Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI 53706, USA.
Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI 53706, USA.
Mol Phylogenet Evol. 2022 Mar;168:107378. doi: 10.1016/j.ympev.2021.107378. Epub 2021 Dec 27.
Excepting a handful of nodes, phylogenetic relationships between chelicerate orders remain poorly resolved, due to both the incidence of long branch attraction artifacts and the limited sampling of key lineages. It has recently been shown that increasing representation of basal nodes plays an outsized role in resolving the higher-level placement of long-branch chelicerate orders. Two lineages have been consistently undersampled in chelicerate phylogeny. First, sampling of the miniaturized order Palpigradi has been restricted to a fragmentary transcriptome of a single species. Second, sampling of Opilioacariformes, a rarely encountered and key group of Parasitiformes, has been restricted to a single exemplar. These two lineages exhibit dissimilar properties with respect to branch length; Opilioacariformes shows relatively low evolutionary rate compared to other Parasitiformes, whereas Palpigradi possibly acts as another long-branch order (an effect that may be conflated with the degree of missing data). To assess these properties and their effects on tree stability, we constructed a phylogenomic dataset of Chelicerata wherein both lineages were sampled with three terminals, increasing the representation of these taxa per locus. We examined the effect of subsampling phylogenomic matrices using (1) taxon occupancy, (2) evolutionary rate, and (3) a principal components-based approach. We further explored the impact of taxon deletion experiments that mitigate the effect of long branches. Here, we show that Palpigradi constitutes a fourth long-branch chelicerate order (together with Acariformes, Parasitiformes, and Pseudoscorpiones), which further destabilizes the chelicerate backbone topology. By contrast, the slow-evolving Opilioacariformes were consistently recovered within Parasitiformes, with certain subsampling practices recovering their placement as the sister group to the remaining Parasitiformes. Whereas the inclusion of Opilioacariformes always resulted in the non-monophyly of Acari with support, deletion of Opilioacariformes from datasets consistently incurred the monophyly of Acari except in matrices constructed on the basis of evolutionary rate. Our results strongly suggest that Acari is an artifact of long- branch attraction.
除了少数几个节点外，由于长枝吸引artifact 的出现以及关键谱系采样的限制，蛛形纲目之间的系统发育关系仍未得到很好的解决。最近的研究表明，增加基础节点的代表性在解决长枝蛛形纲目高级别位置方面起着非常重要的作用。在蛛形纲动物的系统发育中，有两个谱系一直被低估。首先，对微型目节肢动物的采样仅限于一个单一物种的不完整转录组。其次，对 Opilioacariformes 的采样，一种罕见且关键的寄生目，仅限于一个单一的标本。这两个谱系在分支长度上表现出不同的特征；与其他寄生目相比，Opilioacariformes 的进化速度相对较低，而节肢动物可能是另一个长枝目（这种效应可能与缺失数据的程度混淆）。为了评估这些特性及其对树稳定性的影响，我们构建了一个蛛形纲动物的基因组数据集，其中这两个谱系都用三个末端进行了采样，增加了每个基因座的这些分类单元的代表性。我们使用（1）分类单元占有率、（2）进化率和（3）基于主成分的方法来检验基因组矩阵的抽样效果。我们进一步探讨了减轻长枝效应的分类单元删除实验的影响。在这里，我们表明节肢动物构成了第四个长枝蛛形纲目（与蜱螨目、寄生目和伪蝎目一起），这进一步破坏了蛛形纲动物的骨干拓扑结构。相比之下，进化缓慢的 Opilioacariformes 始终在寄生目中被回收，某些抽样方法将它们的位置恢复为与剩余寄生目姐妹群的位置。尽管 Opilioacariformes 的包含总是导致蜱螨目的非单系性，但在基于进化率构建的矩阵中除外，从数据集删除 Opilioacariformes 总是导致蜱螨目的单系性。我们的研究结果强烈表明，蜱螨目是长枝吸引 artifact 的结果。
