印度-太平洋石鲈亚科鱼类DNA条形码及分子系统进化研究
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摘要
为探讨DNA条形码基因COⅠ序列在石鲈亚科鱼类物种鉴定的有效性,本研究分析了印度-太平洋区域的石鲈亚科7个属29种鱼类9个个体长度为651 bp的COⅠ基因序列,利用MEGA 5.0计算石鲈亚科种内与种间的遗传距离,并基于最大简约法与最大似然法构建了其分子系统进化关系。结果显示:石鲈亚科鱼类种间遗传距离在0.021—0.240之间,平均遗传距离0.184;种内遗传距离在0.000—0.009之间,平均0.004。其中种间平均遗传距离(0.184)显著大于种内平均遗传距离(0.004),种间遗传距离是种内的46倍。同时,各物种间遗传距离均大于Hebert推荐区分物种的最小种间遗传距离0.02(2%)。基于COⅠ序列构建的系统进化树,同一物种不同个体间均能聚成独立的单系,表明COⅠ基因可作为石鲈亚科物种准确鉴定的有效条形码基因。同时,系统进化树上,石鲈属是非单系类群,主要形成5个分支,而不同分支的种类与其地理分布存在一定的相关性,与近年部分分子系统地理学的研究观点一致。
To investigate the feasibility of using COⅠ sequences as DNA barcodes to identify Haemulinae species, we determined the 651 bp COⅠ sequences of 91 Haemulinae individuals sampled from 7 genera 29 species, calculated the genetic distances inter- and intra-species using MEGA 5.0, and constructed the molecular phylogenetic trees using maximum parsimony and maximum likelihood methods. The result show that the inter-species genetic distance was 0.021—0.240 in average of 0.184, while that of intra-species was 0.000—0.009 in average of 0.004. The average inter-species value(0.184) is 46 times larger than that of intra-species one(0.004). Moreover, each inter-species genetic distance value is larger than the minimum species identification value 0.200(2%) suggested by Hebert. In the molecular phylogenetic trees, individuals of each species formed an independent monophyletic group, indicating that COⅠ could be used as an effective barcode gene for accurate identification among Haemulinae species. Meanwhile, as the phylogenetic trees show, the Pomadasys fish are non-monophyletic and form 5 independent groups. Such phylogenetic relationships are due to their geographic distribution, which is consistent with the viewpoint of modern molecular phylogeography studies.
To investigate the feasibility of using COⅠ sequences as DNA barcodes to identify Haemulinae species, we determined the 651 bp COⅠ sequences of 91 Haemulinae individuals sampled from 7 genera 29 species, calculated the genetic distances inter- and intra-species using MEGA 5.0, and constructed the molecular phylogenetic trees using maximum parsimony and maximum likelihood methods. The result show that the inter-species genetic distance was 0.021—0.240 in average of 0.184, while that of intra-species was 0.000—0.009 in average of 0.004. The average inter-species value(0.184) is 46 times larger than that of intra-species one(0.004). Moreover, each inter-species genetic distance value is larger than the minimum species identification value 0.200(2%) suggested by Hebert. In the molecular phylogenetic trees, individuals of each species formed an independent monophyletic group, indicating that COⅠ could be used as an effective barcode gene for accurate identification among Haemulinae species. Meanwhile, as the phylogenetic trees show, the Pomadasys fish are non-monophyletic and form 5 independent groups. Such phylogenetic relationships are due to their geographic distribution, which is consistent with the viewpoint of modern molecular phylogeography studies.
