Data from: Phylogenomic interrogation of Arachnida reveals systemic conflicts in phylogenetic signal

Chelicerata represents one of the oldest groups of arthropods, with a fossil record extending to the Cambrian, and is sister group to the remaining extant arthropods, the mandibulates. Attempts to resolve the internal phylogeny of chelicerates have achieved little consensus, due to marked discord in both morphological and molecular hypotheses of chelicerate phylogeny. The monophyly of Arachnida, the terrestrial chelicerates, is generally accepted, but has garnered little support from molecular data, which have been limited either in breadth of taxonomic sampling or in depth of sequencing. To address the internal phylogeny of this group, we employed a phylogenomic approach, generating transcriptomic data for 17 species in combination with existing data, including two complete genomes. We analyzed multiple data sets containing up to 1,235,912 sites across 3,644 loci, using alternative approaches to optimization of matrix composition. Here, we show that phylogenetic signal for the monophyly of Arachnida is restricted to the 500 slowest-evolving genes in the data set. Accelerated evolutionary rates in Acariformes, Pseudoscorpiones, and Parasitiformes potentially engender long-branch attraction artifacts, yielding nonmonophyly of Arachnida with increasing support upon incrementing the number of concatenated genes. Mutually exclusive hypotheses are supported by locus groups of variable evolutionary rate, revealing significant conflicts in phylogenetic signal. Analyses of gene-tree discordance indicate marked incongruence in relationships among chelicerate orders, whereas derived relationships are demonstrably robust. Consistently recovered and supported relationships include the monophyly of Chelicerata, Euchelicerata, Tetrapulmonata, and all orders represented by multiple terminals. Relationships supported by subsets of slow-evolving genes include Ricinulei + Solifugae; a clade comprised of Ricinulei, Opiliones, and Solifugae; and a clade comprised of Tetrapulmonata, Scorpiones, and Pseudoscorpiones. We demonstrate that outgroup selection without regard for branch length distribution exacerbates long-branch attraction artifacts and does not mitigate gene-tree discordance, regardless of high gene representation for outgroups that are model organisms. Arachnopulmonata (new name) is proposed for the clade comprising Scorpiones + Tetrapulmonata (previously named Pulmonata).

螯肢亚门（Chelicerata）是最为古老的节肢动物类群之一，其化石记录可追溯至寒武纪（Cambrian），与其余现生节肢动物类群颚类（mandibulates）互为姊妹群。此前针对螯肢类内部系统发育关系的解析尝试几乎未达成共识，这是因为螯肢类系统发育的形态学假说与分子假说均存在显著冲突。陆生螯肢类类群蛛形纲（Arachnida）的单系性假说虽已被广泛接受，但几乎未获得分子数据的支持——现有分子数据要么在分类群采样广度上存在局限，要么测序深度不足。为解析该类群的内部系统发育关系，本研究采用系统发育组学方法，结合包括2个完整基因组在内的已有数据，新生成了17个物种的转录组数据。本研究针对包含3644个基因座、总计最多1235912个位点的多组数据集，采用多种矩阵构建优化方案开展分析。结果显示，支持蛛形纲单系性的系统发育信号仅存在于数据集内演化速率最慢的500个基因中。螨形总目（Acariformes）、伪蝎目（Pseudoscorpiones）与蜱形总目（Parasitiformes）的演化速率加快，可能引发长枝吸引（long-branch attraction, LBA）假象，随着串联基因数量增加，蛛形纲非单系性的支持率会随之升高。不同演化速率的基因座类群分别支持相互排斥的假说，这表明系统发育信号存在显著冲突。基因树冲突分析结果显示，螯肢类各目之间的系统发育关系存在显著不一致，但衍生的类群关系则表现出较强的稳定性。本研究一致恢复并得到支持的类群关系包括：螯肢亚门、真螯肢亚门（Euchelicerata）、四肺类（Tetrapulmonata），以及所有具有多个代表物种的目级类群的单系性。由慢演化基因子集支持的类群关系包括：巨鞭蝎目（Ricinulei）+避日目（Solifugae）；由巨鞭蝎目、盲蛛目（Opiliones）与避日目构成的一支单系群；以及由四肺类、蝎目（Scorpiones）与伪蝎目构成的一支单系群。本研究证实，若仅选择外类群而不考虑枝长分布情况，会加剧长枝吸引假象，且无法缓解基因树冲突——即便作为外类群的模式生物拥有较高的基因覆盖度。本研究将蝎目与四肺类构成的单系群（此前被称为肺类（Pulmonata））新拟名为蛛肺类（Arachnopulmonata）。