Major Patterns of higher teleostean phylogenies based on complete mitochondrial DNA sequences

最近一项对48种硬骨鱼的完整线粒体DNA序列的初步研究表明，应该在更密集的分类抽样的基础上重新研究更高级别的硬骨鱼系统发育。作为解决高级端骨动物系统发育问题的第二步，我们使用100个有目的地选择的物种的有丝分裂基因组数据重新分析了它们之间的关系，这些物种完全代表了所有高级端骨动物目，除了蝙蝠形目。对每个物种的12个蛋白质编码基因（不包括第3密码子位置）和21个转移RNA （tRNA）基因（仅茎区）的串联核苷酸序列进行非加权和加权最大简约性分析。所得到的树是很好的解决和很大程度上一致，与大多数内部分支支持高统计值。在目前的树中，所有高于序级的主要综合类群（除了Neoteleostei和几个单型类群），如Eurypterygii、Ctenosquamata、Acanthomorpha、Paracanthopterygii、Acanthopterygii和Percomorpha，在当前的树中似乎都是非单系的。这种不一致很大程度上是由于在系统鱼类学中长期存在问题的类群——无足形目、Lampridiformes、多混合形目、蛇形目、Lophiiformes、Beryciformes、Stephanoberyciformes和Zeiformes的位置和/或限制上的差异。其中，蛇形目和Lophiiformes的系统发育位置是完全出乎意料的，因为尽管它们一直被认为是高等硬鱼目（副棘鱼目）中相对原始的类群，但它们被自信地置于硬鱼目的冠群中，在这里被称为Percomorpha。

A recent preliminary study using complete mitochondrial DNA sequences from 48 species of teleosts has suggested that higher teleostean phylogenies should be reinvestigated on the basis of more intensive taxonomic sampling. As a second step towards the resolution of higher teleostean phylogenies, which have been described as the "(unresolved) bush at the top of the tree," we reanalyzed their relationships using mitogenomic data from 100 purposefully-chosen species that fully represented all of the higher teleostean orders, except for the Batrachoidiformes. Unweighted and weighted maximum parsimony analyses were conducted with the data set that comprised concatenated nucleotide sequences from 12 protein-coding genes(excluding 3rd codon positions) and 21 transfer RNA (tRNA) genes (stem regions only) from each species. The resultant trees were well resolved and largely congruent, with most internal branches being supported by high statistical values. All major, comprehensive groups above ordinal level as currently defined in higher teleosts (with the exception of the Neoteleostei and several monotypic groups) , such as the Eurypterygii, Ctenosquamata, Acanthomorpha, Paracanthopterygii , Acanthopterygii , and Percomorpha, appeared to be nonmonophyletic in the present tree. Such incongruities largely resulted from differences in the placement and/or limits of the orders Ateleopodiformes, Lampridiformes, Polymixiiformes, Ophidiiformes, Lophiiformes, Beryciformes, Stephanoberyciformes , and Zeiformes , long-standing problematic taxa in systematic ichthyology. Of these, the resulting phylogenetic positions of the Ophidiiformes and Lophiiformes were totally unexpected, because, although they have consistently been considered relatively primitive groups within higher teleosts (Paracanthopterygii), they were confidently placed within a crown group of teleosts, herein called the Percomorpha.