Data from: Expanding anchored hybrid enrichment to resolve both deep and shallow relationships within the spider tree of life

Background: Despite considerable effort, progress in spider molecular
systematics has lagged behind many other comparable arthropod groups,
thereby hindering family-level resolution, classification, and testing of
important macroevolutionary hypotheses. Recently, alternative targeted
sequence capture techniques have provided molecular systematics a powerful
tool for resolving relationships across the Tree of Life. One of these
approaches, Anchored Hybrid Enrichment (AHE), is designed to recover
hundreds of unique orthologous loci from across the genome, for resolving
both shallow and deep-scale evolutionary relationships within non-model
systems. Herein we present a modification of the AHE approach that expands
its use for application in spiders, with a particular emphasis on the
infraorder Mygalomorphae. Results: Our aim was to design a set of probes
that effectively capture loci informative at a diversity of phylogenetic
timescales. Following identification of putative arthropod-wide loci, we
utilized homologous transcriptome sequences from 17 species across all
spiders to identify exon boundaries. Conserved regions with variable
flanking regions were then sought across the tick genome, three published
araneomorph spider genomes, and raw genomic reads of two mygalomorph taxa.
Following development of the 585 target loci in the Spider Probe Kit, we
applied AHE across three taxonomic depths to evaluate performance:
deep-level spider family relationships (33 taxa, 327 loci); family and
generic relationships within the mygalomorph family Euctenizidae (25 taxa,
403 loci); and species relationships in the North American tarantula genus
Aphonopelma (83 taxa, 581 loci). At the deepest level, all three major
spider lineages (the Mesothelae, Mygalomorphae, and Araneomorphae) were
supported with high bootstrap support. Strong support was also found
throughout the Euctenizidae, including generic relationships within the
family and species relationships within the genus Aptostichus. As in the
Euctenizidae, virtually identical topologies were inferred with high
support throughout Aphonopelma. Conclusions: The Spider Probe Kit, the
first implementation of AHE methodology in Class Arachnida, holds great
promise for gathering the types and quantities of molecular data needed to
accelerate an understanding of the spider Tree of Life by providing a
mechanism whereby different researchers can confidently and effectively
use the same loci for independent projects, yet allowing synthesis of data
across independent research groups.