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

我探讨了系统发育的效用和限制的个别和串联的线粒体基因重建更高层次的关系的硬骨鱼，使用完整的（或接近完整的）线粒体DNA（mtDNA）序列的8个硬骨鱼（包括这三个新确定的序列），其相对系统发育的位置是没有争议的。对上述8种硬骨鱼和2个外类群的13个蛋白质编码基因的核苷酸和氨基酸序列进行了最大简约分析（bichir和shark），表明除了ND5之外，所有的单个蛋白质编码基因都未能恢复预期的同源性，尽管来自22个串联的转移RNA（tRNA）基因的序列被明确地比对，（仅茎区域）成功地恢复了预期的同源性，具有中等的统计学支持。13个蛋白质编码基因在恢复预期的同源性方面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）和非常差（ND4L，ND6，ATPase 8）。尽管这一观察的普遍性尚不清楚，但对13个蛋白质编码基因以相同排序顺序连续连接的分析揭示，包含来自几个排序最高的蛋白质编码基因的核苷酸序列的组合数据集（无第三密码子位置）加上22个串联的tRNA基因（仅茎区），最好地恢复了预期的无性繁殖，所有内部分支得到> 90%的引导值的支持。我们的结论是，明智的选择线粒体基因和适当的数据加权，结合有目的的分类采样，解决更高层次的关系，在硬骨鱼最大简约最优标准的先决条件。

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.