Conflicting signal in transcriptomic markers leads to a poorly resolved backbone phylogeny of Chalcidoid wasps

Chalcidoidea (Hymenoptera) are a megadiverse superfamily of wasps with astounding variation in both morphology and biology. Most species are parasitoids and important natural enemies of insects in terrestrial ecosystems. In this study, we explored a transcriptome-based phylogeny of Chalcidoidea and found that poorly resolved relationships could only be marginally improved by adding more genes (a total of 5,591) and taxa (a total of 65), proof-checking for errors of homology and contamination, and decreasing missing data. Concatenation analyses consistently place Mymaridae and Trichogrammatidae sister to remaining Chalcidoidea. However, our coalescent analyses provide a different hypothesis with a grouping of (Mymaridae (((Trichogrammatidae, Eulophidae), (Encyrtidae, Aphelinidae)), remaining Chalcidoidea)). This hypothesis complicates our hypothesis of egg parasitism as being ancestral in Chalcidoidea. At the deeper nodes, the results uncovered a wide spectrum of gene discordance in the ...小蜂总科（Chalcidoidea）隶属于膜翅目（Hymenoptera），是一个物种多样性极高的蜂类总科，在形态学与生物学特性上均展现出惊人的变异。该总科绝大多数类群为寄生性昆虫，是陆地生态系统中重要的昆虫天敌。本研究基于转录组数据构建了小蜂总科的系统发育树，结果显示，即便新增5591个基因与65个分类单元、校正同源性与污染误差、减少缺失数据比例，原本分辨率不佳的系统发育关系仅能得到极小幅的改善。串联分析（concatenation analysis）始终将缨小蜂科（Mymaridae）与赤眼蜂科（Trichogrammatidae）聚为其余小蜂总科类群的姊妹群。然而本研究的溯祖分析（coalescent analysis）则得到了不同的拓扑结构：（缨小蜂科（（（赤眼蜂科，姬小蜂科（Eulophidae）），（跳小蜂科（Encyrtidae），蚜小蜂科（Aphelinidae））），其余小蜂总科类群））。该拓扑结构使得我们此前提出的"卵寄生为小蜂总科的祖先习性"这一假说变得更为复杂。在更深的系统发育节点处，研究结果揭示了广泛存在的基因冲突现象……