DNA条形码在西藏水系裂腹鱼亚科鱼类鉴定中的研究
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摘要
为确定DNA条形码技术在西藏水系裂腹鱼亚科(Schizothoracinae)物种鉴定中的可行性,利用西藏水系所采集260尾裂腹鱼亚科样本,测定其线粒体细胞色素C氧化酶亚基1(COI)基因片段序列,计算遗传距离,构建系统发育树,并与GenBank中相关序列进行比对。260个样本经检测均获得有效COI基因扩增片段,COI基因碱基组成偏倚明显,A+T含量为54.74%,显著高于G+C含量(45.26%)。基于Kimura双参数模型计算遗传距离,遗传距离阈值设置为0.02时,260个样本可被鉴定到种的为249尾样本,11尾由于样本量少,数据库中存在多个命名,只鉴定到属,其中与形态学鉴定一致的179尾样本,一致率为68.8%,裂腹鱼亚科裸鲤属(Gymnocypris)不能通过COI基因鉴定到种,拉萨裂腹鱼(Schizothoracinae)、异齿裂腹鱼(S.schizothorax oʼconnori)、巨须裂腹鱼(S.macropogon)3个种之间的遗传距离阈值以0.02不能有效鉴别,而遗传距离阈值以0.01作为这3个种的鉴定标准,可达到有效鉴别的目的。基于邻接法构建系统发育树,裂腹鱼亚科鱼类形成一个支持率较高的单系群,Bootstrap检验支持率为99%,系统进化树聚类方式与以遗传距离值为标准的鉴定结果一致,很好地反映了水系物种间的地理和历史联系。
There are more than 40 species of Schizothoracinae in Tibet water system.For the similitude of morphologically between individual within the genus,it is restricted to identified them by traditional morphology.The COI gene fragments from260 individuals of Schizothoracinae were amplified and sequenced to test the applicability of DNA barcode technology in the species identification of schizothoracinae in Tibet water system.Meanwhile,the genetic distance was calculated,the phylogenetic tree was constructed,and the sequences alignment was carried out through the databases of GenBank.This research obtained available gene fragments of the COI from 260 individuals,the base compositions of COI genes were significantly biased.The contents of A+T were 54.74%,which were significantly higher than that of G+C(45.26%).The species identification standard of Schizothroacinae were calculated based on Kimura two parameter model as the genetic distance was set in 0.02.The results showed that 249 individuals among 260 could be identified to the species,however,11 individuals of them were identified as genus because of small sample sizes and multiple naming.The identification results of 179 individuals accorded with morphology,the accordant rate was 68.8%.The individuals in the genus of Gymnocypris of Schizothroacinae could not be identified through DNA barcode technology based on COI gene.Among S.racoma waltoni,S.schizothorax oʼconnori and S. macropogon could not be identified based on the genetic distance value of 0.02,but the value of 0.01 could effective identified.The phylogenetic tree based on Neighbor-Joining method indicated that schizothroachinae was a simple group with 99% approval rating of Bootstrap test.The cluster pattern of phylogenetic tree had the consistent results of identification by standard of genetic distance value.The relationship of geography and history between water system were primely responded by the phylogenetic tree.
There are more than 40 species of Schizothoracinae in Tibet water system.For the similitude of morphologically between individual within the genus,it is restricted to identified them by traditional morphology.The COI gene fragments from260 individuals of Schizothoracinae were amplified and sequenced to test the applicability of DNA barcode technology in the species identification of schizothoracinae in Tibet water system.Meanwhile,the genetic distance was calculated,the phylogenetic tree was constructed,and the sequences alignment was carried out through the databases of GenBank.This research obtained available gene fragments of the COI from 260 individuals,the base compositions of COI genes were significantly biased.The contents of A+T were 54.74%,which were significantly higher than that of G+C(45.26%).The species identification standard of Schizothroacinae were calculated based on Kimura two parameter model as the genetic distance was set in 0.02.The results showed that 249 individuals among 260 could be identified to the species,however,11 individuals of them were identified as genus because of small sample sizes and multiple naming.The identification results of 179 individuals accorded with morphology,the accordant rate was 68.8%.The individuals in the genus of Gymnocypris of Schizothroacinae could not be identified through DNA barcode technology based on COI gene.Among S.racoma waltoni,S.schizothorax oʼconnori and S. macropogon could not be identified based on the genetic distance value of 0.02,but the value of 0.01 could effective identified.The phylogenetic tree based on Neighbor-Joining method indicated that schizothroachinae was a simple group with 99% approval rating of Bootstrap test.The cluster pattern of phylogenetic tree had the consistent results of identification by standard of genetic distance value.The relationship of geography and history between water system were primely responded by the phylogenetic tree.
