Mitogenomic exploration of higher teleostean phylogenies: A case study formoderate-scale evolutionary genomics with 38 newly determined complete mitochondrial DNA sequences
M. Miya et al., Mitogenomic exploration of higher teleostean phylogenies: A case study formoderate-scale evolutionary genomics with 38 newly determined complete mitochondrial DNA sequences, MOL BIOL EV, 18(11), 2001, pp. 1993-2009
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.