Yang Liandong, Zhang Zhaolei, He Shunping
The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei 430072, People's Republic of China; University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China.
Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada; Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada.
Gene. 2015 Jul 25;566(2):242-7. doi: 10.1016/j.gene.2015.04.058. Epub 2015 Apr 24.
The phylogenetic position of Polypteriforme (bichirs) remains elusive, despite extensive research both on morphological and molecular datasets. Unfortunately morphological cladistic analyses and molecular phylogenetic analyses had reached conflicting conclusions, as Polypteriformes were either grouped with lobe-finned fishes (Sarcopterygii) or ray-finned fishes (Actinopterygii), or even classified as their own group, the Brachiopterygii. In this study, we applied a third independent source of datasets, the presence versus absence of microRNAs, to re-investigate the phylogenetic relationship of bichirs. Through deep sequencing of small RNA library, we showed that bichirs should be grouped into ray-finned fishes rather than lobe-finned fishes. Phylogenetic analysis confirmed that bichirs were placed as the most basal member of the ray-finned fishes. Bichirs shared five unique microRNA families with teleostei, which were not found in any other species investigated to date. Bichirs have also retained three of five microRNAs that were previously deemed to be lost exclusively in teleostei. Furthermore, we report more than one hundred novel microRNAs that are unique to bichir. The identification of microRNAs in bichir provides overwhelming evidence for their affinity of ray-finned fishes. The sarcopterygian-like characteristics such as lobed fins, paired ventral lungs, and external gills in juveniles should not be considered as derived traits shared with those of sarcopterygians.
尽管对多鳍鱼目（多鳍鱼）的形态学和分子数据集都进行了广泛研究，但其系统发育位置仍然难以确定。不幸的是，形态学分支分析和分子系统发育分析得出了相互矛盾的结论，因为多鳍鱼目要么与肉鳍鱼类（肉鳍鱼纲）归为一类，要么与辐鳍鱼类（辐鳍鱼纲）归为一类，甚至被归类为它们自己的类群——腕鳍鱼纲。在本研究中，我们应用了数据集的第三个独立来源，即微小RNA的有无，来重新研究多鳍鱼的系统发育关系。通过对小RNA文库的深度测序，我们表明多鳍鱼应归入辐鳍鱼类而非肉鳍鱼类。系统发育分析证实，多鳍鱼是辐鳍鱼类中最基部的成员。多鳍鱼与硬骨鱼纲共有五个独特的微小RNA家族，这些家族在迄今为止研究的任何其他物种中都未发现。多鳍鱼还保留了五个微小RNA中的三个，这些微小RNA以前被认为仅在硬骨鱼纲中丢失。此外，我们报告了一百多种多鳍鱼特有的新型微小RNA。多鳍鱼中微小RNA的鉴定为它们与辐鳍鱼类的亲缘关系提供了压倒性的证据。诸如叶状鳍、成对的腹侧肺和幼鱼的外鳃等类似肉鳍鱼的特征不应被视为与肉鳍鱼类共有的衍生特征。
