Data from: Brooding phylogenomics: Target-capture probe sets for the analysis of ultraconserved elements in the Peracarida

Sequencing via target capture is becoming an important phylogenetic tool
that has been used to great effect with organisms such as insects,
arachnids, and various vertebrate taxa. However, other taxa, such as the
Crustacea, have received limited genomic attention despite the amount of
diversity present within the taxon and the intensity of research on this
group. Here we describe generalized probe sets targeting ultraconserved
elements (UCEs) for members of the crustacean orders Amphipoda and Isopoda
in the superorder Peracarida. These probe sets employ 50-100,000 probes
targeting up to 10,000 UCE loci. In-silico analysis of these probe sets
recovered an average of 5,087 UCE loci; an average of 4,633 unique loci
were retained post-filtering. Phylogenetic analysis of this dataset
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 members of the amphipod families Crangonyctidae and
Gammaridae was conducted. This analysis extracted up to 4,864 unique loci
from the taxa sequenced, with an average of 1,897 loci among all taxa.
Phylogenetic analysis 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.