DOI: 10.5061/dryad.rbnzs7hd1
title: Evolutionary relationships of anglerfishes (Lophiiformes) reconstructed using ultraconserved elements

description: The macroevolutionary consequences of evolving in the deep-sea remain
 poorly understood and are compounded by the fact that convergent
 adaptations for living in this environment makes elucidating phylogenetic
 relationships difficult. Lophiiform anglerfishes exhibit extreme habitat
 and predatory specializations, including the use of a fin-spine system as
 a luring device and unique reproductive strategies where parasitic males
 attach and fuse to females. Despite their notoriety for these odd
 characteristics, evolutionary relationships among these fishes remain
 unclear. We sought to clarify the evolutionary history of Lophiiformes
 using data from 1,000 ultraconserved elements and phylogenomic inference
 methods with particular interest paid to the Ceratioidei (deep-sea
 anglerfishes) and Antennarioidei (frogfishes and handfishes). At the
 suborder level, we recovered similar topologies in separate phylogenomic
 analyses: The Lophioidei (monkfishes) are the sister group to the rest of
 the Lophiiformes, Ogcocephaloidei (batfishes) and Antennarioidei
 (frogfishes) form a sister group, and Chaunacioidei (coffinfishes) and
 Ceratioidei (deep-sea anglerfishes) form a clade. The relationships we
 recover within the ceratioids disagree with most previous phylogenetic
 investigations, which used legacy phylogenetic markers or morphology. We
 recovered non-monophyletic relationships in the Antennarioidei and
 proposed three new families based on molecular and morphological evidence:
 Histiophrynidae, Rhycheridae, and Tathicarpidae. Antennariidae was
 re-evaluated to include what was known as Antennariinae, but not
 Histiophryninae. Non-bifurcating signal in splits network analysis
 indicated reticulations among and within suborders, supporting the
 complicated history of the Lophiiformes previously found with
 morphological data. Although we resolve relationships within
 Antennarioidei, Ceratioidei relationships remain somewhat unclear without
 better taxonomic sampling.
description: We performed target capture of ultraconserved element loci to
 resolve evolutionary relationships among the fish order Lophiiformes
 (i.e., anglerfishes). Library preparation and sequencing was performed at
 Louisiana State University and the RAPiD Genomics Lab (RAPiD Genomics,
 LLC, Gainesville, FL). The HyperPrep Kit was used for library preparation
 as well as the MYbaits UCE Acanthomorph target capture kit, targeting 1341
 UCE loci with 2600 probes using half reaction volumes and recommended
 manufacturer protocols. DNA sequencing was performed in one lane of an
 Illumina HiSeq300-PE150 to obtainn an expected ~30X sequencing coverage.
 Preprocessing and alignment were completed through the Phyluce pipeline
 (v.1.6.8). Assembly was completed using SPAdes (v. 3.12.0). All
 phylogenomic reconstruction was completed with a 75% comlpete data matrix
 equating to 1000 UCE loci.
description: The config files are for cleaning (i.e., illumiprocessor) and
 include the i5i7 adapters, tag sequences, and tag map for all individuals.
 PLEASE NOTE: These files do contain individuals that were pruned
 downstream due to poor resolution AND there are individuals that were
 mislabeled and those whose taxonomy has changed. PLEASE pay attention to
 the code in the sample names. We have included the
 concatenated 75% complete data matrix alignment used to create the
 phylogenomic trees. Again, this does include individuals that were pruned
 downstream and who were re-labeled.