引文
[1]赵新全,祁得林,杨洁.青藏高原代表性土著动物分子进化与适应研究[M].北京:科学出版社,2008:13-69.
[2]曹文宣,陈宜瑜,武云飞,等.裂腹鱼类的起源和演化及其与青藏高原的隆起关系[A]//中国科学院青藏高原综合科学考察队.青藏高原隆起的时代、幅度和形式问题[M].北京:科学出版社,1981.
[3]周建设,李宝海,潘瑛子,等.西藏渔业资源调查研究进展[J].中国农学通报,2013,29(5):53-57.
[4]曹文宣.裂腹鱼亚科鱼类的分类[A]//伍献文.中国鲤科鱼类志[M].上海:上海科学技术出版社,1964:137-197.
[5]徐春燕,沈长春,蔡建堤,等.基于COI基因的福建近海部分仔稚鱼DNA条形码分析[J].中国水产科学,2017,24(6):1176-1183.
[6] Ariagna L,Jose L P D L,Rodet R,et al.DNA barcoding of Cuban freshwater fishes:evidence for cryptic species and taxonomic conflicts [J].Mol Ecol Resour,2010,10(3):421-430.
[7] Alba A,Ana R L,Josino C M,et al.DNA barcoding for conservation and management of Amazonian commercial fish [J].Biol Conserv,2010,143(6):1438-1443.
[8] Mayara A B,Horacio S,Iracilda S,et al.DNA barcoding reveal high substitution rate and mislabeling in croaker fillets(Sciaenidae)marketed in Brazil:The case of “pescada branca”(Cynoscion leiarchus and Plagioscion squamosissimus)[J].Food Res Int,2015,70:40-46.
[9] He D K,Chen Y F.Biogeography and molecular phylogeny of the genus Schizothorax(Teleostei:Cyprinidae)in Chin inferred from cytochrome b sequences [J].J Biogeogr,2006,33(8):1448-1460.
[10]产久林,姜华鹏,刘一萌,等.COI和16S rRNA基因在高原裂腹鱼物种鉴定中的应用[J].水生态学杂志,2015,36(4):98-104.
[11]朱挺兵,刘海平,李学梅,等.西藏鱼类增殖放流初报[J].淡水渔业,2017,47(5):34-39.
[12]黄燕.长江上游特有鱼类DNA条形码研究[D].重庆:西南大学,2014.
[13]乐佩琦,单乡红,林人端,等.中国动物志-硬骨鱼纲,鲤形目(下卷)[M].北京:科学出版社,2000:273-390.
[14]周美玉,陈骁,杨圣云.采用DNA条形码技术对厦门海域鱼卵、仔稚鱼种类的鉴定[J].海洋环境科学,2015,34(1):120-125,135.
[15] Hui L K,Yu T W,Tai S C,et al.Evaluating the accuracy of morphological identification of larval fishes by applying DNA barcoding [J].PLOS one,2013,8(1):1-7.
[16] Robert D W,Tyler S Z,Bronwyn H I,et al.DNA barcoding Astralia?s fish species [J].Philos Trans R Soc B,2005,360(1462):1847-1857.
[17] Zardoy R,Doadrio I.Molecular evidence on the evolutionary and biogeographical patterns of European cyprinids [J].J Mol Evol,1999,49(2):227-237.
[18] Jian H,Qin X,Zhen J S,et al.Identifying earthworms through DNA barcodes [J].Pedobiologia,2007,51(4):301-309.
[19]曹文宣,邓中粦.四川西部及其邻近地区的裂腹鱼类[J].水生生物学集刊,1962,(2):27-53.
[20]张春霖,岳佐和,黄宏金.西藏南部的裸鲤属(Gymnocypris)鱼类[J].动物学报,1964,16(1):139-150.
[21]武云飞,朱松泉.西藏阿里鱼类分类、区系研究及资源概况[A]//西藏阿里地区动植物考察报告[M].北京:科学出版社,1979.
[22] Rudolf M,Kwong S,Gaurav V,et al.DNA barcoding and taxonomy in diptera:A tale of high intraspecific variability and low identification success [J].Systhemat Biol,2006,55(5):715-728.
[23] Collins R A,Cruickshank R H.The seven deadly sins of DNA barcoding [J].Mol Ecol Resour,2013,13(6):969-975.
[24] Maizatul I M,Maryam Z F,Peter B M,et al.Molecular characterization of relatedness among colour variants of Asian Arowana(Scleropages formosus)[J].Gene,2011,490(1-2):47-53.
[25]陈信忠,郭书林,龚艳清.DNA条形码技术在主要观赏鱼物种鉴定中的应用分析[J].渔业研究,2017,39(1):8-14.
[26]何德奎,陈毅峰.高度特化等级裂腹鱼类分子系统发育与生物地理学[J].科学通报,2007,52(3):303-312.
