Data from: Phylogenomic analysis of a rapid radiation of misfit fishes (Syngnathiformes) using ultraconserved elements

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.