Population genomic and phylogenetic analysis of three wireworm (Coleoptera: Elateridae) species

A group of pest species that is resurging as a significant threat to economically important crops worldwide is the larvae of click beetles (Coleoptera: Elateridae), known as wireworms. Here, we produce one of the first wireworm genome assemblies (Limonius californicus), and investigate population genetic structure and phylogenetic relationships of three described species (L. californicus, L. infuscatus, L. canus) across the northwest US and southwest Canada using genome-wide markers (RADseq) and genome skimming. We found two species (L. californicus and L. infuscatus) are comprised of genetically distinct groups that diverged around one million years ago but have no known distinguishing morphological characters, and therefore could be considered cryptic species complexes. Most of the cryptic species have disjunct geographic distributions separated by mountain ranges, but one pair has overlapping distributions, and another pair is separated by no obvious geographic barriers. We also found within-species population structure across relatively short geographic distances (e.g., 25km), but no evidence for distinct populations within a single agricultural field. Genome scans for selection with RADseq data provided evidence for signatures of genomic adaptation associated with changes in pesticide treatment in an experimental agricultural field trial for L. canus. We demonstrate that genomic tools can be a strong asset in the development of effective wireworm control strategies by enabling identification of cryptic species and populations present in a given area, as well as identification of genomic adaptation to pesticide treatment.