Recent technical advances combined with novel computational approaches have promised the acceleration of our understanding of the tree of life. However, when it comes to hyperdiverse and poorly known groups of invertebrates, studies are still scarce. As published phylogenies will be rarely challenged by future taxonomists, careful attention must be paid to potential analytical bias. We present the first molecular phylogenetic hypothesis for the family Chalcididae, a group of parasitoid wasps, with a representative sampling (144 ingroups and seven outgroups) that covers all described subfamilies and tribes, and 82% of the known genera. Analyses of 538 Ultra-Conserved Elements (UCEs) with supermatrix (RAxML and IQTREE) and gene tree reconciliation approaches (ASTRAL, ASTRID) resulted in highly supported topologies in overall agreement with morphology but reveal conflicting topologies for some of the deepest nodes. To resolve these conflicts, we explored the phylogenetic tree space with clustering and gene genealogy interrogation methods, analyzed marker and taxon properties that could bias inferences and performed a thorough morphological analysis (130 characters encoded for 40 taxa representative of the diversity). This joint analysis reveals that UCEs enable attainment of resolution between ancestry and convergent/divergent evolution when morphology is not informative enough, but also shows that a systematic exploration of bias with different analytical methods and a careful analysis of morphological features is required to prevent publication of artifactual results. We highlight a GC content bias for maximum-likelihood approaches, an artifactual mid-point rooting of the ASTRAL tree and a deleterious effect of high percentage of missing data (>85% missing UCEs) on gene tree reconciliation methods. Based on the results we propose a new classification of the family into eight subfamilies and ten tribes that lay the foundation for future studies on the evolutionary history of Chalcididae.

中文翻译：

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超保守元素和形态学相互阐明了Chalcididae（膜翅目，Chalcidoidea）中相互矛盾的系统发育假设

最近的技术进步与新颖的计算方法相结合，有望加速我们对生命之树的理解。然而，当涉及到超多样性和鲜为人知的无脊椎动物群体时，研究仍然很少。由于已发表的系统发育学将很少受到未来分类学家的挑战，因此必须仔细注意潜在的分析偏差。我们提出了 Chalcididae 家族的第一个分子系统发育假说，这是一组寄生蜂，具有代表性的样本（144 个内群和 7 个外群），涵盖了所有描述的亚科和部落，以及 82% 的已知属。使用超矩阵（RAxML 和 IQTREE）和基因树协调方法（ASTRAL，ASTRID）产生了与形态学总体一致的高度支持的拓扑结构，但揭示了一些最深节点的拓扑结构冲突。为了解决这些冲突，我们使用聚类和基因谱系查询方法探索了系统发育树空间，分析了可能导致推断偏差的标记和分类属性，并进行了彻底的形态分析（为代表多样性的 40 个分类群编码了 130 个字符）。这种联合分析表明，当形态学信息不足时，UCEs 能够实现祖先和收敛/发散进化之间的分辨率，但也表明需要使用不同的分析方法对偏差进行系统探索，并对形态特征进行仔细分析，以防止发表人工结果。我们强调了最大似然方法的 GC 内容偏差、ASTRAL 树的人为中点生根以及高百分比缺失数据（>85% 缺失 UCE）对基因树协调方法的有害影响。基于这些结果，我们提出了一个新的家庭分类，分为八个亚科和十个部落，为未来研究Chalcididae的进化史奠定了基础。