Received: 16 May 2018 | Revised: 26 October 2018 | Accepted: 30 October 2018 DOI: 10.1111/1755-0998.12962 RESOURCE ARTICLE Advancing mite phylogenomics: Designing ultraconserved elements for Acari phylogeny Matthew H. Van Dam1 | Michelle Trautwein1 | Greg S. Spicer2 | Lauren Esposito1 1Entomology Department, Institute for Biodiversity Science and Sustainability, Abstract California Academy of Sciences, San Mites (Acari) are one of the most diverse groups of life on Earth; yet, their evolu- Francisco, California tionary relationships are poorly understood. Also, the resolution of broader arachnid 2Department of Biology, San Francisco State University, San Francisco, California phylogeny has been hindered by an underrepresentation of mite diversity in phy- logenomic analyses. To further our understanding of Acari evolution, we design tar- Correspondence Matthew H. Van Dam, Entomology geted ultraconserved genomic elements (UCEs) probes, intended for resolving the Department, Institute for Biodiversity complex relationships between mite lineages and closely related arachnids. We then Science and Sustainability, California Academy of Sciences, San Francisco, test our Acari UCE baits in‐silico by constructing a phylogeny using 13 existing Acari California. genomes, as well as 6 additional taxa from a variety of genomic sources. Our Acari‐ Email: [email protected] specific probe kit improves the recovery of loci within mites over an existing general Funding information arachnid UCE probe set. Our initial phylogeny recovers the major mite lineages, yet Schlinger Foundation; Doolin Foundation for Biodiversity finds mites to be non‐monophyletic overall, with Opiliones (harvestmen) and Ricin- uleidae (hooded tickspiders) rendering Parasitiformes paraphyletic. KEYWORDS Acari, Arachnida, mites, Opiliones, Parasitiformes, partitioning, phylogenomics, Ricinuleidae, ultraconserved elements 1 | INTRODUCTION Babbitt, 2002; Regier et al., 2010; Sharma et al., 2014; Shultz, 2007; Starrett et al., 2017; Wheeler & Hayashi, 1998). Acari, commonly known as mites and ticks, are an extraordinary eco- The class Acari is traditionally comprised of two major lineages logically diverse group that occupy a wide range of niches, from mar- (superorders), Parasitiformes and Acariformes, that are defined pri- ine‐living algae feeders, specialist ectoparasites to soil herbivores. marily on the basis of shared plesiomorphic traits. Parasitiformes and Acari are an old lineage, and their fossil record indicates that they Acariformes have historically been considered to be sister groups lar- may have arisen in the late Silurian, with many extant superfamilies gely based on the lack of convincing evidence that they are not each present as far back as the early Devonian (Lindquist, Krantz, & Wal- other's closest relative (Lindquist et al., 2009). There have been a ter, 2009), and with a burst of diversification during the late Meso- number of studies, however, suggesting that not only are Acari not a zoic (Krantz & Walter, 2009). monophyletic group, but also that the two superorders may be Mites have been particularly problematic for modern systematics, somewhat distant relatives (Dabert, Witalinski, Kazmierski, Olsza- with over 40,000 named species in 540 families, primarily from tem- nowski, & Dabert, 2010; Dunlop & Alberti, 2008; Pepato, da Rocha, perate Eurasia and North America (Lindquist et al., 2009; Walter & & Dunlop, 2010; Van der Hammen, 1989). However, problems pla- Proctor, 1999). Considering the paucity of data from the rest of the gue the higher taxonomy, and for many orders it is unclear, based world, the true species diversity of mites is likely somewhere on few studies of comparative morphology, whether even their between 500,000 and 1 million (Walter & Proctor, 1999). Among placement within the two superorders is correct (Dunlop & Alberti, the major challenges for mite systematics is the small size of most 2008; Klußmann‐Fricke & Wirkner, 2016; Meither & Dunlop, 2016; taxa, the availability of taxonomic expertise to identify them, and the Shultz, 2007). complexities of their position within Arachnida (Fernández & Giribet, While the number of molecular phylogenetic studies on Acari is 2015; Giribet & Edgecombe, 2012; Giribet, Edgecombe, Wheeler, & growing, the majority are based on intrafamilial relationships (Domes, | Mol Ecol Resour. 