Supplementary information of: High Utility of Ultraconserved Elements (UCE) for Disentangling the Elusive Relationships of Tarantulas

Although tarantulas are a widespread, highly diversified, and charismatic spider group, our understanding of their evolution remains limited. A recent transcriptome-based approach, including 16% of the nominal tarantula genera (25), provided the first robust phylogenetic hypothesis of deep tarantula relationships. However, transcriptomics has practical downsides, making it less than ideal for phylogenomic analyses. Ultraconserved Elements (UCE) sequencing, a cost-effective alternative, allows for the simultaneous reading of hundreds of loci and utilizing samples with degraded DNA, including museum material, but its utility for resolving tarantula relationships remains to be tested. In this study, I recovered up to ~850 unique UCE loci from publicly available individual tarantula transcriptomes. Phylogenetic estimation using these loci resulted in topologies identical to those obtained from the published complete transcriptomic datasets, with limited phylogenetic uncertainty restricted to two branches in the tarantula tree of life. I conclude that UCE information has great potential for resolving tarantula relationships and that numerous UCE loci can be harvested from tarantula transcriptomic data. Finally, I provide databases of transcripts and UCE loci for the 27 currently available tarantula genera, facilitating their inclusion in future phylogenomic studies with deeper taxon coverage.

尽管捕鸟蛛是一类分布广泛、类群高度多样且极具魅力的蜘蛛类群，但学界对其演化历程的认知仍较为有限。近期一项基于转录组（transcriptome）的研究纳入了16%的已命名捕鸟蛛属（共计25个属），首次构建了关于捕鸟蛛深层演化关系的稳健系统发育假说。不过转录组学存在实际应用局限，并非系统基因组（phylogenomic）分析的最优选择。超保守元件（Ultraconserved Elements, UCE）测序作为一种经济高效的替代方案，可同时读取数百个基因位点，并适用于降解DNA样本（包括馆藏标本），但其在解析捕鸟蛛演化关系中的实用性仍有待验证。本研究从公开可得的单只捕鸟蛛转录组数据中，成功获取了最多约850个独特的UCE位点。利用这些位点进行系统发育推断得到的拓扑结构，与已发表的完整转录组数据集所得结果完全一致，仅在捕鸟蛛生命之树的两个分支上存在有限的系统发育不确定性。本研究结论表明，UCE数据在解析捕鸟蛛演化关系方面具有巨大潜力，且可从捕鸟蛛转录组数据中挖掘得到大量UCE位点。此外，本研究为当前已有的27个捕鸟蛛属提供了转录本与UCE位点数据库，可为未来开展类群覆盖度更高的系统基因组学研究提供便利。