Takezaki Naoko, Nishihara Hidenori
Life Science Research Center, Kagawa University, Mikicho, Kitagun, Kagawa, Japan
Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Nagatsuta-Cho, Midori-Ku, Yokohama, Kanagawa, Japan.
Genome Biol Evol. 2016 Apr 25;8(4):1208-21. doi: 10.1093/gbe/evw071.
Determining the phylogenetic relationship of two extant lineages of lobe-finned fish, coelacanths and lungfishes, and tetrapods is important for understanding the origin of tetrapods. We analyzed data sets from two previous studies along with a newly collected data set, each of which had varying numbers of species and genes and varying extent of missing sites. We found that in all the data sets the sister relationship of lungfish and tetrapods was constructed with the use of cartilaginous fish as the outgroup with a high degree of statistical support. In contrast, when ray-finned fish were used as the outgroup, which is taxonomically an immediate outgroup of lobe-finned fish and tetrapods, the sister relationship of coelacanth and tetrapods was supported most strongly, although the statistical support was weaker. Even though it is generally accepted that the closest relative is an appropriate outgroup, our analysis suggested that the large divergence of the ray-finned fish as indicated by their long branch lengths and different amino acid frequencies made them less suitable as an outgroup than cartilaginous fish.
确定肉鳍鱼的两个现存谱系——腔棘鱼和肺鱼，与四足动物之间的系统发育关系，对于理解四足动物的起源至关重要。我们分析了来自之前两项研究的数据集以及一个新收集的数据集，每个数据集的物种数量、基因数量以及缺失位点的程度各不相同。我们发现，在所有数据集中，以软骨鱼作为外类群，肺鱼和四足动物的姐妹关系在高度统计支持下得以构建。相比之下，当以辐鳍鱼作为外类群时（从分类学角度来看，辐鳍鱼是肉鳍鱼和四足动物的直接外类群），腔棘鱼和四足动物的姐妹关系得到了最强有力的支持，尽管统计支持较弱。尽管一般认为最近的亲属是合适的外类群，但我们的分析表明，辐鳍鱼因其长分支长度和不同的氨基酸频率所显示出的巨大差异，使其作为外类群不如软骨鱼合适。
