Data from: Episodic radiations in the fly tree of life

Flies are one of four superradiations of insects (along with beetles, wasps, and moths) that account for the majority of animal life on Earth. Diptera includes species known for their ubiquity (Musca domestica house fly), their role as pests (Anopheles gambiae malaria mosquito), and their value as model organisms across the biological sciences (Drosophila melanogaster). A resolved phylogeny for flies provides a framework for genomic, developmental, and evolutionary studies by facilitating comparisons across model organisms, yet recent research has suggested that fly relationships have been obscured by multiple episodes of rapid diversification. We provide a phylogenomic estimate of fly relationships based on molecules and morphology from 149 of 157 families, including 30 kb from 14 nuclear loci and complete mitochondrial genomes combined with 371 morphological characters. Multiple analyses show support for traditional groups (Brachycera, Cyclorrhapha, and Schizophora) and corroborate contentious findings, such as the anomalous Deuterophlebiidae as the sister group to all remaining Diptera. Our findings reveal that the closest relatives of the Drosophilidae are highly modified parasites (including the wingless Braulidae) of bees and other insects. Furthermore, we use micro-RNAs to resolve a node with implications for the evolution of embryonic development in Diptera. We demonstrate that flies experienced three episodes of rapid radiation—lower Diptera (220 Ma), lower Brachycera (180 Ma), and Schizophora (65 Ma)—and a number of life history transitions to hematophagy, phytophagy, and parasitism in the history of fly evolution over 260 million y.

蝇类是构成地球上动物类群绝大多数的四大昆虫超辐射类群（superradiation）之一，其余三类分别为鞘翅目甲虫、膜翅目蜂类与鳞翅目蛾类。双翅目（Diptera）涵盖的物种兼具多重典型特征：如家蝇（Musca domestica）的广布性、冈比亚按蚊（Anopheles gambiae）作为疟疾媒介害虫的危害性，以及黑腹果蝇（Drosophila melanogaster）作为全生物科学领域模式生物的极高科研价值。厘清蝇类的系统发育关系，可为基因组学、发育生物学与进化生物学研究提供框架，助力跨模式生物的比较研究；但近期研究表明，多次快速辐射演化事件模糊了蝇类类群间的演化关联。本研究基于157个蝇类科中的149个科的分子与形态学数据，构建了蝇类类群关系的系统发育组学（phylogenomic）估算结果，所用数据包含14个核基因座（nuclear loci）的30千碱基（kb）序列、完整线粒体基因组（mitochondrial genomes），以及371个形态学性状。多项分析结果支持传统类群划分（短角亚目Brachycera、环裂亚目Cyclorrhapha与有缝组Schizophora），并验证了此前颇具争议的结论——即反常的伪鹬虻科（Deuterophlebiidae）是双翅目其余所有类群的姊妹群。本研究结果显示，果蝇科（Drosophilidae）的近缘类群为高度特化的寄生生物，包括寄生于蜂类及其他昆虫的无翅蜂虱蝇科（Braulidae）。此外，本研究借助微小RNA（microRNAs）厘清了一个系统发育节点，该节点的结果对双翅目胚胎发育的演化具有重要启示意义。本研究证实，蝇类在2.6亿余年的演化历程中经历了三次快速辐射演化事件：分别为低等双翅目（2.2亿年前，220 Ma）、低等短角亚目（1.8亿年前，180 Ma）以及有缝组（6500万年前，65 Ma），同时发生了多次生活史转型，包括吸血习性（hematophagy）、植食性（phytophagy）与寄生习性（parasitism）的演化。