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.

Identifying conserved genomic elements and designing universal bait sets to enrich them

“…To further assess the performance of the principal arachnid bait set, we performed extensive in vitro enrichments of the identified loci as part of a separate manuscript (Starrett et al . in press).…”

“…We empirically test one of the bait sets described below by enriching conserved loci from a diverse group of Arachnids in a separate manuscript (Starrett et al . in press), and we describe a second empirical test of the workflow described here to improve available resources for hymenopteran phylogenetics in Branstetter et al . (in press).…”

A stable phylogenomic classification of Travunioidea (Arachnida, Opiliones, Laniatores) based on sequence capture of ultraconserved elements

“…material 1), including 40 Travunioidea, 14 non-travunioid Laniatores (eight Triaenonychidae, two Synthetonychiidae, and four Grassatores), and single representatives from each of the other three harvestmen suborders. Forty-nine samples were newly sequenced for this study; raw reads for other taxa are from Starrett et al (2017). We included two samples for most travunioid genera (in most cases from two different species), except for Trojanella and Travunia Absolon, 1920, both of which were represented by a single specimen.…”

“…Library preparation followed the general protocol of Starrett et al (2017) and the UCE website (ultraconserved.org), with some modifications. Briefly, libraries were prepared using the KAPA Hyper Prep Kit (Kapa Biosystems), using up to 250 ng DNA (i.e., half reaction of manufacturer’s protocol) as starting material.…”

“…In this paper we utilize DNA sequences derived from capture of ultraconserved elements (UCEs; Faircloth 2017) to reconstruct phylogenomic relationships within Travunioidea. The phylogenetic utility of UCE data at multiple evolutionary scales has been demonstrated in other arachnid lineages (Starrett et al 2017, Hedin et al 2018). Our taxon sample includes 21 of 24 described genera and all currently and historically recognized travunioid families and subfamilies, plus outgroups.…”