Resolving the early divergence pattern of of teleost fish using genome-scale data

Regarding the phylogenetic relationship of the three primary groups of
teleost fishes, Osteoglossomorpha (bonytongues and others), Elopomorpha
(eels and relatives), Clupeocephala (the remaining teleost fish), early
morphological studies hypothesized the first divergence of
Osteoglossomorpha, whereas the recent prevailing view is the first
divergence of Elopomorpha. Molecular studies supported all the possible
relationships of the three primary groups. This study analyzed
genome-scale data from four previous studies: (1) 412 genes from 12
species, (2) 772 genes from 15 species, (3) 1,062 genes from 30 species,
and (4) 491 UCE loci from 27 species. The effects of the species, loci,
and models used on the constructed tree topologies were investigated. In
the analyses of the datasets (1) - (3), although the first divergence of
Clupeocephala that left the other two groups in a sister relationship was
supported by concatenated sequences and gene trees of all the species and
genes, the first divergence of Elopomorpha among the three groups was
supported using species and/or genes with small divergence of sequence and
amino-acid frequencies. This result corresponded to that of the UCE
dataset (4), whose sequence divergence was low, which supported the first
divergence of Elopomorpha with high statistical significance. The increase
in accuracy of the phylogenetic construction by using species and genes
with low sequence divergence was predicted by a phylogenetic
informativeness approach and confirmed by computer simulation. These
results supported that Elopomorpha was the first basal group of teleost
fish to have diverged, consistent with the prevailing view of recent
morphological studies.