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.

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.

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.