title: High phylogenetic utility of an ultraconserved element probe set designed for Arachnida.
abstract: 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.
authors: Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, CA, 92182, USA.
authors: James
authors: J
authors: Starrett
authors: Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, CA, 92182, USA.|Department of Biology, University of California, 900 University Avenue, Riverside, CA, 92521, USA.
authors: Shahan
authors: S
authors: Derkarabetian
authors: Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, CA, 92182, USA.
authors: Marshal
authors: M
authors: Hedin
authors: Department of Biology and Burke Museum of Natural History and Culture, University of Washington, 4331 Memorial Way Northeast, Seattle, WA, 98195, USA.|Moore Laboratory of Zoology, Occidental College, Los Angeles, CA, 90041, USA.
authors: Robert W
authors: RW
authors: Bryson
authors: Moore Laboratory of Zoology, Occidental College, Los Angeles, CA, 90041, USA.
authors: John E
authors: JE
authors: McCormack
authors: Department of Biological Sciences and Museum of Natural Science, Louisiana State University, Baton Rouge, LA, 70803, USA.
authors: Brant C
authors: http://orcid.org/0000-0002-1943-0217
authors: BC
authors: Faircloth
mesh_terms: D000818:Animals; D001097:Arachnida / Q000145:classification* / Q000235:genetics; D015342:DNA Probes; D023281:Genomics; D010802:Phylogeny; D017422:Sequence Analysis, DNA
chemical_list: D015342:DNA Probes
keywords: Araneae; Opiliones; Scorpiones; arthropods; phylogenomics; population genomics; target enrichment; ultraconserved elements