Protein-encoding ultraconserved elements provide a new phylogenomic perspective of Oestroidea flies (Diptera, Calyptratae)

The diverse superfamily Oestroidea with more than 15,000 known species includes among others, blow flies, flesh flies, bot flies, and the diverse tachinid flies. Oestroidea exhibit strikingly divergent morphological and ecological traits, but even with a variety of data sources and inferences there is no consensus on the relationships among major Oestroidea lineages. Phylogenomic inferences derived from targeted enrichment of ultraconserved elements or UCEs have emerged as a promising method for resolving difficult phylogenetic problems at varying timescales. To reconstruct phylogenetic relationships among families of Oestroidea, we obtained UCE loci exclusively derived from the transcribed portion of the genome making them suitable for larger and more integrative phylogenomic studies using other genomic and transcriptomic resources. We analysed datasets containing 37–2,077 UCE loci from 98 representatives of all oestroid families (except Ulurumyiidae and Mystacinobiidae) and seven calyptrate outgroups, with a total concatenated aligned length between 10–550 Mb. About 35% of the sampled taxa consisted of museum specimens (2–92 years old), of which 85% resulted in successful UCE enrichment. Our maximum likelihood and coalescent-based analyses produced well-resolved and highly supported topologies. With the exception of Calliphoridae and Oestridae, all included families were recovered as monophyletic with the following conclusions: Oestroidea is monophyletic with Mesembrinellidae as sister to the remaining oestroid families; Oestridae is paraphyletic with respect to Sarcophagidae; Polleniidae is sister to Tachinidae; Rhinophoridae sister to (Luciliinae (Toxotarsinae (Melanomyinae + Calliphorinae))); Phumosiinae is sister to Chrysomyinae and Bengaliinae is sister to Rhiniidae. These results support the ranking of most calliphorid subfamilies as separate families.

涵盖超15000个已知物种的多样化狂蝇总科（Oestroidea），除其他类群外，还包含丽蝇、麻蝇、皮蝇以及多样的寄蝇。狂蝇总科展现出极为显著的形态与生态特征分化，但即便采用多种数据源与推断方法，学界对该总科主要演化支间的系统发育关系仍未达成共识。基于超保守元件（ultraconserved elements, UCEs）靶向富集的系统基因组学推断，已成为解决不同时间尺度下复杂系统发育难题的有效手段。为重建狂蝇总科各科间的系统发育关系，本研究获取了仅源自基因组转录区域的UCE位点，该类位点可适配结合其他基因组与转录组资源开展更大规模、更具整合性的系统基因组学研究。本研究分析的数据集涵盖98份类群样本（覆盖除乌卢蝇科（Ulurumyiidae）与神秘蝇科（Mystacinobiidae）外的所有狂蝇总科类群，以及7个有瓣蝇类外群），包含37至2077个UCE位点，拼接后的比对序列总长度为10至550 Mb。约35%的采样类群为馆藏标本（标本年代为2至92年），其中85%成功完成UCE富集。本研究的最大似然法与基于溯祖理论的分析均获得了分辨率高、支持度强的系统发育拓扑结构。除丽蝇科（Calliphoridae）与皮蝇科（Oestridae）外，所有纳入分析的类群均恢复为单系群，本研究得出以下结论：狂蝇总科为单系群，中蝇科（Mesembrinellidae）为其余狂蝇总科类群的姊妹群；皮蝇科相对于麻蝇科（Sarcophagidae）为并系群；粉蝇科（Polleniidae）与寄蝇科（Tachinidae）互为姊妹群；鼻蝇科（Rhinophoridae）为（绿蝇亚科（Luciliinae）、弓胫颊蝇亚科（Toxotarsinae）、黑丽蝇亚科（Melanomyinae）与丽蝇亚科（Calliphorinae）构成的演化支）的姊妹群；菲摩斯亚科（Phumosiinae）与金蝇亚科（Chrysomyinae）互为姊妹群，孟加拉蝇亚科（Bengaliinae）与鼻蝇科（Rhiniidae）互为姊妹群。本研究结果支持将多数丽蝇科亚科提升为独立的科。