fish-500-loci-enrichment-probes.fasta.gzFasta file of 120 BP probe sequences commercially synthesized to target UCE loci in ray-finned-fishes.fish-contigs-from-uce-enrichments.tar.gzFASTA file of contigs assembled from raw reads generated by sequencing enriched libraries of several reptile species.fish-lastz-probe-matches-to-uce-contigs.tar.gzLASTZ matches of probes to species-specific contigs in fish-contigs-from-uce-enrichments.tar.gzfish-lastz-probe-matches-to-genome-enabled.tar.gzLASTZ matches of probes to data from genome-enabled fishes.fish-probe-matches-to-uce-contigs.sqlite.gzSQLITE database of LASTZ matches (from fish-lastz-probe-matches-to-uce-contigs.tar.gz) between assembled contigs in fish-contigs-from-uce-enrichments.tar.gz and the UCE probes in fish-500-loci-enrichment-probes.fasta.gz. This database is used to construct data sets containing loci that are shared across taxa and prep data for alignment.fish-probe-matches-to-genome-enabled.sqlite.gzSQLITE database of LASTZ matches between data from genome-enabled taxa and the UCE probes in fish-500-loci-enrichment-probes.fasta.gz. This database is used to construct data sets containing loci that are shared across taxa and prep data for alignment.fish-nexus-files-from-uce-alignment.tar.gzNEXUS alignment files for all taxa across UCE loci, lacking entries for taxa with missing data.fish-nexus-files-with-gaps-from-uce-alignment.tar.gzNEXUS alignment files for all taxa across UCE loci, having entries for taxa with missing data.fish-nexus-file-for-mrbayes.nexus.gzNEXUS-formatted alignment file for use with MRBAYES.fish-phylip-file-for-raxml.phylip.gzPHYLIP formatted alignment file for use with RAXML.fish-partitioned-phylip-file-for-raxml-partitions.txt.gzPartitions for use with RAXML.fish-partitioned-phylip-file-for-raxml.phylip.gzPartitioned PHYLIP file for use with RAXML.fish-phylip-files-for-cloudforest-with-pol_sen-and-aci_ful.tar.gzPHYLIP-formatted alignment file for use with CLOUDFOREST. Polypterus senegalus and Acipenser fulvescens are present in all alignements. Alignment matrices may be incomplete for other taxa.fish-genetree-results-from-cloudforest.tre.gzGene trees generated by CLOUDFOREST.fish-genetree-bootrep-results-from-cloudforest.tar.gzGene tree bootstrap replicates generated by CLOUDFOREST.fish-computer-code-README.txtREADME file providing details about computer code used as part of this research project.

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.