Data from: A phylogenomic perspective on the radiation of ray-finned fishes based upon targeted sequencing of ultraconserved elements (UCEs)

Ray-finned fishes constitute the dominant radiation of vertebrates with over 32,000 species. Although molecular phylogenetics has begun to disentangle major evolutionary relationships within this vast section of the Tree of Life, there is no widely available approach for efficiently collecting phylogenomic data within fishes, leaving much of the enormous potential of massively parallel sequencing technologies for resolving major radiations in ray-finned fishes unrealized. Here, we provide a genomic perspective on longstanding questions regarding the diversification of major groups of ray-finned fishes through targeted enrichment of ultraconserved nuclear DNA elements (UCEs) and their flanking sequence. Our workflow efficiently and economically generates data sets that are orders of magnitude larger than those produced by traditional approaches and is well-suited to working with museum specimens. Analysis of the UCE data set recovers a well-supported phylogeny at both shallow and deep time-scales that supports a monophyletic relationship between Amia and Lepisosteus (Holostei) and reveals elopomorphs and then osteoglossomorphs to be the earliest diverging teleost lineages. Our approach additionally reveals that sequence capture of UCE regions and their flanking sequence offers enormous potential for resolving phylogenetic relationships within ray-finned fishes.辐鳍鱼（Ray-finned fishes）是脊椎动物中演化辐射最为繁盛的类群，现存物种数量超过32000种。尽管分子系统发育学已逐步厘清生命之树这一庞大分支内的主要演化关系，但目前尚无广泛可用的高效采集鱼类系统基因组数据的方法，导致大规模并行测序技术在解决辐鳍鱼类主要辐射演化问题上的巨大潜力尚未得到充分释放。本研究通过靶向富集超保守核DNA元件（ultraconserved nuclear DNA elements, UCEs）及其侧翼序列，从基因组视角探讨了辐鳍鱼类主要类群分化这一长期悬而未决的科学问题。我们的实验流程高效且经济地生成了较传统方法大数个数量级的数据集，且极适用于博物馆标本的研究工作。对UCE数据集的分析在浅时间尺度与深时间尺度下均获得了支持度良好的系统发育树，证实了弓鳍鱼属（Amia）与雀鳝属（Lepisosteus）之间的单系群关系（全骨下纲，Holostei），并揭示海鲢类（elopomorphs）与骨舌鱼类（osteoglossomorphs）依次为真骨鱼类中最早分化的支系。本研究方法同时证实，UCE区域及其侧翼序列的序列捕获技术，在解析辐鳍鱼类内部系统发育关系方面具备巨大应用潜力。