Data from: Taxon sampling to address an ancient rapid radiation: a supermatrix phylogeny of early brachyceran flies (Diptera)

Early diverging brachyceran fly lineages underwent a rapid radiation approximately 180 million years ago, coincident in part with the origin of flowering plants. This region of the fly tree includes 25,000 described extant species with diverse ecological roles such as blood feeding (haematophagy), parasitoidism, predation, pollination, and wood feeding (xylophagy). Early diverging brachyceran lineages were once considered a monophyletic group of families called Orthorrhapha, based on the shared character of a longitudinal break in the pupal skin made during the emergence of the adult. Yet other morphological and molecular evidence generally supports a paraphyletic arrangement of ‘Orthorrhapha,’ with strong support for one orthorrhaphan lineage — dance flies and relatives — as the closest relative to all higher flies (Cyclorrhapha), together called Eremoneura. In order to establish a comprehensive estimate of the relationships among orthorrhaphan lineages using a thorough sample of publicly available data we compiled and analyzed a dataset including 1,217 taxa representing major lineages and 20 molecular markers. Our analyses suggest that ‘Orthorrhapha’ excluding Eremoneura is not monophyletic; instead, we recover two main lineages of early brachyceran flies— Homeodactyla and Heterodactyla. Homeodactyla includes Nemestrinoidea (uniting two parasitic families Acroceridae + Nemestrinidae) as the closest relatives to the large SXT clade, comprised of Stratiomyomorpha, Xylophagidae and Tabanomorpha. Heterodactyla includes Bombyliidae with a monophyletic Asiloidea (exclusive of Bombyliidae) as the closest relatives to Eremoneura. Reducing missing data, modifying the distribution of genes across taxa, and, in particular, removing rogue taxa significantly improved tree resolution and statistical support. Although relying on dense taxonomic sampling and substantial gene coverage, our analyses pinpoint the limited resolving power of Sanger sequencing-era molecular phylogenetic datasets in respect to ancient, hyperdiverse radiations.

短角亚目蝇类（brachyceran fly）的早期分化支系约在1.8亿年前经历了一次快速辐射演化，其时间节点与被子植物的起源部分重合。该蝇类系统树的该分支包含25000个已描述的现生物种，具备多样的生态功能，包括吸血（haematophagy）、拟寄生（parasitoidism）、捕食、传粉以及食木（xylophagy）。

早期分化的短角亚目蝇类支系曾被视为一个单系家族类群，称为直裂类（Orthorrhapha），其共有衍征为成虫羽化时蛹壳会发生纵向开裂。然而其他形态学与分子生物学证据普遍支持“直裂类（Orthorrhapha）”为并系群，且有强有力证据表明其中一个支系——舞虻及其近缘类群——是所有高等蝇类（Cyclorrhapha，环裂亚目）的姊妹群，二者共同构成真脉蝇类（Eremoneura）。

为基于公开可用的全面样本数据，对直裂类支系间的系统发育关系开展全面解析，我们整合并分析了一套数据集：该数据集包含代表主要支系的1217个分类单元，以及20个分子标记。我们的分析显示，排除真脉蝇类（Eremoneura）后的“直裂类”并非单系群；相反，我们恢复了早期短角亚目蝇类的两个主要支系——同趾类（Homeodactyla）与异趾类（Heterodactyla）。

同趾类（Homeodactyla）包含蜂虻总科（Nemestrinoidea，涵盖两个寄生性科：小头虻科（Acroceridae）与蜂虻科（Nemestrinidae）），作为大型SXT演化支的姊妹群；该演化支由水虻下目（Stratiomyomorpha）、木虻科（Xylophagidae）以及虻下目（Tabanomorpha）组成。异趾类（Heterodactyla）包含蜂虻科（Bombyliidae），且单系的食虫虻总科（Asiloidea，不含蜂虻科）是真脉蝇类（Eremoneura）的姊妹群。

减少缺失数据、调整分类单元间的基因分布，尤其是移除异常类群（rogue taxa），可显著提升系统树的分辨率与统计支持度。尽管本研究依赖高密度的分类单元采样与充足的基因覆盖度，但我们的分析明确指出：桑格测序（Sanger sequencing）时代的分子系统发育数据集，难以解析古老且高度多样的辐射演化事件。