引文
毛云涛,甘小妮,王绪祯,2014.基于线粒体COⅠ基因的沙鳅亚科鱼类DNA条形码及其分子系统发育研究.水生生物学报,38(4):737-744
成庆泰,郑葆珊,1987.中国鱼类系统检索.北京:科学出版社,339-341
朱世华,郑文娟,邹记兴等,2006.5种石鲈科鱼类细胞色素b基因序列及分子系统分析.热带海洋学报,25(4):42-45
任岗,章群,钱开诚等,2007.12种石鲈科鱼类线粒体16Sr RNA基因的部分序列分析.热带海洋学报,26(3):48-52
沈世杰,1993.台湾鱼类志.台北:台湾大学动物学系出版,360-363
宋超,于亚男,张涛等,2014.基于线粒体COⅠ基因部分序列的长江口舌鳎科鱼类系统分类研究.动物学杂志,49(5):716-726
孟庆闻,苏锦祥,缪学祖,1995.鱼类分类学.北京:中国农业出版社,636-640
黄宗国,1994.中国海洋生物种类与分布.北京:海洋出版社,708-709
Carpenter K E,Niem V H,2001.FAO Species Identification Guide for Fishery Purposes.ISSN 1020-6868.The Living Marine Resources of the Western Central Pacific.Volume 5:Bony fishes part 3(Menidae to Pomacentridae).FAO,Rome,2961-2989
FAO-FIES,2014.Aquatic Sciences and Fisheries Information System(ASFIS)species list.http://www.fao.org/fishery/collection/asfis/en
Froese R,Pauly D,2013.Fish Base.World Wide Web Electronic Publication.www.fishbase.org,version(9/2013)
Hebert P D N,Cywinska A,Ball S L et al,2003a.Biological identifications through DNA barcodes.Proc R Soc Lond B,270(1512):313-321
Hebert P D N,Ratnasingham S,de Waard J R,2003b.Barcoding animal life:cytochrome c oxidase subunit 1 divergences among closely related species.Proc R Soc Lond B,270(S1):S96-S99
Hubert N,Hanner R,Holm E et al,2008.Identifying Canadian freshwater fishes through DNA barcodes.Plos One,3(6):e2490
Johnson S B,Warén A,Vrijenhoek R C,2008.DNA barcoding of Lepetodrilus limpets reveals cryptic species.J Shellfish Res,27(1):43-51
Jordan D S,Gilbert C H,1882.Synopsis of the fishes of North America.Bulletin of the United States National Museum,16:1-1018
Keskin E,A?damar S,Tarkan A S,2013.DNA barcoding common non-native freshwater fish species in Turkey:Low genetic diversity but high population structuring.Mitochondrial DNA,24(3):276-287
Keskin E,Atar H H,2013.DNA barcoding commercially important fish species of Turkey.Mol Ecol Resour,13(5):788-797
López M,1981.Los"roncadores"del género Pomadasys(Haemulopsis)(Pisces:Haemulidae)de la costa Pacífica de Centro América.Rev Biol Trop,29(1):83-94
Mckay R J,1984.Haemulidae.In:Fischer W,Bianchi G eds.FAO species identification sheets for fishery purposes.Western Indian Ocean(Fishing Area 51).Vol.2.FAO,Rome
Pereira L H G,Hanner R,Foresti F et al,2013.Can DNAbarcoding accurately discriminate megadiverse Neotropical freshwater fish fauna?BMC Genet,14:20
Randall J E,2005.Reef and Shore Fishes of the South Pacific:New Caledonia to Tahiti and the Pitcairn Islands.Honolulu,Hawaii:University of Hawaii Press,720
Sanciangco M D,Rocha L A,Carpenter K E,2011.A molecular phylogeny of the Grunts(Perciformes:Haemulidae)inferred using mitochondrial and nuclear genes.Zootaxa,2966:37-50
Schlei O L,Crête-Lafrenière A,Whiteley A R et al,2008.DNAbarcoding of eight North American coregonine species.Mol Ecol Resour,8(6):1212-1218
Swofford D P,2003.Phylogenetic Analysis Using Parsimony(and Other Methods)Version 10.Sunderland,MA:Sinauer
Tamura K,Peterson D,Peterson N et al,2011.MEGA5:Molecular evolutionary genetics analysis using maximum likelihood,evolutionary distance,and maximum parsimony methods.Mol Biol Evol,28(10):2731-2739
Tavera J J,Acero P A,Balart E F et al,2012.Molecular phylogeny of grunts(Teleostei,Haemulidae),with an emphasis on the ecology,evolution,and speciation history of New World species.BMC Evol Biol,12:57
Thompson J D,Higgins D G,Gibson T J,1994.CLUSTAL W:improving the sensitivity of progressive multiple sequence alignment through sequence weighting,position-specific gap penalties and weight matrix choice.Nucl Acids Res,22(22):4673-4680
Ward R D,Zemlak T S,Innes B H et al,2005.DNA barcoding Australia’s fish species.Phil Trans R Soc B,360:1847-1857
