DOI: 10.5061/dryad.n9g60
title: Data from: Phylogenomic systematics of Ostariophysan fishes: ultraconserved elements support the surprising non-monophyly of Characiformes

description: Ostariophysi is a superorder of bony fishes including more than 10,300
 species in 1,100 genera and 70 families. This superorder is traditionally
 divided into five major groups (orders): Gonorynchiformes (milkfishes and
 sandfishes), Cypriniformes (carps and minnows), Characiformes (tetras and
 their allies), Siluriformes (catfishes), and Gymnotiformes (electric
 knifefishes). Unambiguous resolution of the relationships among these
 lineages remains elusive, with previous molecular and morphological
 analyses failing to produce a consensus phylogeny. In this study, we use
 over 350 ultraconserved element (UCEs) loci comprising five million base
 pairs collected across thirty-five representative ostariophysan species to
 compile one of the most data-rich phylogenies of fishes to date. We use
 these data to infer higher-level (interordinal) relationships among
 ostariophysan fishes, focusing on the monophyly of the Characiformes— one
 the most contentiously debated groups in fish systematics. As with most
 previous molecular studies, we recover a non-monophyletic Characiformes
 with the two monophyletic suborders, Citharinoidei and Characoidei, more
 closely related to other ostariophysan clades than to each other. We also
 explore incongruence between results from different UCE datasets, issues
 of orthology, and the use of morphological characters in combination with
 our molecular data.
description: alignment-data.tar.gzAlignment data for concatenated and coalescent-based analyses. Contents in README.all-contigs-by-taxon.tar.gzAll contigs assembled by Trinity for each taxon in the data set. FASTA format by taxon. Contents in README.astral.tar.gzGene trees and results from coalescent-based (ASTRAL) analyses. Contents in README.bayesian-analyses.tar.gzAll files (samples, parameter estimates, convergence metrics, etc.) from Bayesian analyses. Contents in README.fish-uce-1k-probes.tar.gzProbe set used for UCE enrichment.ml-analyses.tar.gzAll files (best trees, bootreps) from maximum likelihood analyses. Contents in README.taxon-set.txtThe taxon set file for use with PHYLUCE.tip-name-remappings.txtA text file for PHYLUCE that we used to rename tips in each of the trees to fix taxonomy issues, incorrect spellings, etc.trees.tar.gzAll trees generated for this manuscript. In newick format. Contents in README.uce-contigs-by-taxon.tar.gzAll UCE contigs identified for each taxon. FASTA format by taxon. Contents in README.processing-steps.txtText file with step-by-step description of data processing.TableS1.xlsxSupplemental Table 1: Number of reads, total number of base pairs sequenced, mean length of adapter- and quality-trimmed reads, 95 CI of trimmed read length, minimum read length, maximum read length, and median length for reads sequenced, by platform, from ostariophysan libraries enriched for UCEs (table also includes outgroup taxa, indicated with an asterisk).TableS2.xlsxSupplemental Table 2: Number of contigs assembled, total number of base pairs sequenced, mean contig length, 95 CI of contig length, minimum contig length, maximum contig length, median contig length, and number of contigs &gt; 1 Kb in length from reads sequenced, by platform, from ostariophysan libraries enriched for UCEs (table also includes outgroup taxa, indicated with an asterisk).TableS3.xlsxSupplemental Table 3: Number of UCE loci enriched, total number of base pairs in all UCE loci, mean length of UCE loci, 95 CI of UCE locus length, minimum UCE locus length, maximum UCE locus length, median UCE locus length, number of UCE loci having a length &gt; 1 Kb, UCE locus coverage, percentage of reads on-target, and percentage of on-target reads that were unique from reads assembled, by platform, from ostariophysan libraries enriched for UCEs (table also includes outgroup taxa, indicated with an asterisk). We collected Danio rerio UCE data from the danRer7 genome assembly.Fig_S1.pdfSupplemental Figure 1: Morphology based ML and Bayesian phylogeny. Support values on every node was (BPP &gt;0.99 and bootstrap support of 100).Fig_S2.pdfSupplemental Figure 2: Results from ML analyses of ostariophysans using ultraconserved elements, with 50% complete data coverage, data not partitioned but concatenated.Fig_S3.pdfSupplemental Figure 3. Results from Bayesian analyses of ostariophysans using ultraconserved elements, with 50% complete data coverage, partitioned and concatenated.Fig_S4.pdfSupplemental Figure 4. Results from ML analyses of ostariophysans using ultraconserved elements, with 50% complete data coverage, partitioned and concatenated.Fig_S5.pdfSupplemental Figure 5: Results from ML analyses of ostariophysans using ultraconserved elements, with 75% complete data coverage, not partitioned but concatenated.Fig_S6.pdfSupplemental Figure 6: Results from ML and Bayesian analyses of ostariophysans using ultraconserved elements, with 75% complete data coverage, partitioned, and all data concatenated.Fig_S7.pdfSupplemental Figure 7: ASTRAL phylogeny of ostariophysans using ultraconserved elements with 50% data coverage, using a coalescent species tree approach. Internodes that were found to potentially be in the anomaly zone are shown with dashed lines (see text).Fig_S8.pdfSupplemental Figure 8: Result from a Bayesian analysis using ultraconserved elements (partitioned) and morphology, with 50% complete UCE data coverage.Fig_S9.pdfSupplemental Figure 9: Result from a ML analysis using ultraconserved elements (partitioned) and morphology, with 50% complete UCE data coverage.Fig_S10.pdfSupplemental Figure 10: Result from a Bayesian analysis using ultraconserved elements (partitioned) and morphology, with 75% complete UCE data coverage.Fig_S11.pdfSupplemental Figure 11: Result from a ML analysis using ultraconserved elements (partitioned) and morphology, with 75% complete UCE data coverage.