Brooding Phylogenomics: Target-Capture Probe Sets for the Analysis of Ultraconserved Elements in the Peracarida

Sequencing via target capture has been used to great effect in phylogenetic studies of organisms such as insects, arachnids and vertebrates. However, other taxa have received limited genomic attention despite their diversity and the intensity of research on such groups. Here, we describe generalised probe sets targeting ultraconserved elements (UCEs) for members of the crustacean orders Amphipoda and Isopoda in the superorder Peracarida. These sets employ ~10,000-100,000 probes targeting up to 10,000 loci. In silico analyses of these probe sets recovered an average of 5087 loci, while an average of 4633 was retained post-filtering. Phylogenetic analysis of these datasets resulted in well-supported trees that align with previously reconstructed relationships among the taxa selected while also providing resolution of previously uncertain nodes. Following the in silico analysis, an in vitro analysis targeting several amphipod and isopod families was conducted. This analysis extracted up to 4864 unique loci from the taxa sequenced, with an average of 1897 loci among all taxa. This represents an order-of-magnitude increase versus previously published sets, which were only able to recover < 250 UCEs among peracarid taxa. Phylogenetic analyses of the data generated in vitro resulted in well-supported trees that were resolved at both shallow and deep taxonomic levels. Both analyses demonstrate the utility of these probe sets for phylogenomic research within the Peracarida. Additional attention to members of the superorder using target enrichment will doubtlessly assist in resolving poorly understood aspects of their evolutionary history and expand current knowledge of this group.