Evolutionary biologists have long sought to disentangle phylogenetic relationships among taxa spanning the tree of life, an increasingly important task as anthropogenic influences have caused, and are expected to continue to cause, population declines and species extinctions, particularly in insects. Advances in DNA sequencing techniques have increasingly facilitated the ability of researchers to apply genomic methods to phylogenetic analyses, even for non-model organisms which have historically lacked the genomic resources to do so. Phylogenetic relationships within the stonefly genus Suwallia (Insecta: Plecoptera: Chloroperlidae) are poorly understood, and have never been assessed using molecular data. We used DNA sequence data from genome-wide ultraconserved element loci to generate the first molecular phylogeny for the group and assess its monophyly. Our results reveal that the monospecific chloroperlid Neaviperla forcipata renders Suwallia paraphyletic, and we recommend a taxonomic revision for its inclusion in Suwallia. We also found that Palearctic and Nearctic Suwallia do not form reciprocally monophyletic clades, and that a biogeographic history including dispersal, vicariance, and founder event speciation via jump dispersal best explains the geographic distribution of this group. Moreover, some Suwallia species (e.g., S. amoenacolens, S. kerzhneri, S. marginata, S. pallidula, and S. starki) exhibit pronounced cryptic diversity that is worthy of further investigation. These findings provide a first glimpse into the evolutionary history of Suwallia, improve our understanding of stonefly diversity, and highlight areas where additional research is needed.

We extracted genomic DNA from museum specimens (see Fig. 1 and Table S1 for sampling information). We captured UCEs using baits that were developed for Hemipterans and Hymenopterans, and sequenced them using an Illumina HiSeq (150 bp paired end reads). Raw data were processed using the PHYLUCE pipeline, and we generated a 50% matrix of UCE loci. We reconstructed a lineage tree from a concatenated UCE data set, and then used two coalescent-based phylogenetic approaches to estimate species trees. We also conducted a biogeographic analysis to evaluate various biogeographic models for these stoneflies. 

All trees and nexus files from our lineage tree reconstruction, and two species tree reconstructions (ASTRAL-III and SVDQuartets) are included herein, as are raw data and R scripts for BioGeoBEARs analysis.