Supplementary material for Klementz et al. (2025) Exploring genome architecture as a source of phylogenetic characters for resolving the apulmonate arachnid polytomy. Molecular Phylogenetics and Evolution.

Chromosome-level genome assemblies are powerful tools for identifying the presence of rare genomic changes that can overcome phylogenetically intractable problems. Chelicerata, the sister group to the remaining arthropods, harbors a soft polytomy at the base of an internal node named Euchelicerata, which is variably resolved across phylogenomic studies. As a result, seven orders, comprising horseshoe crabs and six apulmonate arachnid lineages, exhibit highly unstable placements from one study to the next, typically with maximal nodal support. Here, we analyzed recently released chromosome-level genomes of two of these orders, Opiliones (harvestmen) and Solifugae (camel spiders). We show that both Opiliones and Solifugae exhibit an unduplicated genome condition, as inferred from analysis of gene clusters, microRNAs, and macrosynteny. These results are congruent with phylogenomic studies that have refuted traditional morphological placements of Opiliones and Solifugae as close relatives of orders within Arachnopulmonata, a subset of six arachnid orders that are united by a shared whole genome duplication. Additionally, we examine irreversible chromosome fusion-with-mixing events as potential sources of phylogenetic data. We show that while fusion and mixing events are common in apulmonate arachnids, multiple mixing events support incompatible unrooted tree topologies. These results suggest that fusion and mixing events have evolved convergently in the chelicerate tree of life, particularly for extant lineages with a small number of chromosomes. Overall, our findings demonstrate that broader sampling of chelicerate genomes and establishment of genomic resources for key missing orders are essential to unlocking the potential of rare genomic changes as phylogenetic data sources.

染色体水平基因组组装（chromosome-level genome assemblies）是识别稀有基因组变异的有力工具，这类变异可用于破解系统发育研究中的棘手难题。螯肢亚门（Chelicerata）作为其余节肢动物的姊妹群，在名为真螯肢亚门（Euchelicerata）的内部节点基部存在一处软多歧支（soft polytomy），该节点在不同系统基因组学研究中的分辨率存在显著差异。因此，包含鲎类与6个无肺蛛形纲动物（apulmonate arachnid）支系在内的7个蛛形纲目，其系统发育位置在不同研究中表现出极强的不稳定性，即便此类节点的支持度往往达到最高。本研究分析了上述7个目中两个类群新近发布的染色体水平基因组：盲蛛目（Opiliones，俗称长脚盲蛛）与避日目（Solifugae，俗称骆驼蜘蛛）。通过对基因簇、微小RNA（microRNAs）以及宏共线性（macrosynteny）的分析，我们发现盲蛛目与避日目的基因组均未经历复制事件。该结果与此前多项系统基因组学研究的结论一致——这些研究驳斥了传统形态学观点，即认为盲蛛目与避日目是有肺蛛形亚纲（Arachnopulmonata）内多个类群的近亲；有肺蛛形亚纲包含6个蛛形纲目，其共同特征为经历过一次全基因组复制（whole genome duplication）事件。此外，本研究还将不可逆的染色体融合混合事件（chromosome fusion-with-mixing）作为潜在的系统发育数据来源进行了分析。研究发现，尽管融合混合事件在无肺蛛形纲动物中较为常见，但多起混合事件却支持彼此不相容的无根树拓扑结构（unrooted tree topologies）。该结果表明，染色体融合混合事件在螯肢亚门的生命之树中呈现趋同演化特征，尤其在染色体数目较少的现存支系中更为显著。综上，本研究结果表明，若要充分挖掘稀有基因组变异作为系统发育数据来源的潜力，亟需扩大螯肢亚门基因组的采样范围，并为尚未完成基因组测序的关键类群建立基因组资源库。