Aphids (Aphididae) are intensively studied due to their significance as pests and their captivating biological traits. Despite this interest, the evolutionary history of this insect family is poorly understood. Recent phylogenomic analyses have produced conflicting topologies, complicating our understanding of aphid trait evolution. In this work, we aimed to unravel the backbone phylogeny of aphids. We sequenced partial and whole mitochondrial genomes from 87 species. We additionally sequenced 42 nuclear loci across 95 aphid species and sourced 146 genes from 12 new and 61 published genomes from aphid obligate endosymbiont, Buchnera aphidicola. We obtained data from these three sources for a subset of aphid species, facilitating a comparative analysis of their signal. Our analyses confirm the monophyly of most subfamilies, validating current taxonomic classifications. However, relationships between subfamilies remain contentious in both mitochondrial and nuclear phylogenies. The topologies obtained with Buchnera are fully resolved but disagree with host phylogenies at deep evolutionary scales and conflict with views on the evolution of aphid morphology. We discuss alternative hypotheses for these discrepancies. Finally, the paucity of phylogenetic information at deep timescales may stem from an initial rapid radiation. Though challenging to establish, this scenario may inherently hinder resolution in aphid phylogenetics.

中文翻译：

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蚜虫系统发育中线粒体、核和共生体基因组之间的不一致：谁说的是实话？


蚜虫（Aphididae）因其作为害虫的重要性及其迷人的生物学特性而受到深入研究。尽管有这样的兴趣，但人们对该昆虫家族的进化历史知之甚少。最近的系统发育分析产生了相互矛盾的拓扑，使我们对蚜虫性状进化的理解复杂化。在这项工作中，我们的目的是揭示蚜虫的系统发育骨架。我们对 87 个物种的部分和完整线粒体基因组进行了测序。我们还对 95 个蚜虫物种的 42 个核基因座进行了测序，并从蚜虫专性内共生体 Buchnera aphidicola 的 12 个新基因组和 61 个已发表的基因组中获取了 146 个基因。我们从这三个来源获得了蚜虫物种子集的数据，有助于对其信号进行比较分析。我们的分析证实了大多数亚科的单系性，验证了当前的分类学分类。然而，亚科之间的关系在线粒体和核系统发育中仍然存在争议。 Buchnera 获得的拓扑结构已完全解析，但与深层进化尺度上的宿主系统发育不一致，并且与蚜虫形态进化的观点相冲突。我们讨论这些差异的替代假设。最后，深时间尺度的系统发育信息的缺乏可能源于最初的快速辐射。尽管建立起来具有挑战性，但这种情况可能本质上阻碍蚜虫系统发育的解决。