Data from: Target gene enrichment in the cyclophyllidean cestodes, the most diverse group of tapeworms

The Cyclophyllidea is the most diverse order of tapeworms, encompassing
species that infect all classes of terrestrial tetrapods including humans
and domesticated animals. Available phylogenetic reconstructions based
either on morphology or molecular data lack the resolution to allow
scientists to either propose a solid taxonomy or infer evolutionary
associations. Molecular markers available for the Cyclophyllidea mostly
include ribosomal DNA and mitochondrial loci. In this study, we identified
3,641 single-copy nuclear coding loci by comparing the genomes of
Hymenolepis microstoma, Echinococcus granulosus, and Taenia solium. We
designed RNA baits based on the sequence of H. microstoma, and applied
target enrichment and Illumina sequencing to test the utility of those
baits to recover loci useful for phylogenetic analyses. We captured DNA
from five species of tapeworms representing two families of
cyclophyllideans. We obtained an average of 3,284 (90%) of the targets
from the test samples and then used captured sequences (2,181,361 bp in
total; fragment size ranging from 301 bp to 6,969 bp) to reconstruct a
phylogeny for the five test species plus the three species for which
genomic data are available. The results were consistent with the current
consensus regarding cyclophyllidean relationships. To assess the potential
for our method to yield informative genetic variation at intraspecific
scales, we extracted 14,074 single nucleotide polymorphisms (SNPs) from
alignments of four Arostrilepis macrocirrosa and two A. cooki and
successfully inferred their relationships. The results showed that our
target gene tools yield datasets that provide robust inferences at a range
of taxonomic scales in the Cyclophyllidea.