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.辐鳍鱼类（Ray-finned Fishes）是脊椎动物中物种辐射演化最繁盛的类群，现存物种超过32000种。尽管分子系统发育学（molecular phylogenetics）已开始厘清生命之树这一庞大类群内的主要演化关系，但目前尚无广泛可用的方法可高效采集鱼类的系统基因组学数据，致使大规模并行测序技术在解析辐鳍鱼类主要辐射演化事件中的巨大潜力尚未得到充分释放。本研究通过对超保守核DNA元件（ultraconserved nuclear DNA elements, UCEs）及其侧翼序列进行靶向富集，为辐鳍鱼类主要类群的多样化这一长期悬而未决的科学问题提供了基因组层面的研究视角。本研究的实验流程可高效且经济地生成较传统方法高出数个数量级的数据集，且非常适用于处理博物馆馆藏标本。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，该树支持弓鳍鱼属（Amia）与雀鳝属（Lepisosteus）构成单系群（全骨鱼下纲，Holostei），并揭示海鲢类与骨舌鱼类依次为最早分化的真骨鱼支系。此外，本研究的方法还证实，对UCE区域及其侧翼序列进行序列捕获，可为解析辐鳍鱼类内部的系统发育关系提供巨大应用潜力。