Limits of exon capture efficiency for phylogenomics using nudibranch gastropods (Mollusca: Heterobranchia) as a case...

Target capture is an effective tool for phylogenomic reconstruction of evolutionary histories. This sequencing methodology is cost-effective and allows the use of older or poorly preserved specimens. One important consideration while applying target capture is the rate of divergence of the group under study. The success of this approach depends on the distance of the bait set with the target taxon, affecting the sequencing efficiency and the ability to extract the target loci. However, the threshold distance at which the efficiency decreases is still unclear, varying between studies and taxonomic groups. In nudibranch mollusks, an exon capture bait set was designed for the suborder Doridina. However, the usefulness of this bait set in other clades has not been explored. We investigate the efficiency and taxonomic limits of target capture sequencing in evolutionarily distant taxa, testing the capacity of inferring the evolutionary relationships throughout the order Nudibranchia. Seventy-nine species across two diverse suborders and 12 superfamilies were sequenced using an exon capture bait set designed for Doridina. Although species of the suborder Cladobranchia were successfully sequenced, a decrease in the number of captured genes is observed, showing that the capture efficiency significantly decreases after a threshold bait-to-target DNA distance of 18%. Even so, the results obtained from phylogenetic analyses shed light on relationships among nudibranch taxa, addressing questions that have remained controversial due to the lack of support in previous analyses, such as the position of the genus Doridoxa within Doridina, supporting Phyllidioidea as monophyletic or the paraphyletic nature of Chromodoridoidea.