Despite application of genome-scale datasets, the phylogenetic placement of scorpions within arachnids remains contentious between two different phylogenetic data classes. Paleontologists continue to recover scorpions in a basally branching position, partly owing to their morphological similarity to extinct marine orders like Eurypterida (sea scorpions). Phylogenomic datasets consistently recover scorpions in a derived position, as the sister group of Tetrapulmonata (a clade of arachnids that includes spiders). To adjudicate between these hypotheses using a rare genomic change (RGC), we leveraged the recent discovery of ancient paralogy in spiders and scorpions to assess phylogenetic placement. We identified homologs of four transcription factors required for appendage patterning (dachshund, homothorax, extradenticle, and optomotor blind) in arthropods that are known to be duplicated in spiders. Using genomic resources for a spider, a scorpion, and a harvestman, we conducted gene tree analyses and assayed expression patterns of scorpion gene duplicates. Here we show that scorpions, like spiders, retain two copies of all four transcription factors, whereas arachnid orders like mites and harvestmen bear a single copy. A survey of embryonic expression patterns of the scorpion paralogs closely matches those of their spider counterparts, with one paralog consistently retaining the putatively ancestral pattern found in the harvestman, as well as the mite, and/or other outgroups. These data comprise a rare genomic change in chelicerate phylogeny supporting the inference of a distal placement of scorpions. Beyond demonstrating the diagnostic power of developmental genetic data as a phylogenetic data class, a derived placement of scorpions within the arachnids, together with an array of stem-group Paleozoic scorpions that occupied marine habitats, effectively rules out a scenario of a single colonization of terrestrial habitat within Chelicerata, even in tree topologies contrived to recover the monophyly of Arachnida.

中文翻译：

---

发育基因表达作为系统发育数据类别：支持蛛形纲的单生。

尽管应用了基因组规模的数据集，但在两个不同的系统发育数据类别之间，蝎子在蜘蛛体内的系统发育位置仍然存在争议。古生物学家继续将蝎子恢复到基部分支的位置，部分原因是它们的形态与灭绝的海象，如Eurypterida（海蝎）在形态上相似。系统生物学数据集始终如一地将蝎子恢复为蝎形纲（包括蜘蛛的蛛形纲）的姊妹群。为了使用罕见的基因组变化（RGC）判断这些假设，我们利用蜘蛛和蝎子中古代寄生虫的最新发现来评估系统发生位置。我们确定了附件模式（腊肠，同胸，齿外和视动盲）在已知可在蜘蛛中复制的节肢动物中。利用蜘蛛，蝎子和收割者的基因组资源，我们进行了基因树分析并测定了蝎子基因重复序列的表达模式。在这里，我们显示蝎子像蜘蛛一样，保留了所有四个转录因子的两个副本，而蜘蛛纲的螨虫和收割者则拥有一个副本。一项对蝎子旁系同源物的胚胎表达方式的调查非常接近其蜘蛛对应体的胚胎表达方式，其中一种旁系同源物始终保留着收割者，螨虫和/或其他外来群体中发现的推定祖先的形态。这些数据包括螯合物系统发育中罕见的基因组变化，支持了蝎子向远侧放置的推断。