Mitogenomic exploration of higher teleostean phylogenies: A case study for moderate-scale evolutionary genomics with 38 newly determined complete mitochondrial DNA sequences
Mitogenomic exploration of higher teleostean phylogenies: A case study for moderate-scale evolutionary genomics with 38 newly determined complete mitochondrial DNA sequences
复制标题
DOI：
10.1093/oxfordjournals.molbev.a003741
复制
发表时间：
2001-11-01
影响因子：
10.7
通讯作者：
Nishida, M
中科院分区：
文献类型：
--
作者：
Miya, M;Kawaguchi, A;Nishida, M
虽然高层次的有机体关系的充分解决显然需要更长的DNA序列比目前正在分析的，时间和资源的限制，在获得这样的序列从许多类群的困难。对于鱼类，这些困难已经克服了一个完整的线粒体基因组（有丝分裂基因组），它采用了长PCR技术和许多鱼类通用的PCR引物测序的PCR为基础的方法的发展。此外，最近的研究表明，这些有丝分裂基因组学数据是有用的，并在解决长期存在的争议更高层次的关系telcosts的决定性。作为解决高等硬骨鱼类关系的第一步，这被描述为“树顶的（未解决的）灌木”，我们使用48个有目的地选择的硬骨鱼类的有丝分裂基因组数据研究了关系，其中38个是在本研究期间新确定的（共632，315 bp），使用上述方法。最大简约法和最大似然分析进行了数据集，包括连接的核苷酸序列从12个蛋白质编码基因（不包括ND 6基因和第三密码子位置）和22个转移RNA（tRNA）基因（干区）从48个物种。从这两种方法得到的两棵树得到了很好的解决，很大程度上是一致的，许多内部分支支持高统计值。树拓扑结构本身，然而，表现出相当大的变化，从以前的形态学为基础的分支假设，后者被自信地拒绝的有丝分裂基因组数据。这种不一致主要是由于系统发育的位置或长期存在的问题类群的限制，这是相当出乎意料的，从以前的形态和分子分析。我们的结论是，目前的研究提供了一个基础和指导方针，为今后的调查硬骨鱼进化的有丝分裂基因组学和有目的的高密度分类采样，随后的测序工作，和系统发育分析，其有丝分裂基因组可能是决定性的，在解决持久的争议更高层次的关系硬骨鱼，最多样化的组的所有脊椎动物，包括超过23,500现存物种。
Although adequate resolution of higher-level relationships of organisms apparently requires longer DNA sequences than those currently being analyzed, limitations of time and resources present difficulties in obtaining such sequences from many taxa. For fishes, these difficulties have been overcome by the development of a PCR-based approach for sequencing the complete mitochondrial genome (mitogenome), which employs a long PCR technique and many fish-versatile PCR primers. In addition, recent studies have demonstrated that such mitogenomic data are useful and decisive in resolving persistent controversies over higher-level relationships of telcosts. As a first step toward resolution of higher teleostean relationships, which have been described as the "(unresolved) bush at the top of the tree," we investigated relationships using mitogenomic data from 48 purposefully chosen teleosts, of which those from 38 were newly determined during the present study (a total of 632,315 bp), using the above method. Maximum-parsimony and maximum-likelihood analyses were conducted with the data set that comprised concatenated nucleotide sequences from 12 protein-coding genes (excluding the ND6 gene and third codon positions) and 22 transfer RNA (tRNA) genes (stem regions only) from the 48 species. The resultant two trees from the two methods were well resolved and largely congruent, with many internal branches supported by high statistical values. The tree topologies themselves, however, exhibited considerable variation from the previous morphology-based cladistic hypotheses, with most of the latter being confidently rejected by the mitogenomic data. Such incongruence resulted largely from the phylogenetic positions or limits of long-standing problematic taxa, which were quite unexpected from previous morphological and molecular analyses. We concluded that the present study provided a basis of and guidelines for future investigations of teleostean evolutionary mitogenomics and that purposeful higher-density taxonomic sampling, subsequent sequencing efforts, and phylogenetic analyses of their mitogenomes may be decisive in resolving persistent controversies over higher-level relationships of teleosts, the most diversified group of all vertebrates, comprising over 23,500 extant species.