DNA barcoding Australia's fish species
DNA barcoding Australia's fish species
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DOI：
10.1098/rstb.2005.1716
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发表时间：
2005-10-29
影响因子：
6.3
通讯作者：
Hebert, PDN
中科院分区：
文献类型：
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作者：
Ward, RD;Zemlak, TS;Hebert, PDN
对 207 种鱼类（主要是澳大利亚海洋鱼类）的线粒体细胞色素氧化酶亚基 I 基因 (cox1) 的 655 bp 区域进行了测序（条形码）。大多数物种由多个标本代表，并生成了 754 个序列。 143 种硬骨鱼的 GC 含量高于 61 种鲨鱼和鳐鱼（47.1% 比 42.2%），这主要是由于前者密码子 3 位的 GC 含量较高（41.1% 比 29.9%）。鳐鱼的 GC 值高于鲨鱼（44.7% 比 41.0%），这主要是由于鳐鱼第三个密码子位置的 GC 值更高（36.3% 比 26.8%）。种内、属内、科内、目内和纲内木村二参数（K2P）平均距离分别为0.39%、9.93%、15.46%、22.18%和23.27%。所有物种都可以通过它们的 cox1 序列来区分，尽管两个物种中的每一个的单个个体都具有同系物的单倍型特征。尽管 DNA 条形码旨在开发物种识别系统，但数据中仍存在一些明显的系统发育信号。在所有 754 个序列的邻接树中，明显有四个主要簇：银鲛科动物、鳐鱼、鲨鱼和硬骨鱼。属内的物种总是聚集在一起，科内的属通常也是如此。对三个分类群——角鲨属的角鲨、扁头鱼科的平头鱼和金枪鱼属的金枪鱼——进行了更仔细的研究。引导后发现的进化枝总体上与预期相符。来自被指定为角鲨属物种 B 至 F 的操作分类单位的个体形成了单独的进化枝，支持了每个物种都是独立物种的形态学证据。我们得出的结论是，cox1 测序或“条形码”可用于识别鱼类物种。
Two hundred and seven species of fish, mostly Australian marine fish, were sequenced (barcoded) for a 655 bp region of the mitochondrial cytochrome oxidase subunit I gene (cox1). Most species were represented by multiple specimens, and 754 sequences were generated. The GC content of the 143 species of teleosts was higher than the 61 species of sharks and rays (47.1% versus 42.2%), largely due to a higher GC content of codon position 3 in the former (41.1% versus 29.9%). Rays had higher GC than sharks (44.7% versus 41.0%), again largely due to higher GC in the 3rd codon position in the former (36.3% versus 26.8%). Average within-species, genus, family, order and class Kimura two parameter (K2P) distances were 0.39%, 9.93%, 15.46%, 22.18% and 23.27%, respectively. All species could be differentiated by their cox1 sequence, although single individuals of each of two species had haplotypes characteristic of a congener. Although DNA barcoding aims to develop species identification systems, some phylogenetic signal was apparent in the data. In the neighbour-joining tree for all 754 sequences, four major clusters were apparent: chimaerids, rays, sharks and teleosts. Species within genera invariably clustered, and generally so did genera within families. Three taxonomic groups-dogfishes of the genus Squalus, flatheads of the family Platycephalidae, and tunas of the genus Thunnus-were examined more closely. The clades revealed after bootstrapping generally corresponded well with expectations. Individuals from operational taxonomic units designated as Squalus species B through F formed individual clades, supporting morphological evidence for each of these being separate species. We conclude that cox1 sequencing, or 'barcoding', can be used to identify fish species.