Abstract
Abstract The beetle suborder A dephaga 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 H ymenoptera. Recently, a UCE bait set was developed for C oleoptera using polyphagan genomes and a member of the order S trepsiptera 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 C oleoptera. Our final dataset included 305 UCE loci for 18 representatives of all adephagan families except A spidytidae, 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 G yrinidae sister to G eadephaga and all other adephagans. Haliplidae was recovered as sister to D ytiscoidea, with H ygrobiidae and A mphizoidae successive sisters to D ytiscidae. Finally, N oteridae was recovered as monophyletic and sister to M eruidae. Given the success of UCE data for resolving phylogenetic relationships within A dephaga, we suggest the potential for further resolution of relationships within A dephaga using UCEs with improved taxon sampling, and by developing Adephaga‐specific probes.