Spider-specific probe set for ultraconserved elements offers new perspectives on the evolutionary history of spiders (Arachnida, Araneae)

Phylogenomic methods have proven useful for resolving deep nodes and recalcitrant groups in the spider tree of life. Across arachnids, transcriptomic approaches may generate thousands of loci, and target-capture methods, using the previously designed arachnid-specific probe-set, can target a maximum of about 1,000 loci. Here, we develop a specialized target-capture probe set for spiders that contains over 2,000 ultraconserved elements (UCEs) and then demonstrate the utility of this probe set through sequencing and phylogenetic analysis. We designed the “spider-specific” probe set using three spider genomes (Loxosceles, Parasteatoda and Stegodyphus) and ensured that the newly designed probe-set include UCEs from the previously designed Arachnida probe set. The new “spider-specific” probes were used to sequence UCE loci in 51 specimens. The remaining samples included five spider genomes and taxa that were enriched using Arachnida probe set. The “spider-specific” probes were also used to gather loci from a total of 84 representative taxa across Araneae. On mapping these 84 taxa to the Arachnida probe set, we captured at most 710 UCE loci, while the spider specific probe set captured up to 1,547 UCE loci from the same taxon sample. Phylogenetic analyses using Maximum Likelihood and coalescent methods corroborate most nodes resolved by recent transcriptomic analyses, but not all (e.g., UCE data suggests monophyly of “symphytognathoids”). Our preferred analysis based on topology tests, suggests monophyly of the “symphytognathoids” (the miniature orb-weavers), which in previous studies has only been supported by a combination of morphological and behavioral characters.

系统发育基因组学方法已被证实可用于解析蜘蛛生命之树中的深层节点与疑难类群。在蛛形纲类群中，转录组学方法可获得数千个基因座，而采用此前设计的蛛形纲特异性探针组的靶向捕获测序法，最多可靶向约1000个基因座。本研究开发了一款针对蜘蛛的专属靶向捕获探针组，其包含超过2000个超保守元件（ultraconserved elements, UCEs），并通过测序与系统发育分析验证了该探针组的实用性。我们基于褐隐蛛属（Loxosceles）、拟肥腹蛛属（Parasteatoda）以及诡蛛属（Stegodyphus）的三个蜘蛛基因组，设计了这款“蜘蛛特异性”探针组，并确保新探针组涵盖了此前设计的蛛形纲探针组中的超保守元件。我们利用这款新的“蜘蛛特异性”探针对51份标本的超保守元件基因座进行了测序。剩余样本包括5份蜘蛛基因组，以及采用蛛形纲探针组完成富集的类群。该“蜘蛛特异性”探针还被用于从蜘蛛目（Araneae）的共计84个代表性类群中获取基因座。将这84个类群比对至蛛形纲探针组时，最多可捕获710个超保守元件基因座；而采用蜘蛛特异性探针组时，从同一类群样本中最多可捕获1547个超保守元件基因座。采用最大似然法与溯祖法进行的系统发育分析，验证了近期转录组学研究中解析出的多数节点，但并非全部（例如，超保守元件数据支持短尾蛛类群（symphytognathoids）为单系群）。我们基于拓扑检验得到的最优分析结果显示，短尾蛛类群（即微型园蛛类）为单系群，而此前的相关研究仅通过形态学与行为学特征的组合支持这一结论。