Phylogenomic Systematics of Ostariophysan Fishes: Ultraconserved Elements Support the Surprising Non-Monophyly of Characiformes

Prosanta Chakrabarty, Louisiana State University
Brant C. Faircloth, Louisiana State University
Fernando Alda, Louisiana State University
William B. Ludt, Louisiana State University
Caleb D. McMahan, Louisiana State University
Thomas J. Near, Yale University
Alex Dornburg, North Carolina State Museum of Natural Sciences
James S. Albert, University of Louisiana at Lafayette
Jairo Arroyave, Universidad Nacional Autónoma de México
Melanie L.J. Stiassny, American Museum of Natural History
Laurie Sorenson, Louisiana State University
Michael E. Alfaro, University of California, Los Angeles


© The Author(s) 2017. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved. Ostariophysi is a superorder of bony fishes including more than 10,300 species in 1100 genera and 70 families. This superorder is traditionally divided into five major groups (orders): Gonorynchiformes (milkfishes and sandfishes), Cypriniformes (carps and minnows), Characiformes (tetras and their allies), Siluriformes (catfishes), and Gymnotiformes (electric knifefishes). Unambiguous resolution of the relationships among these lineages remains elusive, with previous molecular and morphological analyses failing to produce a consensus phylogeny. In this study, we use over 350 ultraconserved element (UCEs) loci comprising 5million base pairs collected across 35 representative ostariophysan species to compile one of the most data-rich phylogenies of fishes to date. We use these data to infer higher level (interordinal) relationships among ostariophysan fishes, focusing on themonophyly of the Characiformes-one of themost contentiously debated groups in fish systematics. As withmost previous molecular studies,we recover a non-monophyletic Characiformes with the two monophyletic suborders, Citharinoidei and Characoidei, more closely related to other ostariophysan clades than to each other. We also explore incongruence between results from different UCE data sets, issues of orthology, and the use of morphological characters in combination with our molecular data.