Data from: High phylogenetic utility of an ultraconserved element probe set designed for Arachnida

Arachnida is an ancient, diverse, and ecologically important animal group
that contains a number of species of interest for medical, agricultural,
and engineering applications. Despite their importance, many aspects of
the arachnid tree of life remain unresolved, hindering comparative
approaches to arachnid biology. Biologists have made considerable efforts
to resolve the arachnid phylogeny; yet, limited and challenging
morphological characters, as well as a dearth of genetic resources, have
hindered progress. Here, we present a genomic toolkit for arachnids
featuring hundreds of conserved DNA regions (ultraconserved elements or
UCEs) that allow targeted sequencing of any species in the arachnid tree
of life. We used recently developed capture probes designed from conserved
regions of available arachnid genomes to enrich a sample of loci from 32
diverse arachnids. Sequence capture returned an average of 487 UCE loci
for all species, with a range from 170 to 722. Phylogenetic analysis of
these UCEs produced a highly resolved arachnid tree with relationships
largely consistent with recent transcriptome-based phylogenies. We also
tested the phylogenetic informativeness of UCE probes within the spider,
scorpion, and harvestman orders, demonstrating the utility of these
markers at shallower taxonomic scales, and suggesting that these loci will
be useful for species-level differences. This probe set will open the door
to phylogenomic and population genomic studies across the arachnid tree of
life, enabling systematics, species delimitation, species discovery, and
conservation of these diverse arthropods.