Exon markers have a long history of use in phylogenetics of ray‐finned fishes, the most diverse clade of vertebrates with more than 35,000 species. As the number of published genomes increases, it has become easier to test exons and other genetic markers for signals of ancient duplication events and filter out paralogues that can mislead phylogenetic analysis. We present seven new probe sets for current target‐capture phylogenomic protocols that capture 1,104 exons explicitly filtered for paralogues using gene trees. These seven probe sets span the diversity of teleost fishes, including four sets that target five hyperdiverse percomorph clades which together comprise ca. 17,000 species (Carangaria, Ovalentaria, Eupercaria, and Syngnatharia + Pelagiaria combined). We additionally included probes to capture legacy nuclear exons and mitochondrial markers that have been commonly used in fish phylogenetics (despite some exons being flagged for paralogues) to facilitate integration of old and new molecular phylogenetic matrices. We tested these probes experimentally for 56 fish species (eight species per probe set) and merged new exon‐capture sequence data into an existing data matrix of 1,104 exons and 300 ray‐finned fish species. We provide an optimized bioinformatics pipeline to assemble exon capture data from raw reads to alignments for downstream analysis. We show that legacy loci with known paralogues are at risk of assembling duplicated sequences with target‐capture, but we also assembled many useful orthologous sequences that can be integrated with many PCR‐generated matrices. These probe sets are a valuable resource for advancing fish phylogenomics because targeted exons can easily be extracted from increasingly available whole genome and transcriptome data sets, and also may be integrated with existing PCR‐based exon and mitochondrial data.

中文翻译：

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用于各级鱼类系统基因组学的外显子探针组和生物信息学管道

外显子标记在射线鳍鱼类的系统发育中有着悠久的历史，该鱼类是拥有超过 35,000 种物种的最多样化的脊椎动物进化枝。随着已发表基因组数量的增加，测试外显子和其他遗传标记的古代复制事件信号并过滤掉可能误导系统发育分析的旁系同源物变得更加容易。我们为当前的目标捕获系统基因组方案提供了七个新的探针组，这些方案捕获了 1,104 个使用基因树明确过滤旁系同源物的外显子。这七个探针组涵盖了硬骨鱼的多样性，其中四个探针组针对五个高度多样化的超形进化枝，这些进化枝共同构成了大约。17,000 种（Carangaria、Ovalentaria、Eupercaria 和 Syngnatharia + Pelagiaria 组合）。我们还包括用于捕获鱼类系统发育中常用的遗留核外显子和线粒体标记的探针（尽管一些外显子被标记为旁系同源物），以促进新旧分子系统发育矩阵的整合。我们针对 56 种鱼类（每个探针组 8 种）对这些探针进行了实验测试，并将新的外显子捕获序列数据合并到包含 1,104 个外显子和 300 种射线鳍鱼类的现有数据矩阵中。我们提供优化的生物信息学管道，将外显子捕获数据从原始读数组装到下游分析的比对。我们表明，具有已知旁系同源物的传统位点存在通过目标捕获组装重复序列的风险，但我们也组装了许多有用的直系同源序列，这些序列可以与许多 PCR 生成的矩阵整合。