The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, PR China.
Sci Rep. 2012;2:665. doi: 10.1038/srep00665. Epub 2012 Sep 18.
The actinopterygians comprise nearly one-half of all extant vertebrate species and are very important for human well-being. However, the phylogenetic relationships among certain groups within the actinopterygians are still uncertain, and debates about these relationships have continued for a long time. Along with the progress achieved in sequencing technologies, phylogenetic analyses based on multi-gene sequences, termed phylogenomic approaches, are becoming increasingly common and often result in well-resolved and highly supported phylogenetic hypotheses. Based on the transcriptome sequences generated in this study and the extensive expression data currently available from public databases, we obtained alignments of 274 orthologue groups for 26 scientifically and commercially important actinopterygians, representing 17 out of 44 orders within the class Actinopterygii. Using these alignments and probabilistic methods, we recovered relationships between basal actinopterygians and teleosts, among teleosts within protacanthopterygians and related lineages, and also within acanthomorphs. These relationships were recovered with high confidence.
肉鳍鱼类包含了现存脊椎动物物种的近一半，对人类福祉非常重要。然而，肉鳍鱼类内部某些群体之间的系统发育关系仍然不确定，关于这些关系的争论已经持续了很长时间。随着测序技术的进步，基于多基因序列的系统发育分析（称为系统基因组学方法）变得越来越普遍，并且通常会产生分辨率高且得到高度支持的系统发育假说。基于本研究生成的转录组序列和当前可从公共数据库获得的广泛表达数据，我们获得了 26 种具有科学和商业重要性的肉鳍鱼类的 274 个直系同源物组的比对，代表了硬骨鱼纲 44 个目中的 17 个目。使用这些比对和概率方法，我们重建了基础肉鳍鱼类和硬骨鱼类之间的关系，在原棘鳍鱼类和相关谱系内以及棘鳍鱼类内的关系也得到了重建。这些关系得到了高度置信的重建。
