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

最近利用48种硬骨鱼的完整线粒体DNA序列进行的初步研究表明，高等硬骨鱼的系统发育应该在更密集的分类样本的基础上进行重新研究。作为解决高等硬骨动物系统发育的第二步，我们使用了100个有目的地选择的物种的有丝基因组数据来重新分析它们之间的关系，这些物种完全代表了除蝙蝠形目之外的所有高等硬骨动物目。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(仅茎区域)的串联核苷酸序列进行了未加权和加权最大简约分析。得到的树分辨率很好，基本上是一致的，大多数内部分支得到了高统计值的支持。所有在高等硬骨动物中定义的序级以上的主要的、综合的类群(除了新龙骨和几个单型类群)，例如Eurypterygii、Ctenosquamata、棘形目、Paracanthopterygii、Acanthopterygii和Percomforma，在本树上似乎是非单系的。这种不一致很大程度上是由于在鱼类学系统学中长期存在问题的分类单元--棘足目、鳗形目、多混目、蛇形目、鹿形目、贝形目、石龙目和泽鱼目在位置和/或界限上的差异。其中，蛇形目和蛇形目的系统发育位置完全出乎人们的意料，因为尽管它们一直被认为是高等硬骨鱼(副刺龙目)中相对原始的类群，但它们自信地被归入硬骨鱼的一个冠群，在这里被称为Percomforma。

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.