Data from: High phylogenetic utility of an ultraconserved element probe set designed for Arachnida
Starrett, James, San Diego State University
Derkarabetian, Shahan, San Diego State University, University of California System
Hedin, Marshal, San Diego State University
Bryson Jr., Robert W., Louisiana State University
McCormack, John E., Occidental College
Faircloth, Brant C., Louisiana State University of Alexandria
Bryson, Robert W., Occidental College, University of Washington
Published Oct 19, 2016 on Dryad.
Cite this dataset
Starrett, James et al. (2016). Data from: High phylogenetic utility of an ultraconserved element probe set designed for Arachnida [Dataset]. Dryad. https://doi.org/10.5061/dryad.5k3j3
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.
Zip file with Trinity assemblies for all samples in fasta format
Concatenated matrices in phylip for all data sets used in the study.
National Science Foundation, Award: DEB-1354558, DEB-1242260