Cao Y, Waddell P J, Okada N, Hasegawa M
Institute of Statistical Mathematics, Tokyo, Japan.
Mol Biol Evol. 1998 Dec;15(12):1637-46. doi: 10.1093/oxfordjournals.molbev.a025891.
A remarkable example of a misleading mitochondrial protein tree is presented, involving ray-finned fishes, coelacanths, lungfishes, and tetrapods, with sea lampreys as an outgroup. In previous molecular phylogenetic studies on the origin of tetrapods, ray-finned fishes have been assumed as an outgroup to the tetrapod/lungfish/coelacanth clade, an assumption supported by morphological evidence. Standard methods of molecular phylogenetics applied to the protein-encoding genes of mitochondria, however, give a bizarre tree in which lamprey groups with lungfish and, therefore, ray-finned fishes are not the outgroup to a tetrapod/lungfish/coelacanth clade. All of the dozens of published phylogenetic methods, including every possible modification to maximum likelihood known to us (such as inclusion of site heterogeneity and exclusion of potentially misleading hydrophobic amino acids), fail to place the ray-finned fishes in a biologically acceptable position. A likely cause of this failure may be the use of an inappropriate outgroup. Accordingly, we have determined the complete mitochondrial DNA sequence from the shark, Mustelus manazo, which we have used as an alternative and more proximal outgroup than the lamprey. Using sharks as the outgroup, lungfish appear to be the closest living relative of tetrapods, although the possibility of a lungfish/coelacanth clade being the sister group of tetrapods cannot be excluded.
文中给出了一个关于误导性线粒体蛋白树的显著例子，涉及硬骨鱼、腔棘鱼、肺鱼和四足动物，并以海七鳃鳗作为外类群。在之前关于四足动物起源的分子系统发育研究中，硬骨鱼被假定为四足动物/肺鱼/腔棘鱼进化枝的外类群，这一假设得到了形态学证据的支持。然而，将分子系统发育的标准方法应用于线粒体的蛋白质编码基因时，却得出了一个奇怪的树状图，其中七鳃鳗与肺鱼归为一类，因此硬骨鱼并非四足动物/肺鱼/腔棘鱼进化枝的外类群。所有已发表的几十种系统发育方法，包括我们所知的对最大似然法的每一种可能修改（如纳入位点异质性和排除潜在误导性的疏水氨基酸），都无法将硬骨鱼置于生物学上可接受的位置。这种失败的一个可能原因可能是使用了不合适的外类群。因此，我们测定了条纹斑竹鲨的完整线粒体DNA序列，并将其用作比七鳃鳗更合适且更接近的外类群。以鲨鱼作为外类群时，肺鱼似乎是四足动物现存的最近亲缘物种，尽管肺鱼/腔棘鱼进化枝作为四足动物姐妹群的可能性也不能排除。
