The Calyptratae, one of the most species‐rich fly clades, only originated and diversified after the Cretaceous–Palaeogene extinction event and yet exhibit high species diversity and a diverse array of life history strategies including predation, phytophagy, saprophagy, haematophagy and parasitism. We present the first phylogenomic analysis of calyptrate relationships. The analysis is based on 40 species representing all calyptrate families and on nucleotide and amino acid data for 1456 single‐copy protein‐coding genes obtained from shotgun sequencing of transcriptomes. Topologies are overall well resolved, robust and largely congruent across trees obtained with different approaches (maximum parsimony, maximum likelihood, coalescent‐based species tree, four‐cluster likelihood mapping). Many nodes have 100% bootstrap and jackknife support, but the true support varies by more than one order of magnitude [Bremer support from 3 to 3427; random addition concatenation analysis (RADICAL) gene concatenation size from 10 to 1456]. Analyses of a Dayhoff‐6 recoded amino acid dataset also support the robustness of many clades. The backbone topology Hippoboscoidea+(Fanniidae+(Muscidae+((Anthomyiidae–Scathophagidae)+Oestroidea))) is strongly supported and most families are monophyletic (exceptions: Anthomyiidae and Calliphoridae). The monotypic Ulurumyiidae is either alone or together with Mesembrinellidae as the sister group to the rest of Oestroidea. The Sarcophagidae are sister to Mystacinobiidae+Oestridae. Polleniinae emerge as sister group to Tachinidae and the monophyly of the clade Calliphorinae+Luciliinae is well supported, but the phylogenomic data cannot confidently place the remaining blowfly subfamilies (Helicoboscinae, Ameniinae, Chrysomyinae). Compared to hypotheses from the Sanger sequencing era, many clades within the muscoid grade are congruent but now have much higher support. Within much of Oestroidea, Sanger era and phylogenomic data struggle equally with regard to finding well‐supported hypotheses.

中文翻译：

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Calyptratae 的系统发育分析：解决双翅目主要辐射内的系统发育关系

Calyptratae 是物种最丰富的蝇进化枝之一，仅在白垩纪-古近纪灭绝事件之后才起源和多样化，但仍表现出高度的物种多样性和多样化的生活史策略，包括捕食、植食、腐食、吸血和寄生。我们提出了第一个 calyptrate 关系的系统发育分析。该分析基于代表所有 calyptrate 家族的 40 个物种以及从转录组鸟枪测序中获得的 1456 个单拷贝蛋白质编码基因的核苷酸和氨基酸数据。拓扑总体上得到了很好的解决，鲁棒性并且在使用不同方法（最大简约、最大似然、基于合并的物种树、四簇似然映射）获得的树之间基本一致。许多节点具有 100% 引导程序和折刀支持，但真实支持度相差不止一个数量级【布雷默支持度从 3 到 3427；随机添加串联分析 (RADICAL) 基因串联大小从 10 到 1456]。对 Dayhoff-6 重新编码的氨基酸数据集的分析也支持了许多进化枝的稳健性。主干拓扑 Hippoboscoidea+(Fanniidae+(Muscidae+((Anthomyiidae–Scathophagidae)+Oestroidea))) 得到强烈支持，并且大多数科是单系的（例外：Anthomyiidae 和 Calliphoridae）。单型乌鲁鲁米科单独或与 Mesembrinellidae 一起作为其他 Oestroidea 的姊妹组。Sarcophagidae 是 Mystacinobiidae+Oestridae 的姐妹。Polleninae 作为 Tachinidae 的姐妹群出现，并且分支 Calliphorinae + Luciliinae 的单系得到了很好的支持，但是系统发育数据不能确定地放置剩余的苍蝇亚科（Helicoboscinae、Ameniinae、Chrysomyinae）。与 Sanger 测序时代的假设相比，粘液级内的许多进化枝是一致的，但现在得到了更高的支持。在 Oestroidea 的大部分中，Sanger 时代和系统发育数据在寻找有充分支持的假设方面同样挣扎。