A novel probe set for the phylogenomics and evolution of RTA spiders

Spiders are important models for evolutionary studies of web building,
sexual selection and adaptive radiation. The recent development of probes
for UCE-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 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.