2019;19:465–475. wileyonlinelibrary.com/journal/men © 2018 John Wiley & Sons Ltd 465 466 | VAN DAM ET AL. Norton, Maraun, & Scheu, 2007; Dowling & OConnor, 2010; Hen- our understanding of Acari evolution, here we design a custom UCE dricks, Flannery, & Spicer, 2013; Klimov & OConnor, 2008; Klimov & probe set specific to Acari based on 13 existing mite genomes. UCE OConnor, 2013; Murrell, Campbell, & Barker, 2001; Maraun et al. probe kits are typically designed with fewer genomes, but we 2004; Mans, de Klerk, Pienaar, de Castro, & Latif, 2012; Pachl et al., included nearly all available mite genomes to enhance the probe kit's 2012). A number of taxa‐rich phylogenetic studies have addressed potential effectiveness across this hyperdiverse, ancient group. We the evolutionary relationships within the major mite lineages Acari- then test this probe set in‐silico on 2 additional mites and 3 other formes and Parasitiformes based primarily on ribosomal and mito- arachnid libraries, as well as Merostomata (horseshoe crab) in order chondrial DNA (Dabert et al., 2010; Klimov et al., 2018; Klompen, to evaluate its effectiveness at recovering the mite phylogeny. Lekveishvili, & Black, 2007; Murrell et al., 2005; Pepato & Klimov, 2015; Pepato et al., 2010). These studies present conflicting frame- 2 | MATERIALS AND METHODS works of the higher‐level relationships that have yet to be tested by large‐scale phylogenomic data. Some points of conflict are the 2.1 | Study group monophyly of Acari and Parasitiformes, and the closest relatives to Parasitiformes and Acariformes (Garwood & Dunlop, 2014; Giribet, We used 13 publicly available mite genomes to design a probe set 2018; Pepato & Klimov, 2015). specifically for Acari (Table 1). The taxa represented in the probe The placement of Acari within Arachnida and their closest arach- design included representatives of most, but not all, major divisions nid relatives are unclear. Various hypotheses have been proposed, of mites. We then performed an in‐silico test of the probes on these including Acaramorpha sistergroup relationship between Acari and taxa, plus 2 additional mites, as well as the putatively related arach- Ricinulei (hooded tickspiders). Acaramorpha, however, has not been nids groups hooded tickspider (Order Ricinulei) and saddleback har- recovered in several molecular analyses (Garwood & Dunlop, 2014; vestman (Order Opiliones). A spider and a horseshoe crab were used Legg, Sutton, & Edgecombe, 2013; Pepato & Klimov, 2015). Giribet as outgroups. The data for the additional taxa were in the form of 3 (2018) described the problem, “The relationships of Pseudoscorpi- additional genomes (Dermatophagoides pteronyssinus, Limulus polyphe- ones, Palpigradi, Ricinulei, Solifugae, Opiliones and the two acarine mus, Stegodyphus mimosarum), 2 low coverage “shotgun” libraries clades are however poorly understood and they conflict in virtually (Cryptocellus goodnighti, Mitopus morio) and 1 UCE bait capture data every published analysis of arachnid relationships.” As such, the set (Neomolgus littoralis) (Table 1). potential sister groups to either Acari or its major lineages seem wide‐ranging. 2.2 | Identification of loci and “bait” design Ultraconserved genomic elements (UCEs) (sensu Faircloth et al., 2012), provide a powerful approach to sequence many independent Our workflow follows that of Faircloth, 2017, and we used PHYLUCE regions of the genome for phylogenetic inference. UCEs have pro- scripts (Faircloth, 2016; Faircloth et al., 2012). All programs hereafter ven useful in resolving evolutionary relationships at multiple phylo- beginning with “phyluce” are PYTHON programs part of the PHYLUCE genetic scales, both shallow and deep (Blaimer et al., 2015; Faircloth, package. Specifically, we used art (Huang, Li, Myers, & Marth, 2012) Sorenson, Santini, & Alfaro, 2013; JeŠovnik et al., 2017; Moyle et al., to simulate paired‐end, error‐free reads for each genome that we 2016; Van Dam et al., 2017). While UCEs have been developed then used to align to our “base” genome. We simulated 100 bp across many insect and arachnid orders (Faircloth, 2017; Starrett paired end reads at 2× coverage across each genome, and these et al., 2017), few authors have designed custom UCE probes within reads were then merged. We selected Tetranychus urticae (GenBank these orders (with the exception of ants, Branstetter, Longino, Ward, accession number: GCA_000239435.1) as the “base” genome & Faircloth, 2017). Taxon‐specific probes target UCE loci with more because it is relatively complete and because its phylogenetic place- specificity and in greater numbers (Branstetter et al., 2017; Faircloth, ment, according to our preliminary analyses, is neither early diverging Branstetter, White, & Brady, 2015). UCEs, like many other genomic nor recently diverging within Acari. subsampling methods, rely on oligonucleotide “bait” capture proce- In order to align the genomes to the “base” and look for homolo- dures (Brewer & Bond, 2013) that can be particularly useful when gous sections, we used stampy (Lunter & Goodson, 2011). We set relying on specimens with degraded DNA (Blaimer, Lloyd, Guillory, & the substitution