Soil has become a major hotspot of biodiversity studies, yet the pattern and timing of the evolution of soil organisms are poorly known because of the scarcity of paleontological data. To overcome this limitation, we conducted a genome-based macroevolutionary study of an ancient, diversified, and widespread lineage of soil fauna, the elongate-bodied springtails (class Collembola, order Entomobryomorpha). To build the first robust backbone phylogeny of this previously refractory group, we sampled representatives of major higher taxa (6 out of 8 families, 11 out of 16 subfamilies) of the order with an emphasis on the most problematic superfamily Tomoceroidea, applied whole-genome sequencing methods, and compared the performance of different combinations of data sets (universal single-copy orthologs [USCO] vs. ultraconserved elements]) and modeling schemes. The fossil-calibrated timetree was used to reconstruct the evolution of body size, sensory organs, and pigmentation to establish a time frame of the ecomorphological divergences. The resultant trees based on different analyses were congruent in most nodes. Several discordant nodes were carefully evaluated by considering method fitness, morphological information, and topology test. The evaluation favored the well-resolved topology from analyses using USCO amino acid matrices and complex site-heterogeneous models (CAT$+$GTR and LG$+$PMSF (C60)). The preferred topology supports the monophyletic superfamily Tomoceroidea as an early-diverging lineage and a sister relationship between Entomobryoidea and Isotomoidea. The family Tomoceridae was recovered as monophyletic, whereas Oncopoduridae was recovered as paraphyletic, with Harlomillsia as a sister to Tomoceridae and hence deserving a separate family status as Harlomillsiidae Yu and Zhang fam. n. Ancestral Entomobryomorpha were reconstructed as surface-living, supporting independent origins of soil-living groups across the Paleozoic-Mesozoic, and highlighting the ancient evolutionary interaction between aboveground and belowground fauna. [Collembola; phylogenomics; soil-living adaptation; whole-genome sequencing.].

中文翻译：

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细长体弹尾的系统基因组学揭示了在很长一段时间内从地上栖息地到地下栖息地的独立过渡。

土壤已成为生物多样性研究的主要热点，但由于古生物学数据的稀缺，土壤生物演化的模式和时间却鲜为人知。为了克服这一限制，我们对一种古老的、多样化的、广泛分布的土壤动物谱系——细长的跳尾虫（跳虫类，昆虫纲）进行了一项基于基因组的宏观进化研究。为了建立这个先前难以控制的组的第一个强大的骨干系统发育，我们对主要高级分类群（8 个科中的 6 个，16 个亚科中的 11 个）的代表进行了采样，重点是最有问题的超科 Tomoceroidea，应用了全基因组测序方法，并比较了数据集的不同组合（通用单拷贝直系同源物 [USCO] 与 超守恒元素]）和建模方案。化石校准的时间树用于重建体型、感觉器官和色素沉着的演变，以建立生态形态差异的时间框架。基于不同分析的结果树在大多数节点中是一致的。通过考虑方法适应度、形态信息和拓扑测试，仔细评估了几个不一致的节点。该评估有利于使用 USCO 氨基酸矩阵和复杂的位点异质模型（CAT$+$GTR 和 LG$+$PMSF (C60)）分析得到的良好解析拓扑。首选拓扑支持单系超科 Tomoceroidea 作为早期分化的谱系和 Entomobryoidea 和 Isotomoidea 之间的姐妹关系。Tomoceridae科被恢复为单系，而 Oncopoduridae 则作为并系群被发现，而 Harlomillsia 是 Tomoceridae 的姐妹，因此值得作为 Harlomillsiidae Yu 和 Zhang fam 的单独家庭地位。n. 祖先昆虫纲被重建为地表生活，支持古生代-中生代土壤生物群的独立起源，并突出了地上和地下动物群之间古老的进化相互作用。[跳虫；系统基因组学；土壤生活适应；全基因组测序。]。并强调地上和地下动物群之间古老的进化相互作用。[跳虫；系统基因组学；土壤生活适应；全基因组测序。]。并强调地上和地下动物群之间古老的进化相互作用。[跳虫；系统基因组学；土壤生活适应；全基因组测序。]。