DOI: 10.5061/dryad.w9ghx3fns
title: Ultraconserved elements data for Amarsipus and Pelagiaria

description: Amarsipus carlsbergi is a rare mesopelagic fish distributed in
 the Indian and Pacific Oceans, and is the only species classified in the
 family Amarsipidae. Since its description in 1969, phylogenetic hypotheses
 have varied regarding its relationship with other percomorph lineages, but
 most have indicated a close relationship with the traditional suborder
 Stromateoidei. Molecular phylogenies place families previously classified
 in Stromateoidei within a diverse clade– Pelagiaria– that includes fishes
 such as tunas, cutlassfishes, and pomfrets. A recent analysis of a small
 number of loci resolved a clade containing Amarsipus and
 the stromateoid lineage Tetragonurus. A subsequent
 high-throughput sequence phylogeny based on ultraconserved elements (UCEs)
 of Pelagiaria lacked Amarsipus, but revealed both strong support
 for stromateoid paraphyly and high levels of gene tree incongruence. We
 gathered UCE sequence data for 610 UCE loci
 from Amarsipus and integrate these with samples from all
 remaining pelagiarian families. This provides a taxonomically
 comprehensive phylogenomic framework to test the evolutionary
 relationships of Amarsipus, and evaluate the support for
 stromateoid monophyly. As in previous studies, our analyses find high
 levels of gene tree topological discordance with regard to some deeper
 pelagiarian inter-relationships. However, we
 resolve Amarsipus as the sister lineage of a clade
 containing Tetragonurus and a family not considered a
 stromateoid lineage, Chiasmodontidae. This relationship is supported by
 both high gene tree concordance and node support. Our analyses also
 provide strong support for the paraphyly of Stromateoidei, casting
 uncertainty on previous hypotheses of the evolution of morphological
 traits across members of Pelagiaria. 
description: We generated alignments from UCE data from the following
 studies:  Friedman et al. 2019. A phylogenomic
 framework for Pelagiarian fishes (Acanthomorpha: Percomorpha) highlights
 mosaic evolution in the open ocean. Proceedings of the Royal Society
 B. https://doi.org/10.1098/rspb.2019.1502 Campbell, M.A. et al. 2018. Multilocus phylogenetic analysis of the first molecular data from the rare and monotypic Amarsipidae places the family within the Pelagiaria and highlights limitations of existing datasets in resolving pelagiarian interrelationships. Molecular Phylogenetics and Evolution. https://doi.org/10.1016/j.ympev.2018.03.008 We also include multilocus phylogenies inferred with ExaBayes, IQTree, and ASTRAL. 
description: A directory containing individual UCE locus alignments are in the
 zipped file named Amarsipus_UCE_alignments.zip.
 Bayesian (ExaBayes) and maximum likelihood (IQTree) phylogenies
 generated from concatenated analysis of these UCE loci attached as the
 files named: Amarsipus_exabayes_concat.tre and
 Amarsipus_IQTree_concat.tre ASTRAL species trees are
 named as: ASTRAL_bs15_collapsed.tre;
 ASTRAL_bs30_collapsed.tre; ASTRAL_bs45_collapsed; and
 ASTRAL_no_collapse.tre. These trees were generated in
 ASTAL using IQTree-generated UCE loci gene trees. Each ASTRAL analysis was
 performed on these gene trees for which nodes were collapsed at varying
 thresholds of bootstrap support. These thresholds of bootstrap support
 used were 15, 30, or 45, as well as a tree for which no node collapsing on
 gene trees was performed, as indicated by the tree file name.