Mitogenomic exploration of higher teleostean phylogenies: A case study formoderate-scale evolutionary genomics with 38 newly determined complete mitochondrial DNA sequences

Although adequate resolution of higher-level relationships of organisms app arently requires longer DNA sequences than those currently being analyzed, limitations of time and resources present difficulties in obtaining such se quences from many taxa. For fishes, these difficulties have been overcome b y the development of a PCR-based approach for sequencing the complete mitoc hondrial genome (mitogenome), which employs a long PCR technique and many f ish-versatile PCR primers. In addition, recent studies have demonstrated th at such mitogenomic data are useful and decisive in resolving persistent co ntroversies over higher-level relationships of telcosts. As a first step to ward resolution of higher teleostean relationships, which have been describ ed as the "(unresolved) bush at the top of the tree," we investigated relat ionships using mitogenomic data from 48 purposefully chosen teleosts, of wh ich those from 38 were newly determined during the present study (a total o f 632,315 bp), using the above method. Maximum-parsimony and maximum-likeli hood analyses were conducted with the data set that comprised concatenated nucleotide sequences from 12 protein-coding genes (excluding the ND6 gene a nd third codon positions) and 22 transfer RNA (tRNA) genes (stem regions on ly) 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, exhibi ted considerable variation from the previous morphology-based cladistic hyp otheses, with most of the latter being confidently rejected by the mitogeno mic data. Such incongruence resulted largely from the phylogenetic position s or limits of long-standing problematic taxa, which were quite unexpected from previous morphological and molecular analyses. We concluded that the p resent study provided a basis of and guidelines for future investigations o f teleostean evolutionary mitogenomics and that purposeful higher-density t axonomic 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.