Data from: Resolving relationships among the megadiverse butterflies and moths with a novel pipeline for Anchored Phylogenomics

The advent of next-generation sequencing technology has allowed for the
collection of large portions of the genome for phylogenetic analysis.
Hybrid enrichment and transcriptomics are two techniques that leverage
next-generation sequencing and have shown much promise. However, methods
for processing hybrid enrichment data are still limited. We developed a
pipeline for anchored hybrid enrichment (AHE) read assembly, orthology
determination, contamination screening, and data processing for sequences
flanking the target “probe” region. We apply this approach to study the
phylogeny of butterflies and moths (Lepidoptera), a megadiverse group of
more than 157,000 described species with poorly understood deep-level
phylogenetic relationships. We introduce a new, 855 locus anchored hybrid
enrichment kit for Lepidoptera phylogenetics and compare resulting trees
to those from transcriptomes. The enrichment kit was designed from
existing genomes, transcriptomes and expressed sequence tag (EST) data and
was used to capture sequence data from 54 species from 23 lepidopteran
families. Phylogenies estimated from AHE data were largely congruent with
trees generated from transcriptomes, with strong support for relationships
at all but the deepest taxonomic levels. We combine AHE and transcriptomic
data to generate a new Lepidoptera phylogeny, representing 76 exemplar
species in 42 families. The tree provides robust support for many
relationships, including those among the seven butterfly families. The
addition of AHE data to an existing transcriptomic dataset lowers node
support along the Lepidoptera backbone, but firmly places taxa with AHE
data on the phylogeny. To examine the efficacy of AHE at different
taxonomic levels, phylogenetic analyses were also conducted on a sister
group representing a more recent divergence, the Saturniidae and
Sphingidae. These analyses utilized sequences from the probe region and
data flanking it, nearly doubled the size of the dataset; all resulting
trees were well supported. We hope that our data processing pipeline,
hybrid enrichment gene set, and approach of combining AHE data with
transcriptomes will be useful for the broader systematics community.