DOI: 10.5061/dryad.v7f76
title: Data from: Phylogenomic analysis of a rapid radiation of misfit fishes (Syngnathiformes) using ultraconserved elements

description: Phylogenetics is undergoing a revolution as large-scale molecular datasets
 reveal unexpected but repeatable rearrangements of clades that were
 previously thought to be disparate lineages. One of the most unusual
 clades of fishes that has been found using large-scale molecular datasets
 is an expanded Syngnathiformes including traditional long-snouted
 syngnathiform lineages (Aulostomidae, Centriscidae, Fistulariidae,
 Solenostomidae, Syngnathidae), as well as a diverse set of largely
 benthic-associated fishes (Callionymoidei, Dactylopteridae, Mullidae,
 Pegasidae) that were previously dispersed across three orders. The
 monophyly of this surprising clade of fishes has been upheld by recent
 studies utilizing both nuclear and mitogenomic data, but the relationships
 among major lineages within Syngnathiformes remain ambiguous; previous
 analyses have inconsistent topologies and are plagued by low support at
 deep divergences between the major lineages. In this study, we use a
 dataset of ultraconserved elements (UCEs) to conduct the first
 phylogenomic study of Syngnathiformes. UCEs have been effective markers
 for resolving deep phylogenetic relationships in fishes and, combined with
 increased taxon sampling, we expected UCEs to resolve problematic
 syngnathiform relationships. Overall, UCEs were effective at resolving
 relationships within Syngnathiformes at a range of evolutionary
 timescales. We find consistent support for the monophyly of traditional
 long-snouted syngnathiform lineages (Aulostomidae, Centriscidae,
 Fistulariidae, Solenostomidae, Syngnathidae), which better agrees with
 morphological hypotheses than previously published topologies from
 molecular data. This result was supported by all Bayesian and maximum
 likelihood analyses, was robust to differences in matrix completeness and
 potential sources of bias, and was highly supported in coalescent-based
 analyses in ASTRAL when matrices were filtered to contain the most
 phylogenetically informative loci. While Bayesian and maximum likelihood
 analyses found support for a benthic-associated clade (Callionymidae,
 Dactylopteridae, Mullidae, and Pegasidae) as sister to the long-snouted
 clade, this result was not replicated in the ASTRAL analyses. The base of
 our phylogeny is characterized by short internodes separating major
 syngnathiform lineages and is consistent with the hypothesis of an ancient
 rapid radiation at the base of Syngnathiformes. Syngnathiformes therefore
 present an exciting opportunity to study patterns of morphological
 variation and functional innovation arising from rapid but ancient
 radiation.
description: NCBI Accession
 InformationText file indicating
 accession numbers for raw-reads in NCBI SRA and accession numbers for
 assembled UCE contigs for each species in NCBI GenBank.AccessionInfo.txtUCE alignmentsCleaned and trimmed MAFFT alignments for each UCE in the 75 and 95 percent complete matricesuce_alignments.zipConcatenated alignments of UCEsConcatenated alignments and charsets for the 95p and 75p matrices used in ExaBayes and RAxML analyses, as well as best-fit partitioning schemes from Partition Finder and RY-coded matrices.concatenated_alignments.zipASTRAL filesInput and output files for all ASTRAL analyses of 75p and 95p matricesASTRAL_input_output.zipPhylogenetic TreesFiles containing all trees presented in the publicationtrees.zipTrinity AssembliesDe novo Trinity assemblies of raw-reads for all individuals included in our published study.trinity_assemblies_dryad.zipExaBayes outputInput and output files for the ExaBayes analyses of the 75p and 95p datasetsExaBayes_output.zip