Reassessing the phylogeny of Cyphophthalmi with phylogenomics: A UCE-based phylogeny of mite harvesters (Opiliones)

Cyphophthalmi (the mite harvesters) are a group of Opiliones with broad interest due to their species being classic examples of short-range endemics and displaying model biogeographical patterns for poor dispersers. Cyphophthalmi phylogeny has received attention using morphology, Sanger-based sequencing data, or transcriptomics. Here we turn to a new type of data, ultraconserved elements (UCEs) and provide a first phylogeny for the entire suborder Cyphophthalmi using such data and including representatives from 36 of the 46 currently recognized genera. Phylogenetic analysis of four occupancy matrices (50%, 75%, 90% and 95%), for a total of 840, 567, 129, and 23 loci, respectively, yielded a well resolved phylogeny with monophyly of Pettalidae, Parasironidae, Stylocellidae and Troglosironidae. However, Neogoveidae appeared paraphyletic with respect to Ogoveidae in all datasets and to Troglosironidae in some, and the traditional Sironidae, which was monophyletic, now appeared paraphyletic with respect to the recently erected family Parasironidae. Our phylogenomic results using UCE data resolve the position of several problematic genera (e.g., Pettalus) and add support to other parts of the tree that received low support in Sanger-based phylogenies. Our work also stresses the possibility to add museum samples to phylogenies although methods for optimizing DNA yield from such small-bodied specimens need further improvement. Finally, this backbone phylogeny demonstrates the feasibility of an all-species phylogeny using UCEs for Cyphophthalmi, and by extension, for all Opiliones.