Key Laboratory of Zoological Systematics and Application of Hebei Province, Institute of Life Science and Green Development, College of Life Sciences, Hebei University, Baoding, Hebei, 071002, China.
School of Life Sciences, Southwest University, Chongqing, 400700, China.
Cladistics. 2023 Apr;39(2):116-128. doi: 10.1111/cla.12523. Epub 2023 Jan 31.
Spiders are important models for evolutionary studies of web building, sexual selection and adaptive radiation. The recent development of probes for UCE (ultra-conserved element)-based phylogenomic studies has shed light on the phylogeny and evolution of spiders. However, the two available UCE probe sets for spider phylogenomics (Spider and Arachnida probe sets) have relatively low capture efficiency within spiders, and are not optimized for the retrolateral tibial apophysis (RTA) clade, a hyperdiverse lineage that is key to understanding the evolution and diversification of spiders. In this study, we sequenced 15 genomes of species in the RTA clade, and using eight reference genomes, we developed a new UCE probe set (41 845 probes targeting 3802 loci, labelled as the RTA probe set). The performance of the RTA probes in resolving the phylogeny of the RTA clade was compared with the Spider and Arachnida probes through an in-silico test on 19 genomes. We also tested the new probe set empirically on 28 spider species of major spider lineages. The results showed that the RTA probes recovered twice and four times as many loci as the other two probe sets, and the phylogeny from the RTA UCEs provided higher support for certain relationships. This newly developed UCE probe set shows higher capture efficiency empirically and is particularly advantageous for phylogenomic and evolutionary studies of RTA clade and jumping spiders.
蜘蛛是研究结网、性选择和适应性辐射等进化问题的重要模型。最近，基于 UCE（超保守元件）的系统发育基因组学研究探针的发展，揭示了蜘蛛的系统发育和进化。然而，蜘蛛系统发育基因组学中现有的两个 UCE 探针集（蜘蛛和蛛形纲探针集）在蜘蛛内部的捕获效率相对较低，并且没有针对 RTA（retrolateral tibial apophysis）进化枝进行优化，RTA 进化枝是理解蜘蛛进化和多样化的关键。在这项研究中，我们对 RTA 进化枝的 15 个物种的基因组进行了测序，并使用 8 个参考基因组，开发了一个新的 UCE 探针集（针对 3802 个基因座的 41845 个探针，标记为 RTA 探针集）。通过对 19 个基因组进行的计算机模拟测试，比较了 RTA 探针在解决 RTA 进化枝系统发育中的表现与蜘蛛和蛛形纲探针的表现。我们还在 28 个主要蜘蛛谱系的蜘蛛物种上进行了新探针集的实证测试。结果表明，RTA 探针集比其他两个探针集多回收了两倍和四倍的基因座，来自 RTA UCE 的系统发育为某些关系提供了更高的支持。这个新开发的 UCE 探针集在实证上显示出更高的捕获效率，特别有利于 RTA 进化枝和跳蛛的系统发育和进化研究。
