An Opiliones-specific ultraconserved element probe set with a near-complete family-level phylogeny

Testing ultraconserved elements (UCEs) for phylogenetic inference across bivalves (Mollusca: Bivalvia)

Bivalves constitute an important resource for fisheries and as cultural objects. Bivalve phylogenetics has had a long tradition using both morphological and molecular characters, and genomic resources are available for a good number of commercially important species. However, relationships among bivalve families have been unstable and major conflicting results exist between mitogenomics and results based on Sanger-based amplicon sequencing or phylotranscriptomics. Here we design and test an ultraconserved elements probe set for the class Bivalvia with the aim to use hundreds of loci without the need to sequence full genomes or transcriptomes, which are expensive and complex to analyze, and to open bivalve phylogenetics to museum specimens. Our probe set successfully captured 1,513 UCEs for a total of 263,800 bp with an average length of 174.59 ± 3.44 per UCE (ranging from 28 to 842 bp). Phylogenetic testing of this UCE probe set across Bivalvia and within the family Donacidae using different data matrices and methods for phylogenetic inference shows promising results at multiple taxonomic levels. In addition, our probe set was able to capture large numbers of UCEs for museum specimens collected before 1900 and from DNAs properly stored, of which many museums and laboratories are well stocked. Overall, this constitutes a novel and useful resource for bivalve phylogenetics.

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.

New species of Paktongius and convergent evolution of the gonyleptoid-like habitus in Southeast Asian Assamiidae (Opiliones: Laniatores)

The armored harvestman family Assamiidae (Arachnida: Opiliones: Laniatores) is widely distributed throughout the Old World tropics, specifically throughout tropical Asia and Central Africa. However, the systematics and intrafamilial relationships of the group remain poorly understood. This can be largely attributed to the complicated taxonomic history of the group, which is exemplified by poorly supported subfamily classifications and the prevalence of monotypic genera. Here, we describe four new species of the formerly monotypic genus Paktongius Suzuki, 1969, using specimens collected from Laos, Thailand, and West Malaysia, suggesting a degree of microendemism within the group, which underscores the need for greater sampling of the southeast Asian arachnofauna. Recent phylogenetic analysis has also suggested that Mysorea thaiensis Suzuki, 1985 nests within a clade composed of Paktongius distinctus Suzuki, 1969 and the species described herein (P. suzukii sp. nov., P. spiculosus sp. nov., P. paritensis sp. nov., P. furculus sp. nov.). We therefore transfer Mysorea thaiensis to Paktongius (P. thaiensis comb. nov.). We also comment on the unique morphology of this highly derived group of harvestmen, which appears to suggest convergent evolution of the gonyleptoid-like morphology, complete with the characteristic exaggerated leg four coxae and laterally expanded scutum.