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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蚜虫系统发育学中线粒体、核和共生体基因组之间的不一致：谁在说真话？


蚜虫 （Aphididae） 因其作为害虫的重要性和迷人的生物特性而受到深入研究。尽管有这种兴趣，但人们对这个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结构，使我们对蚜虫性状进化的理解复杂化。在这项工作中，我们旨在解开蚜虫的主干系统发育。我们对 87 个物种的部分和整个线粒体基因组进行了测序。我们还对 95 种蚜虫的 42 个核位点进行了测序，并从 12 个新的和 61 个已发表的基因组中获取了 146 个基因，这些基因组来自蚜虫专性内共生体 Buchnera aphidicola。我们从这三个来源获得了蚜虫物种子集的数据，有助于对它们的信号进行比较分析。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。使用 Buchnera 获得的拓扑结构已完全解析，但在深层进化尺度上与宿主系统发育不一致，并且与蚜虫形态进化的观点相冲突。我们讨论了这些差异的替代假设。最后，深时间尺度上系统发育信息的缺乏可能源于最初的快速辐射。尽管难以建立，但这种情况可能本质上阻碍了蚜虫系统发育学的解决。