Betancur-R Ricardo, Broughton Richard E, Wiley Edward O, Carpenter Kent, López J Andrés, Li Chenhong, Holcroft Nancy I, Arcila Dahiana, Sanciangco Millicent, Cureton Ii James C, Zhang Feifei, Buser Thaddaeus, Campbell Matthew A, Ballesteros Jesus A, Roa-Varon Adela, Willis Stuart, Borden W Calvin, Rowley Thaine, Reneau Paulette C, Hough Daniel J, Lu Guoqing, Grande Terry, Arratia Gloria, Ortí Guillermo
The George Washington University.
PLoS Curr. 2013 Apr 18;5:ecurrents.tol.53ba26640df0ccaee75bb165c8c26288. doi: 10.1371/currents.tol.53ba26640df0ccaee75bb165c8c26288.
The tree of life of fishes is in a state of flux because we still lack a comprehensive phylogeny that includes all major groups. The situation is most critical for a large clade of spiny-finned fishes, traditionally referred to as percomorphs, whose uncertain relationships have plagued ichthyologists for over a century. Most of what we know about the higher-level relationships among fish lineages has been based on morphology, but rapid influx of molecular studies is changing many established systematic concepts. We report a comprehensive molecular phylogeny for bony fishes that includes representatives of all major lineages. DNA sequence data for 21 molecular markers (one mitochondrial and 20 nuclear genes) were collected for 1410 bony fish taxa, plus four tetrapod species and two chondrichthyan outgroups (total 1416 terminals). Bony fish diversity is represented by 1093 genera, 369 families, and all traditionally recognized orders. The maximum likelihood tree provides unprecedented resolution and high bootstrap support for most backbone nodes, defining for the first time a global phylogeny of fishes. The general structure of the tree is in agreement with expectations from previous morphological and molecular studies, but significant new clades arise. Most interestingly, the high degree of uncertainty among percomorphs is now resolved into nine well-supported supraordinal groups. The order Perciformes, considered by many a polyphyletic taxonomic waste basket, is defined for the first time as a monophyletic group in the global phylogeny. A new classification that reflects our phylogenetic hypothesis is proposed to facilitate communication about the newly found structure of the tree of life of fishes. Finally, the molecular phylogeny is calibrated using 60 fossil constraints to produce a comprehensive time tree. The new time-calibrated phylogeny will provide the basis for and stimulate new comparative studies to better understand the evolution of the amazing diversity of fishes.
鱼类的生命之树尚不稳定，因为我们仍缺乏一个涵盖所有主要类群的全面系统发育树。对于一大类传统上被称为鲈形目鱼类的硬骨鱼来说，情况最为严峻，其不确定的亲缘关系已经困扰鱼类学家一个多世纪了。我们对鱼类谱系间高级别亲缘关系的了解大多基于形态学，但分子研究的迅速涌入正在改变许多已确立的系统发育概念。我们报告了一个涵盖所有主要谱系代表的硬骨鱼全面分子系统发育树。为1410个硬骨鱼分类单元收集了21个分子标记（1个线粒体基因和20个核基因）的DNA序列数据，外加4种四足动物和2种软骨鱼外类群（共1416个终端）。硬骨鱼的多样性由1093个属、369个科以及所有传统认可的目来体现。最大似然树为大多数主干节点提供了前所未有的分辨率和高自展支持率，首次定义了全球鱼类系统发育树。该树的总体结构与先前形态学和分子研究的预期一致，但出现了重要的新分支。最有趣的是，鲈形目鱼类中高度的不确定性现在被解析为9个得到充分支持的超目类群。鲈形目长期以来被许多人视为一个多系分类的“废纸篓”，现在在全球系统发育中首次被定义为一个单系类群。我们提出了一个反映我们系统发育假设的新分类法，以促进关于鱼类生命之树新发现结构的交流。最后，利用60个化石约束对分子系统发育树进行校准，以生成一个全面的时间树。新的时间校准系统发育树将为新的比较研究提供基础，并激发新的比较研究，以更好地理解鱼类惊人多样性的演化。
