism data.Bioinformatics,25(11):1451-1452.
Lu Y,Wang B,Huang H,Tian Y J,Dong J H,Lu M J,Yang D L.2008.The interferon-alpha gene family of Marmota himalayana,a Chinese marmot species with susceptibility to woodchuck hepatitis virus infection.Developmental & Comparative Immunology,32(4):445-457.
Ma Y,Wang H.2010.Epidemiologic characteristics of natural foci of plague in Qinghai Province from 1999 to 2009.Chinese Journal Endemiology,29(6):42-44.(in Chinese)
Ma Z J,Zhong J C,Han J L,Xu J T,Bai W L,Li J Y,Cairang D Z,Jin X Y,Zhang J.2010.Genetic diversity and demographic history of wild yak (Bos grunniens mutus) inferred from mtDNA D-loop sequences.African Journal of Biotechnology,9(46):7805-7810.
Millar C L,Libby W J.1991.Strategies for conserving clinal,ccotypic ,and disjunct population diversity in widespread species.In:Fald D A,Holsinger K E eds.Genetics and Conservation of Rare Plants.New York:Oxford University Press,149-170.
Mipam T D,Wen Y L,Fu C X,Li S R,Zhao H W,Ai Y,Li L,Zhang L,Zou D Q.2012.Maternal phylogeny of newly-found yak population in China.International Journal of Molecular Sciences,13(9):11455-11470.
Mora M S,Lessa E P,Cutrera A P,Kittlein M J,Vassallo A.2007.Phylogeographical structure in the subterranean tuco-tuco Ctenomys talarum (Rodentia:Ctenomyidae):contrasting the demographic consequences of regional and habitat-specific histories.Molecular Ecology,16(16):3453-3465.
Nei M.1987.Molecular Evolutionary Genetics.New York:Columbia University Press.
Nicolas V,Bryja J,Akpatou B,Konecny A,Lecompte E,Colyn M,Lalis A,Couloux A,Denys C,Granjon L.2008.Comparative phylogeography of two sibling species of forest-dwelling rodent (Praomys rostratus and P.tullbergi) in West Africa:different reactions to past forest fragmentation.Molecular Ecology,17(23):5118-5134.
Niu Y D,Li M Wei F W,Feng Z J.2001.Reliability of mtDNA as molecular marker and its perspective.Hereditas,23(6):593-598.(in Chinese)
Saccone C,Gissi C,Lanave C,Larizza A,Pesole G,Reyes A.2000.Evolution of the mitochondrial generic system:an over view.Gene,261(1):153-159.
Slatkin M,Barton N H.1989.A comparison of three indirect methods for estimating average levels of gene flow.Evolution,43:1349-1368.
Su B,Fu Y X,Wang Y X,Jin L,Chakraborty R.2001.Genetic diversity and population history of the red p and a as inferred from mitochondrial DNA sequence variations.Mol Biol Evol,18(6):70-76.
Tajima F.1989.Statistical method for testing the neutral mutation hypothesis by DNA polymorphism.Genetics,123(3):585-595.
Tajima F.1996.The amount of DNA polymorphism maintained in a finite population when the neutral mutation rate varies among sites.Genetics,143(3):1457-1465.
Tamura K,Stecher G,Peterson D,Filipski A,Kumar S.2013.MEGA 6:molecular evolutionary genetics analysis version 6.0.Molecular Biology Evolution,30(12):2725-2729.
Thompson J D,Gibson T J,Plewniak F,Jeanmougin F,Higgins D G.1997.The Clustal X windows interface:flexible strategies for multiple sequence alignment aided by quality analysis tools.Nucleic Acid Research,25(24):4876-4882.
Wright S.1949.The gentical structure of populations.Annals of Eugenics,15(1):323-354.
Xu J H,Wang L L,Xue H L,Wang Y S,Xu L X.2009.Microsatellite variation and genetic diversity in Marmota himalayana.Chinese Journal of Zoology,44(2):34-40.(in Chinese)
Xu W,Jameson D,Tang B,Higgs P G.2006.The relationship between the rate of molecular evolution and the rate of genome rearrangement in animal mitochondrial genomes.Journal Molecular Evolution,63(3):375-392.
Zhang T J,Li H F,Chen K W,Chang H,Tang Q P,Zhang J X.2007.Analysis on the genetic polymorphism and systematic evolution in domestic ducks by mitochondrial DNA D-loop region.Acta Veterinaria et Zootechnica Sinica,38(11):1168-1175.(in Chinese)
Zhou H,Li D Q,Zhang Y G,Yi X R,Liu Y.2006.Study on mitochondrial DNA genetic diversity of Tibetan antelope.Hereditas,28(3):299-305.(in Chinese)
牛屹东,李明,魏辅文,冯祚建.2001.线粒体DNA用作分子标记的可靠性和研究前景.遗传,23(6):593-598.
马英,王虎.2010.1990-2009年青海省鼠疫流行病学分析,中国地方病学杂志,29(6):42-44
李安意,王宝菊,田拥军,江敏,鲍俊杰,郝友华,喻植群,陆蒙吉,杨东亮.2006.中国早獭IL-10分子的克隆和序列分折.医学分子生物学杂志,3(5):344-346.
李增超,夏霖,杨奇森,梁孟元.2005.塔里木兔种群遗传结构的初步探讨.兽类学报,25(3):224-228.
张汤杰,李慧芳,陈宽维,常洪,汤青萍,张晶鑫.2007.利用线粒体D-loop区分析家鸭品种遗传多态性与系统进化.畜牧兽医学报,38(11):1168-1175.
陈星,沈永义,张亚平.2012.线粒体DNA在分子进化研究中的应用.动物学研究,33(6):566-573.
陈钦铭,叶子聪,夏寅明.1992.对不同年龄喜马拉雅旱獭大脑皮质结构与血液气体测定的比较研究.兽类学报,12(1):25-30.
周惠,李迪强,张于光,易湘蓉,刘毅.2006.藏羚羊mtDNA D-loop区遗传多样性研究.遗传,28(3):299-305.
徐金会,王琳琳,薛慧良,王玉山,徐来祥.2009.喜马拉雅旱獭种群微卫星变异及遗传多样性.动物学杂志,44(2):34-40.
黄凰,杨燕,刘嘉,张振华,田拥军,王宝菊,郝友华,杨东亮.2006.中国旱獭去唾液酸糖蛋白受体H1和H2亚基糖基识别域的原核表达及复性.医学分子生物学杂志,3(4):255-259.
常勇斌,杨奇森,温知新,夏霖,吕雪,程继龙,Andrey A L,侯建华,葛德燕.2016.间颅鼠兔的种群遗传结构和历史演化动态.兽类学报,36(4):373-387.
蔡振媛,张同作,慈海鑫,唐利洲,连新明,刘建全,苏建平.2007.高原鼢鼠线粒体谱系地理学和遗传多样性.兽类学报,27(2):130-137.