Department of Biological Sciences, The George Washington University, Washington, DC, USA.
Department of Entomology, Smithsonian Institution, National Museum of Natural History, Washington, DC, USA.
Mol Ecol Resour. 2020 Jan;20(1):185-203. doi: 10.1111/1755-0998.13099. Epub 2019 Oct 28.
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 includes 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 suggest monophyly of 'symphytognathoids'). Our preferred hypothesis 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 behavioural characters.
系统发生基因组学方法已被证明对解决蜘蛛生命树中的深节点和顽固类群非常有用。在蛛形纲动物中，转录组方法可能会产生数千个基因座，而目标捕获方法（使用之前设计的蛛形纲特异性探针组）最多可以靶向约 1000 个基因座。在这里，我们开发了一种专门针对蜘蛛的目标捕获探针组，其中包含超过 2000 个超保守元件（UCEs），然后通过测序和系统发育分析证明了该探针组的实用性。我们使用三个蜘蛛基因组（Loxosceles、Parasteatoda 和 Stegodyphus）设计了“蜘蛛特异性”探针组，并确保新设计的探针组包含以前设计的蛛形纲探针组中的 UCEs。新的“蜘蛛特异性”探针用于对 51 个标本的 UCE 基因座进行测序。其余样本包括五个蜘蛛基因组和使用蛛形纲探针组富集的类群。“蜘蛛特异性”探针还用于从 84 个代表类群的总类群中收集基因座。在将这些 84 个分类群映射到蛛形纲探针组时，我们最多捕获了 710 个 UCE 基因座，而蜘蛛特异性探针组则从同一分类群样本中捕获了多达 1547 个 UCE 基因座。使用最大似然和合并方法进行的系统发育分析证实了最近转录组分析解决的大多数节点，但并非全部（例如，UCE 数据表明“拟态蛛形类”的单系性）。基于拓扑测试的我们首选假设表明，“拟态蛛形类”（微型圆网蜘蛛）的单系性，在以前的研究中，这种单系性仅得到形态学和行为特征的结合支持。
