Data from: Phylogenomic systematics of Ostariophysan fishes: ultraconserved elements support the surprising non-monophyly of Characiformes

Ostariophysi is a superorder of bony fishes including more than 10,300
species in 1,100 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 five million base
pairs collected across thirty-five 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 the monophyly of the Characiformes— one
the most contentiously debated groups in fish systematics. As with most
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 datasets, issues
of orthology, and the use of morphological characters in combination with
our molecular data.