Ultraconserved elements data for Amarsipus and Pelagiaria

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. 

Methods
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.