In Silico Assessment of Probe-Capturing Strategies and Effectiveness in the Spider Sub-Lineage Araneoidea (Order: Araneae)

Reduced-representation sequencing (RRS) has made it possible to identify hundreds thousands of genetic markers for phylogenomic analysis the testing phylogenetic hypotheses in non-model taxa. The use customized probes capture (i.e., ultraconserved element (UCE) approach) further boosted efficiency collecting markers. Three UCE probe sets pertaining spiders (Araneae) have been published, including one suborder Mesothelae (an early diverged spider group), Araneae, and Arachnida. In current study, we developed a set specifically superfamily Araneoidea spiders. We then combined three Araneoidea, Arachnid into fourth set. effectiveness 4 sets, used captured loci 15 genomes silico (6 from Araneoidea). outperformed all other terms number loci. Araneae most included species. reconstruction trees using four data matrices generated 50% 75% occupancies indicated that node linked Stegodyphus + RTA (retrolateral tibial apophysis) clade unstable nodal supports bootstrap values, gCFs, sCFs. Our results strongly indicate developing ad hoc sub-lineages is important cases where origins lineage are ancient (e.g., ~380 MYA).