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.骨鳔总目（Ostariophysi）是硬骨鱼的一个总目，涵盖110个属、70个科，共计超过10300个物种。传统上，该总目被划分为5个主要类群（目）：鼠鱚目（Gonorynchiformes，包含虱目鱼与沙鱼类）、鲤形目（Cypriniformes，包含鲤类与鲦鱼）、脂鲤目（Characiformes，包含脂鲤及其近缘类群）、鲶形目（Siluriformes，即鲶鱼）以及电鳗目（Gymnotiformes，即电刀鱼）。明确解析这些类群间的系统发育关系仍颇具挑战，此前的分子与形态学分析均未能得到一致的系统发育树。本研究选取了覆盖35个代表性骨鳔总目物种的350余个超保守元件（ultraconserved element, UCE）位点，共计包含500万个碱基对，以此构建了迄今数据量最为丰富的鱼类系统发育研究之一。我们利用这些数据推断骨鳔总目鱼类的高阶（目间）系统发育关系，重点聚焦于脂鲤目的单系性——这是鱼类分类学中争议最为激烈的类群之一。与多数此前的分子研究结果一致，本研究发现脂鲤目并非单系群：其下两个单系亚目——琴脂鲤亚目（Citharinoidei）与脂鲤亚目（Characoidei）——与其他骨鳔总目演化支的亲缘关系，反而比二者彼此间的亲缘关系更近。本研究还探讨了不同UCE数据集所得结果间的不一致性、直系同源性问题，以及将形态学特征与分子数据结合使用的相关议题。