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.辐鳍鱼类是脊椎动物中演化辐射最为繁盛的类群，现存物种超过32000种。尽管分子系统发育学已开始厘清生命之树这一庞大分支内的主要演化亲缘关系，但目前尚无广泛可用的高效采集鱼类系统发育组学数据的方法，致使大规模并行测序技术在解析辐鳍鱼类主要类群辐射演化时的巨大潜力尚未得到充分发挥。在此研究中，我们通过靶向富集超保守核DNA元件（ultraconserved nuclear DNA elements, UCEs）及其侧翼序列，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。本研究的实验流程能够高效且经济地生成规模较传统方法高出数个数量级的数据集，且极适用于博物馆标本的相关研究。对UCE数据集的分析结果，在浅层与深层演化时间尺度上均获得了支持度优良的系统发育树：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），并揭示海鲢下纲（Elopomorphs）与骨舌鱼超目（Osteoglossomorphs）依次为真骨鱼类中最早分化的演化支。本研究方法同时证实，针对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的系统发育关系方面具备巨大应用潜力。