No abstract

The beetle suborder Adephaga has been the subject of many phylogenetic reconstructions utilizing a variety of data sources and inference methods. However, no strong consensus has yet emerged on the relationships among major adephagan lineages. Ultraconserved elements (UCEs) have proved useful for inferring difficult or unresolved phylogenies at varying timescales in vertebrates, arachnids and Hymenoptera. Recently, a UCE bait set was developed for Coleoptera using polyphagan genomes and a member of the order Strepsiptera as an outgroup. Here, we examine the utility of UCEs for reconstructing the phylogeny of adephagan families, in the first in vitro application a UCE bait set in Coleoptera. Our final dataset included 305 UCE loci for 18 representatives of all adephagan families except Aspidytidae, and two polyphagan outgroups, with a total concatenated length of 83 547 bp. We inferred trees using maximum likelihood analyses of the concatenated UCE alignment and coalescent species tree methods (astral ii, ASTRID, svdquartets). Although the coalescent species tree methods had poor resolution and weak support, concatenated analyses produced well-resolved, highly supported trees. Hydradephaga was recovered as paraphyletic, with Gyrinidae sister to Geadephaga and all other adephagans. Haliplidae was recovered as sister to Dytiscoidea, with Hygrobiidae and Amphizoidae successive sisters to Dytiscidae. Finally, Noteridae was recovered as monophyletic and sister to Meruidae. Given the success of UCE data for resolving phylogenetic relationships within Adephaga, we suggest the potential for further resolution of relationships within Adephaga using UCEs with improved taxon sampling, and by developing Adephaga-specific probes.

Adephaga is the second largest suborder of beetles (Coleoptera) and they serve as important arthropod predators in both aquatic and terrestrial ecosystems. The suborder is divided into Geadephaga comprising terrestrial families and Hydradephaga for aquatic lineages. Despite numerous studies, phylogenetic relationships among the adephagan families and monophyly of the Hydradephaga itself remain in question.Here we conduct a comprehensive phylogenomic analysis of the suborder using ultraconserved elements (UCEs). This study presents the first in vitro test of a newly developed UCE probe set customized for use within Adephaga that includes both probes tailored specifically for the suborder, alongside generalized Coleoptera probes previously found to work in adephagan taxa. We assess the utility of the entire probe set, as well as comparing the tailored and generalized probes alone for reconstructing evolutionary relationships. Our analyses recovered strong support for the paraphyly of Hydradephaga with whirligig beetles (Gyrinidae) placed as sister to all other adephagan families. Geadephaga was strongly supported as monophyletic and placed sister to a clade composed of Haliplidae + Dytiscoidea. Monophyly of Dytiscoidea was strongly supported with relationships among the dytiscoid families resolved and strongly supported. Relationships among the subfamilies of Dytiscidae were strongly supported but largely incongruent with prior phylogenetic estimates for the family. The results of our UCE probe comparison showed that tailored probes alone outperformed generalized probes alone, as well as the full combined probe set (containing both types of probes), under decreased taxon sampling. When taxon sampling was increased, the full combined probe set outperformed both tailored probes and generalized probes alone. This study provides further evidence that UCE probe sets customized for a focal group result in a greater number of recovered loci and substantially improve phylogenomic analysis.

No abstract

Notomicrinae (Coleoptera: Noteridae) is a subfamily of minute and ecologically diverse aquatic beetles distributed across the Southeast Asia, Oceania, and the Americas. We investigate the evolution of Notomicrinae and construct the first species-level phylogeny within Noteridae using five nuclear and mitochondrial gene fragments. We focus on the genus Notomicrus Sharp (Coleoptera: Noteridae), sampling 13 of the 17 known Notomicrus species and an additional 11 putative undescribed species. We also include Phreatodytes haibaraensis Uéno (Coleoptera: Noteridae). Datasets are analyzed in Maximum Likelihood and Bayesian frameworks. With these, we 1) estimate divergence times among notomicrine taxa and reconstruct the biogeographical history of the group, particularly testing the hypothesis of Gondwanan vicariance between Old World and New World Notomicrus; 2) additionally, we assess ecological plasticity within Notomicrinae in the context of the phylogeny; and 3) finally, we test the monophyly of tentative species groups within Notomicrus and place putative new taxa. We recover a monophyletic Notomicrinae, with Phreatodytes sister to Notomicrus. We estimate the crown age of Notomicrinae to be ca. 110 Mya. The crown age of Notomicrus is recovered as ca. 75 Mya, there diverging into reciprocally monophyletic Old and New World clades, suggesting Gondwanan vicariance. Our phylogenetic estimate indicates a strong degree of ecological plasticity within Notomicrinae, with habitat switching occurring in recently diverging taxa. Finally, we recover five main species groups in Notomicrus, one Old World, Four New World, with tentative affirmation of the placement of undescribed species.