Data from: High phylogenetic utility of an ultraconserved element probe set designed for Arachnida

Arachnida is an ancient, diverse, and ecologically important animal group that contains a number of species of interest for medical, agricultural, and engineering applications. Despite their importance, many aspects of the arachnid tree of life remain unresolved, hindering comparative approaches to arachnid biology. Biologists have made considerable efforts to resolve the arachnid phylogeny; yet, limited and challenging morphological characters, as well as a dearth of genetic resources, have hindered progress. Here, we present a genomic toolkit for arachnids featuring hundreds of conserved DNA regions (ultraconserved elements or UCEs) that allow targeted sequencing of any species in the arachnid tree of life. We used recently developed capture probes designed from conserved regions of available arachnid genomes to enrich a sample of loci from 32 diverse arachnids. Sequence capture returned an average of 487 UCE loci for all species, with a range from 170 to 722. Phylogenetic analysis of these UCEs produced a highly resolved arachnid tree with relationships largely consistent with recent transcriptome-based phylogenies. We also tested the phylogenetic informativeness of UCE probes within the spider, scorpion, and harvestman orders, demonstrating the utility of these markers at shallower taxonomic scales, and suggesting that these loci will be useful for species-level differences. This probe set will open the door to phylogenomic and population genomic studies across the arachnid tree of life, enabling systematics, species delimitation, species discovery, and conservation of these diverse arthropods.

蛛形纲（Arachnida）是一类古老、多样且在生态系统中具有核心意义的动物类群，包含诸多在医学、农业及工程应用领域具备研究价值的物种。尽管该类群具有如此重要的地位，但其生命之树的诸多分支仍未得到解析，这阻碍了蛛形纲生物学的比较研究进展。生物学家已为解析蛛形纲系统发育关系付出了大量努力，但有限且难以获取的形态学性状，加之遗传资源的匮乏，进一步阻碍了相关研究的推进。本研究面向蛛形纲开发了一套基因组学工具包，其包含数百个保守DNA区域——超保守元件（ultraconserved elements, UCEs），可实现对蛛形纲生命之树中任意物种的靶向测序。研究团队利用基于现有蛛形纲基因组保守区域设计的新型捕获探针，对32个不同蛛形纲物种的基因座进行了富集。序列捕获实验为每个物种平均获得487个UCE基因座，覆盖范围为170至722个。对这些UCE进行系统发育分析后，得到了分辨率极高的蛛形纲系统发育树，其物种间亲缘关系与近期基于转录组的系统发育研究结果基本一致。本研究还测试了UCE探针在蜘蛛目、蝎目和盲蛛目内的系统发育信息效能，结果表明这类分子标记在较低分类阶元尺度上同样具备应用价值，且提示这些基因座可有效用于物种水平的差异分析。这套捕获探针将为跨蛛形纲生命之树的系统基因组学与种群基因组学研究打开大门，为这类多样节肢动物的分类学研究、物种界定、物种发现及物种保护提供有力支撑。