Use of mitochondrial genomic information in telestean molecular phylogenetics: A new approach using long PCR technique

我利用八种硬骨鱼的完整(或接近完整)线粒体DNA(MtDNA)序列(包括这三个新确定的序列)，探索了单个和串联的线粒体基因在重建硬骨鱼高级关系中的系统发育作用和局限性，它们的相对系统发育位置是没有争议的。对上述8种硬骨鱼和两个外群(Bichir和Shark)13个蛋白质编码基因的核苷酸和氨基酸序列的最大简约分析表明，除ND5外，所有单个蛋白质编码基因都未能恢复预期的系统发育，尽管22个串联转移RNA(TRNA)基因(仅茎段)的明确比对序列在适度的统计支持下成功地恢复了预期的系统发育。13个编码蛋白质的基因在恢复预期的系统发育中的系统发育性能大致分为五个组，即。很好(ND5，ND4，COIII，COI)，良好(COII，Cytb)，中等(ND3，ND2)，差(ND1，ATPase 6)，很差(ND4L，ND6，ATPase 8)。尽管这一观察结果的普遍性尚不清楚，但对13个编码蛋白质的基因以相同的排序顺序连续连接的分析表明，由几个排名最高的蛋白质编码基因(没有第三个密码子位置)的核苷酸序列加上22个连接的tRNA基因(仅限于茎区域)组成的组合数据集最好地恢复了预期的系统发育，所有内部分支都得到了引导值的90%支持。我们的结论是，明智地选择线粒体基因和适当的数据加权，结合有目的的分类抽样，是在最大简约性最优标准下解决硬骨鱼更高水平关系的先决条件。

I explored the phylogenetic utility and limits of the individual and concatenated mitochondrial genes for reconstructing the higher-level relationships of teleosts, using the complete (or nearly complete) mitochondrial DNA (mtDNA) sequences of eight teleosts (including those three newly-determined sequences), whose relative phylogenetic positions were noncontroversial. Maximum-parsimony analyses of the nucleotide and amino acid sequences of 13 protein-coding genes from the above eight teleosts, plus two outgroups (bichir and shark), indicated that all of the individual protein-coding genes, with the exception of ND5, failed to recover the expected phylogeny, although unambiguously aligned sequences from 22 concatenated transfer RNA (tRNA) genes (stem regions only) recovered the expected phylogeny successfully with moderate statistical support. The phylogenetic performance of the 13 protein-coding genes in recovering the expected phylogeny was roughly classified into five groups, viz. very good (ND5, ND4, COIII, COI), good (COII, cyt b), medium (ND3, ND2), poor (ND1, ATPase 6), and very poor (ND4L, ND6, ATPase 8). Although the universality of this observation was unclear, analysis of successive concatenation of the 13 protein-coding genes in the same ranking order revealed that the combined data sets comprising nucleotide sequences from the several top ranked protein-coding genes (no 3rd codon positions) plus the 22 concatenated tRNA genes (stem regions only), best recovered the expected phylogeny, with all internal branches being supported by bootstrap values >90%. We concluded that judicious choice of mitochondrial genes and appropriate data weighting, in conjunction with purposeful taxonomic sampling, are prerequisites for resolving higher-level relationships in teleosts under the maximum-parsimony optimality criterion.