Strugnell Jan, Norman Mark, Jackson Jennifer, Drummond Alexei J, Cooper Alan
Molecular Evolution, Department of Zoology, South Parks Road, Oxford OX1 3PS, UK.
Mol Phylogenet Evol. 2005 Nov;37(2):426-41. doi: 10.1016/j.ympev.2005.03.020. Epub 2005 Jun 2.
The resolution of higher level phylogeny of the coleoid cephalopods (octopuses, squids, and cuttlefishes) has been hindered by homoplasy among morphological characters in conjunction with a very poor fossil record. Initial molecular studies, based primarily on small fragments of single mitochondrial genes, have produced little resolution of the deep relationships amongst coleoid cephalopod families. The present study investigated this issue using 3415 base pairs (bp) from three nuclear genes (octopine dehydrogenase, pax-6, and rhodopsin) and three mitochondrial genes (12S rDNA, 16S rDNA, and cytochrome oxidase I) from a total of 35 species (including representatives of each of the higher level taxa). Bayesian analyses were conducted on mitochondrial and nuclear genes separately and also all six genes together. Separate analyses were conducted with the data partitioned by gene, codon/rDNA, gene+codon/rDNA or not partitioned at all. In the majority of analyses partitioning the data by gene+codon was the appropriate model with partitioning by codon the second most selected model. In some instances the topology varied according to the model used. Relatively high posterior probabilities and high levels of congruence were present between the topologies resulting from the analysis of all Octopodiform (octopuses and vampire "squid") taxa for all six genes, and independently for the datasets of mitochondrial and nuclear genes. In contrast, the highest levels of resolution within the Decapodiformes (squids and cuttlefishes) resulted from analysis of nuclear genes alone. Different higher level Decapodiform topologies were obtained through the analysis of only the 1st+2nd codon positions of nuclear genes and of all three codon positions. It is notable that there is strong evidence of saturation among the 3rd codon positions within the Decapodiformes and this may contribute spurious signal. The results suggest that the Decapodiformes may have radiated earlier and/or had faster rates of evolution than the Octopodiformes. The following taxonomic conclusions are drawn from our analyses: (1) the order Octopoda and suborders Cirrata, Incirrata, and Oegopsida are monophyletic groups; (2) the family Spirulidae (Ram's horn squids) are the sister taxon to the family Sepiidae (cuttlefishes); (3) the family Octopodidae, as currently defined, is paraphyletic; (4) the superfamily Argonautoidea are basal within the suborder Incirrata; and (5) the benthic octopus genera Benthoctopus and Enteroctopus are sister taxa.
头足纲软体动物（章鱼、鱿鱼和乌贼）高级系统发育关系的解析一直受到形态特征同塑性以及化石记录非常匮乏的阻碍。最初的分子研究主要基于单个线粒体基因的小片段，对头足纲软体动物各家族之间的深层关系几乎没有解析清楚。本研究使用来自35个物种（包括各高级分类单元的代表）的三个核基因（章鱼碱脱氢酶、pax-6和视紫红质）和三个线粒体基因（12S rDNA、16S rDNA和细胞色素氧化酶I）的3415个碱基对（bp）来研究这个问题。分别对线粒体基因和核基因以及所有六个基因一起进行贝叶斯分析。对数据按基因、密码子/rDNA、基因+密码子/rDNA进行划分或根本不划分进行单独分析。在大多数分析中，按基因+密码子划分数据是合适的模型，按密码子划分是第二被选择最多的模型。在某些情况下，拓扑结构根据所使用的模型而有所不同。对所有六个基因以及独立地对线粒体和核基因数据集进行分析所得到的拓扑结构之间，八腕总目（章鱼和幽灵蛸）所有分类单元的拓扑结构具有相对较高的后验概率和高度的一致性。相比之下，十足目（鱿鱼和乌贼）内最高水平的解析结果来自仅对核基因的分析。通过仅分析核基因的第1+2密码子位置和所有三个密码子位置获得了不同的高级十足目拓扑结构。值得注意的是，有强有力的证据表明十足目内第3密码子位置存在饱和现象，这可能会产生虚假信号。结果表明，十足目可能比八腕总目辐射得更早和/或进化速度更快。从我们的分析中得出以下分类学结论：（1）八腕目以及深海乌贼亚目、普通乌贼亚目和开眼亚目是单系类群；（2）旋壳乌贼科（旋壳乌贼）是乌贼科（乌贼）的姐妹分类单元；（3）目前定义的章鱼科是并系的；（4）船蛸总科在深海乌贼亚目内是基部类群；（5）底栖章鱼属的深海章鱼属和真蛸属是姐妹分类单元。
