Data from: Multi-locus phylogenetic analysis reveals the pattern and tempo of bony fish evolution

Over half of all vertebrates are “fishes”, which exhibit enormous diversity in morphology, physiology, behavior, reproductive biology, and ecology. Investigation of fundamental areas of vertebrate biology depend critically on a robust phylogeny of fishes, yet evolutionary relationships among the major actinopterygian and sarcopterygian lineages have not been conclusively resolved. Although a consensus phylogeny of teleosts has been emerging recently, it has been based on analyses of various subsets of actinopterygian taxa, but not on a full sample of all bony fishes. Here we conducted a comprehensive phylogenetic study on an unprecedented combination of broad taxonomic sampling of actinopterygian and sarcopterygian lineages (with a chondrichthyan outgroup) using a molecular data set of 21 independent loci. These data yielded a resolved phylogenetic hypothesis for extant Osteichthyes, including 1) reciprocally monophyletic Sarcopterygii and Actinopterygii, as currently understood, with polypteriforms as the first diverging lineage within Actinopterygii; 2) a monophyletic group containing gars and bowfin (= Holostei) as sister group to Teleostei; and 3) the earliest diverging lineage among teleosts being Elopomorpha, rather than Osteoglossomorpha. Relaxed-clock dating analysis employing a set of 24 newly applied fossil calibrations reveals divergence times that are more consistent with paleontological estimates than previous studies. Establishing a new phylogenetic pattern with accurate divergence dates for bony fishes illustrates several areas where the fossil record is incomplete and provides critical new insights on diversification of this important vertebrate group.脊椎动物中超过一半为鱼类，其在形态学、生理学、行为学、生殖生物学以及生态学方面展现出极高的多样性。对脊椎动物生物学基础领域的研究高度依赖可靠的鱼类系统发育框架，但目前辐鳍鱼类（Actinopterygii）与肉鳍鱼类（Sarcopterygii）主要类群间的演化关系仍未得到明确解析。尽管近期真骨鱼下纲（Teleostei）的共识系统发育框架逐渐成型，但此类研究多基于辐鳍鱼类类群的不同子集进行分析，并未涵盖所有硬骨鱼类的完整样本。本研究针对辐鳍鱼类与肉鳍鱼类类群（辅以软骨鱼类（Chondrichthyes）外类群）开展了前所未有的宽分类采样组合，并基于21个独立基因座的分子数据集完成了全面的系统发育分析。本数据集为现生硬骨鱼纲（Osteichthyes）构建了得到解析的系统发育假说，具体包括：1）如当前认知般互为单系群的肉鳍鱼类与辐鳍鱼类，其中多鳍鱼目（Polypteriformes）为辐鳍鱼类中最早分化的类群；2）包含雀鳝与弓鳍鱼（即全骨鱼下纲（Holostei））的单系群，该类群与真骨鱼下纲互为姊妹群；3）真骨鱼类中最早分化的类群为海鲢总目（Elopomorpha），而非骨舌鱼总目（Osteoglossomorpha）。本研究采用24个新建立的化石校准点开展宽松分子钟定年（relaxed-clock dating）分析，结果显示的分化时间相较于以往研究更符合古生物学估算结果。本研究为硬骨鱼类构建了兼具准确分化时间的全新系统发育格局，该成果揭示了古生物记录存在缺失的多个领域，并为这一重要脊椎动物类群的演化辐射研究提供了关键的全新认知。