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

我利用8种硬鱼的完整（或近乎完整）线粒体DNA （mtDNA）序列（包括这3种新确定的序列）探索了个体和串联线粒体基因在重建硬鱼之间更高层次关系方面的系统发育效用和局限性，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2个外群（bichir和shark）的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，所有单独的蛋白质编码基因都未能恢复预期的系统发育，尽管22个连接的转移RNA （tRNA）基因（仅在干区）的明确对齐序列成功恢复了预期的系统发育，并得到了适度的统计支持。13个蛋白编码基因在恢复预期系统发育中的系统发育表现大致分为5组，即非常好（ND5、ND4、COIII、COI）、良好（COII、cyt b）、中等（ND3、ND2）、差（ND1、ATPase 6）和极差（ND4L、ND6、ATPase 8）。虽然这一观察结果的普遍性尚不清楚，但对13个蛋白质编码基因按相同顺序连续串联的分析表明，由几个排名靠前的蛋白质编码基因（没有第3密码子位置）和22个串联的tRNA基因（仅茎区）组成的组合数据集最能恢复预期的系统发育，所有内部分支都得到bootstrap值>90%的支持。我们的结论是，明智的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，是在最大简约最优准则下解决硬骨鱼更高层次关系的先决条件。

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.