成庆泰,郑葆珊,1987.中国鱼类系统检索.北京:科学出版社,339-341
朱世华,郑文娟,邹记兴等,2006.5种石鲈科鱼类细胞色素b基因序列及分子系统分析.热带海洋学报,25(4):42-45
任岗,章群,钱开诚等,2007.12种石鲈科鱼类线粒体16Sr RNA基因的部分序列分析.热带海洋学报,26(3):48-52
沈世杰,1993.台湾鱼类志.台北:台湾大学动物学系出版,360-363
宋超,于亚男,张涛等,2014.基于线粒体COⅠ基因部分序列的长江口舌鳎科鱼类系统分类研究.动物学杂志,49(5):716-726
孟庆闻,苏锦祥,缪学祖,1995.鱼类分类学.北京:中国农业出版社,636-640
黄宗国,1994.中国海洋生物种类与分布.北京:海洋出版社,708-709
Carpenter K E,Niem V H,2001.FAO Species Identification Guide for Fishery Purposes.ISSN 1020-6868.The Living Marine Resources of the Western Central Pacific.Volume 5:Bony fishes part 3(Menidae to Pomacentridae).FAO,Rome,2961-2989
FAO-FIES,2014.Aquatic Sciences and Fisheries Information System(ASFIS)species list.http://www.fao.org/fishery/collection/asfis/en
Froese R,Pauly D,2013.Fish Base.World Wide Web Electronic Publication.www.fishbase.org,version(9/2013)
Hebert P D N,Cywinska A,Ball S L et al,2003a.Biological identifications through DNA barcodes.Proc R Soc Lond B,270(1512):313-321
Hebert P D N,Ratnasingham S,de Waard J R,2003b.Barcoding animal life:cytochrome c oxidase subunit 1 divergences among closely related species.Proc R Soc Lond B,270(S1):S96-S99
Hubert N,Hanner R,Holm E et al,2008.Identifying Canadian freshwater fishes through DNA barcodes.Plos One,3(6):e2490
Johnson S B,Warén A,Vrijenhoek R C,2008.DNA barcoding of Lepetodrilus limpets reveals cryptic species.J Shellfish Res,27(1):43-51
Jordan D S,Gilbert C H,1882.Synopsis of the fishes of North America.Bulletin of the United States National Museum,16:1-1018
Keskin E,A?damar S,Tarkan A S,2013.DNA barcoding common non-native freshwater fish species in Turkey:Low genetic diversity but high population structuring.Mitochondrial DNA,24(3):276-287
Keskin E,Atar H H,2013.DNA barcoding commercially important fish species of Turkey.Mol Ecol Resour,13(5):788-797
López M,1981.Los"roncadores"del género Pomadasys(Haemulopsis)(Pisces:Haemulidae)de la costa Pacífica de Centro América.Rev Biol Trop,29(1):83-94
Mckay R J,1984.Haemulidae.In:Fischer W,Bianchi G eds.FAO species identification sheets for fishery purposes.Western Indian Ocean(Fishing Area 51).Vol.2.FAO,Rome
Pereira L H G,Hanner R,Foresti F et al,2013.Can DNAbarcoding accurately discriminate megadiverse Neotropical freshwater fish fauna?BMC Genet,14:20
Randall J E,2005.Reef and Shore Fishes of the South Pacific:New Caledonia to Tahiti and the Pitcairn Islands.Honolulu,Hawaii:University of Hawaii Press,720
Sanciangco M D,Rocha L A,Carpenter K E,2011.A molecular phylogeny of the Grunts(Perciformes:Haemulidae)inferred using mitochondrial and nuclear genes.Zootaxa,2966:37-50
Schlei O L,Crête-Lafrenière A,Whiteley A R et al,2008.DNAbarcoding of eight North American coregonine species.Mol Ecol Resour,8(6):1212-1218
Swofford D P,2003.Phylogenetic Analysis Using Parsimony(and Other Methods)Version 10.Sunderland,MA:Sinauer
Tamura K,Peterson D,Peterson N et al,2011.MEGA5:Molecular evolutionary genetics analysis using maximum likelihood,evolutionary distance,and maximum parsimony methods.Mol Biol Evol,28(10):2731-2739
Tavera J J,Acero P A,Balart E F et al,2012.Molecular phylogeny of grunts(Teleostei,Haemulidae),with an emphasis on the ecology,evolution,and speciation history of New World species.BMC Evol Biol,12:57
Thompson J D,Higgins D G,Gibson T J,1994.CLUSTAL W:improving the sensitivity of progressive multiple sequence alignment through sequence weighting,position-specific gap penalties and weight matrix choice.Nucl Acids Res,22(22):4673-4680
Ward R D,Zemlak T S,Innes B H et al,2005.DNA barcoding Australia’s fish species.Phil Trans R Soc B,360:1847-1857