[2]曹文宣,陈宜瑜,武云飞,等.裂腹鱼类的起源和演化及其与青藏高原的隆起关系[A]//中国科学院青藏高原综合科学考察队.青藏高原隆起的时代、幅度和形式问题[M].北京:科学出版社,1981.
[3]周建设,李宝海,潘瑛子,等.西藏渔业资源调查研究进展[J].中国农学通报,2013,29(5):53-57.
[4]曹文宣.裂腹鱼亚科鱼类的分类[A]//伍献文.中国鲤科鱼类志[M].上海:上海科学技术出版社,1964:137-197.
[5]徐春燕,沈长春,蔡建堤,等.基于COI基因的福建近海部分仔稚鱼DNA条形码分析[J].中国水产科学,2017,24(6):1176-1183.
[6] Ariagna L,Jose L P D L,Rodet R,et al.DNA barcoding of Cuban freshwater fishes:evidence for cryptic species and taxonomic conflicts [J].Mol Ecol Resour,2010,10(3):421-430.
[7] Alba A,Ana R L,Josino C M,et al.DNA barcoding for conservation and management of Amazonian commercial fish [J].Biol Conserv,2010,143(6):1438-1443.
[8] Mayara A B,Horacio S,Iracilda S,et al.DNA barcoding reveal high substitution rate and mislabeling in croaker fillets(Sciaenidae)marketed in Brazil:The case of “pescada branca”(Cynoscion leiarchus and Plagioscion squamosissimus)[J].Food Res Int,2015,70:40-46.
[9] He D K,Chen Y F.Biogeography and molecular phylogeny of the genus Schizothorax(Teleostei:Cyprinidae)in Chin inferred from cytochrome b sequences [J].J Biogeogr,2006,33(8):1448-1460.
[10]产久林,姜华鹏,刘一萌,等.COI和16S rRNA基因在高原裂腹鱼物种鉴定中的应用[J].水生态学杂志,2015,36(4):98-104.
[11]朱挺兵,刘海平,李学梅,等.西藏鱼类增殖放流初报[J].淡水渔业,2017,47(5):34-39.
[12]黄燕.长江上游特有鱼类DNA条形码研究[D].重庆:西南大学,2014.
[13]乐佩琦,单乡红,林人端,等.中国动物志-硬骨鱼纲,鲤形目(下卷)[M].北京:科学出版社,2000:273-390.
[14]周美玉,陈骁,杨圣云.采用DNA条形码技术对厦门海域鱼卵、仔稚鱼种类的鉴定[J].海洋环境科学,2015,34(1):120-125,135.
[15] Hui L K,Yu T W,Tai S C,et al.Evaluating the accuracy of morphological identification of larval fishes by applying DNA barcoding [J].PLOS one,2013,8(1):1-7.
[16] Robert D W,Tyler S Z,Bronwyn H I,et al.DNA barcoding Astralia?s fish species [J].Philos Trans R Soc B,2005,360(1462):1847-1857.
[17] Zardoy R,Doadrio I.Molecular evidence on the evolutionary and biogeographical patterns of European cyprinids [J].J Mol Evol,1999,49(2):227-237.
[18] Jian H,Qin X,Zhen J S,et al.Identifying earthworms through DNA barcodes [J].Pedobiologia,2007,51(4):301-309.
[19]曹文宣,邓中粦.四川西部及其邻近地区的裂腹鱼类[J].水生生物学集刊,1962,(2):27-53.
[20]张春霖,岳佐和,黄宏金.西藏南部的裸鲤属(Gymnocypris)鱼类[J].动物学报,1964,16(1):139-150.
[21]武云飞,朱松泉.西藏阿里鱼类分类、区系研究及资源概况[A]//西藏阿里地区动植物考察报告[M].北京:科学出版社,1979.
[22] Rudolf M,Kwong S,Gaurav V,et al.DNA barcoding and taxonomy in diptera:A tale of high intraspecific variability and low identification success [J].Systhemat Biol,2006,55(5):715-728.
[23] Collins R A,Cruickshank R H.The seven deadly sins of DNA barcoding [J].Mol Ecol Resour,2013,13(6):969-975.
[24] Maizatul I M,Maryam Z F,Peter B M,et al.Molecular characterization of relatedness among colour variants of Asian Arowana(Scleropages formosus)[J].Gene,2011,490(1-2):47-53.
[25]陈信忠,郭书林,龚艳清.DNA条形码技术在主要观赏鱼物种鉴定中的应用分析[J].渔业研究,2017,39(1):8-14.
[26]何德奎,陈毅峰.高度特化等级裂腹鱼类分子系统发育与生物地理学[J].科学通报,2007,52(3):303-312.