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.

24Exon markers have a long history of use in phylogenetics of ray-finned fishes, the most diverse 25 clade of vertebrates with more than 35,000 species. As the number of published genomes 26 increases, it has become easier to test exons and other genetic markers for signals of ancient 27 duplication events and filter out paralogs that can mislead phylogenetic analysis. We present 28 seven new probe sets for current target-capture phylogenomic protocols that capture 1,104 exons 29 explicitly filtered for paralogs using gene trees. These seven probe sets span the diversity of 30 teleost fishes, including four sets that target five hyper-diverse percomorph clades which 31 together comprise ca. 17,000 species (Carangaria, Ovalentaria, Eupercaria, and Syngnatharia + 32 Pelagiaria combined). We additionally included probes to capture exon markers that have been 33 commonly used in fish phylogenetics, despite some being flagged for paralogs, to facilitate 34 integration of old and new molecular phylogenetic matrices. We tested these probes and merged 35 new exon-capture sequence data into an existing data matrix of 1,105 exons and 300 ray-finned 36 fish species. We provide an optimized bioinformatics pipeline to assemble exon capture data 37 from raw reads to alignments for downstream analysis. We show that loci with known paralogs 38 are at risk of assembling duplicated sequences with target-capture, but we also assembled many 39 useful orthologous sequences. These probe sets are a valuable resource for advancing fish 40 phylogenomics because they can be easily extracted from increasingly available whole genome 41 and transcriptome datasets, and also may be integrated with existing PCR-based exon and 42 mitochondrial datasets. 43 44 Exon markers have played a pivotal role in resolving phylogenetic relationships among ray-46 finned fishes (Li et al. 2007;Near et al. 2012;Betancur-R. et al. 2013;Betancur-R et al. 2017; 47 Hughes et al. 2018;Rabosky et al. 2018). Identification of these exons has typically involved the 48 comparison of a small number of fish model genomes. For example, a suite of 154 single-copy 49 exons conserved enough for PCR amplification was identified by Li et al. (2007). This study 50 used a reciprocal BLAST approach on two genomes, the pufferfish Takifugu rubripes and the 51 zebrafish Danio rerio, with 10 exons initially optimized with PCR primers for sequencing (Li et 52 al. 2007). These exons demonstrated their utility for resolving previously enigmatic relationships 53 among fishes (Li et al. 2008), and were the basis for largescale reappraisals of the ray-finned fish 54