Ultraconserved elements show utility in phylogenetic inference of Adephaga (Coleoptera) and suggest paraphyly of ‘Hydradephaga’

• Published in: Systematic entomology Vol. 42; no. 4; pp. 786 - 795
• Main Authors: BACA, STEPHEN M., ALEXANDER, ALANA, GUSTAFSON, GREY T., SHORT, ANDREW E. Z.
• Format: Journal Article
• Language: English
• Published: Oxford, UK Blackwell Publishing Ltd 01.10.2017; Wiley Subscription Services, Inc
• Subjects: Adephaga; Arachnida; baits; Coleoptera; data collection; Data processing; DNA probes; Dytiscidae; genome; Genomes; Gyrinidae; Haliplidae; Hymenoptera; loci; monophyly; Noteridae; paraphyly; Phylogenetics; Phylogeny; sisters; Strepsiptera; Trees; vertebrates
• ISSN: 0307-6970; 1365-3113
• DOI: 10.1111/syen.12244

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. The first phylogenetic study in Coleoptera to explore the utility of ultraconserved elements (UCEs) for reconstructing relationships of the suborder Adephaga. Hydradephaga is recovered as paraphyletic, with Gyrinidae sister to Geadephaga and all other adephagans. UCE data successfully reconstructed the phylogenetic relationships of Adephaga with the potential for further resolution following improved taxon sampling and Adephaga‐specific probe design.