Data from: The tree of life and a new classification of bony fishes

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.

鱼类生命之树仍处于动态演变之中，目前学界仍缺乏涵盖所有主要类群的全面系统发育研究。其中以传统上被称为鲈形总目（Percomorphs）的大型棘鳍鱼类演化支面临的问题最为严峻：其类群间的系统发育关系长期悬而未决，这一难题已困扰鱼类学家长达一个多世纪。此前学界对鱼类支系间高阶系统发育关系的认知大多基于形态学证据，但近年来分子研究的大量涌现正不断改写诸多已确立的系统学认知。本研究构建了涵盖所有主要类群代表类群的硬骨鱼类全面分子系统发育树：共采集了1410个硬骨鱼类群、4个四足动物类群以及2个软骨鱼外类群（总计1416个终端分类单元）的21个分子标记序列数据，其中包含1个线粒体基因与20个核基因。样本覆盖了硬骨鱼类1093个属、369个科，以及所有传统认定的目级类群，充分体现了硬骨鱼类的物种多样性。本研究通过最大似然法构建的系统发育树实现了前所未有的分辨率，且多数主干节点拥有较高的自举支持值，首次构建了全球性的鱼类系统发育框架。该系统发育树的整体结构与此前形态学及分子研究的预期相符，但同时也揭示了多个全新的重要演化支。最具突破性的是，此前长期存在争议的鲈形总目类群间的关系已被厘清为9个具有强支持度的超目级演化支。曾被诸多学者视为多系混杂的“分类垃圾桶”的鲈形目（Perciformes），在本次全球系统发育框架中首次被界定为单系群。本研究提出了一套契合本次系统发育假说的全新分类系统，便于学界就鱼类生命之树的全新结构开展学术交流。最后，本研究通过60个化石校准点对分子系统发育树进行时间校准，构建了全面的时间校准系统发育树（时间树）。这套全新的时间校准系统发育树将为后续研究提供坚实基础，并推动更多比较生物学研究的开展，助力学界更深入地解析鱼类惊人多样性的演化历程。