Use of mitogenomic information in teleostean molecular phylogenetics: A tree-based exploration under the maximum-parsimony optimality criterion

We explored the phylogenetic utility and limits of the individual and conca tenated mitochondrial genes for reconstructing the higher-level relationshi ps of teleosts, using the complete (or nearly complete) mitochondrial DNA s equences of eight teleosts (including three newly determined sequences), wh ose relative phylogenetic positions were noncontroversial. Maximum-parsimon y 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 except ion of ND5, failed to recover the expected phylogeny, although unambiguousl y aligned sequences from 22 concatenated transfer RNA (tRNA) genes (stem re gions only) recovered the expected phylogeny successfully with moderate sta tistical support. The phylogenetic performance of the 13 protein-coding gen es in recovering the expected phylogeny was roughly classified into five gr oups, viz. very good (ND5, ND4, COIII, COI), good (COII, cyt b), medium (ND 3, ND2), poor (ND1, ATPase 6), and very poor (ND4L, ND6, ATPase 8). Althoug h the universality of this observation was unclear, analysis of successive concatenation of the 13 protein-coding genes in the same ranking order reve aled that the combined data sets comprising nucleotide sequences from the s everal top-ranked protein-coding genes (no 3rd codon positions) plus the 22 concatenated tRNA genes (stem regions only) best recovered the expected ph ylogeny, with all internal branches being supported by bootstrap values >90 %. We conclude that judicious choice of mitochondrial genes and appropriate data weighting, in conjunction with purposeful taxonomic sampling, are pre requisites for resolving higher-level relationships in teleosts under the m aximum-parsimony optimality criterion. (C) 2000 Academic Press.