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）是最古老的节肢动物类群之一，其化石记录可追溯至寒武纪，且与其余现存节肢动物——颚亚门类群（mandibulates）互为姊妹群。此前针对螯肢亚门内部系统发育关系的解析尝试始终难以达成共识，这是因为螯肢亚门系统发育的形态学与分子学假说均存在显著冲突。作为陆生螯肢类群的蛛形纲（Arachnida）单系性虽已被广泛认可，但几乎未获得分子数据的支持：这类分子数据要么在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，结合包含2个完整基因组的已有数据，新生成了17个物种的转录组（transcriptomic）数据。我们分析了多组数据集，这些数据集涵盖3644个基因座、最多1235912个比对位点，并采用多种不同策略对序列矩阵的组成进行优化。本研究结果显示，支撑蛛形纲单系性的系统发育信号仅局限于数据集中进化速率最慢的500个基因。真螨目（Acariformes）、伪蝎目（Pseudoscorpiones）与寄螨目（Parasitiformes）的进化速率加快，可能引发长枝吸引（long-branch attraction）假象，导致随着串联基因数量的增加，蛛形纲非单系性的支持率不断提升。进化速率各异的基因座组会支持互斥的系统发育假说，这揭示了不同基因的系统发育信号间存在显著冲突。对基因树冲突的分析表明，螯肢亚门各目之间的系统发育关系存在显著不一致，但衍生的高阶系统发育关系则表现出可靠的稳定性。被一致恢复并得到支持的系统发育关系包括：螯肢亚门、真螯肢亚门（Euchelicerata）、四肺类（Tetrapulmonata），以及所有由多个终端类群代表的目均呈现单系性。由慢速进化基因子集支持的系统发育关系包括：有鞭目（Ricinulei）+ 避日目（Solifugae）；由有鞭目、盲蛛目（Opiliones）与避日目组成的单系支系；以及由四肺类、蝎目（Scorpiones）与伪蝎目组成的单系支系。本研究证实，不考虑枝长分布的外类群（outgroup）选择会加剧长枝吸引假象，且无法缓解基因树冲突——即便作为模式生物的外类群拥有极高的基因覆盖度。蛛肺类（Arachnopulmonata，新拟名称）被提议用于包含蝎目与四肺类的单系支系，该支系此前被称为肺类（Pulmonata）。