DOI: 10.5061/dryad.j015n
title: Data from: A phylogenomic perspective on the radiation of ray-finned fishes based upon targeted sequencing of ultraconserved elements (UCEs)

description: 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.
description: 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.