Disjunction between canola distribution and the genetic structure of its recently described pest, the canola flower midge (Contarinia brassicola)

Population genomics is a useful tool to support integrated pest management as it can elucidate population dynamics, demography, and histories of invasion. Here, we use a restriction site‐associated DNA sequencing approach combined with whole‐genome amplification (WGA) to assess genomic population structure of a newly described pest of canola, the diminutive canola flower midge, Contarinia brassicola. Clustering analyses recovered little geographic structure across the main canola production region but differentiated several geographically disparate populations at edges of the agricultural zone. Given a lack of alternative hypotheses for this pattern, we suggest these data support alternative hosts for this species and thus our canola‐centric view of this midge as a pest has limited our understanding of its biology. These results speak to the need for increased surveying efforts across multiple habitats and other potential hosts within Brassicaceae to improve both our ecological and evolutionary knowledge of this species and contribute to effective management strategies. We additionally found that use of WGA prior to library preparation was an effective method for increasing DNA quantity of these small insects prior to restriction site‐associated DNA sequencing and had no discernible impact on genotyping consistency for population genetic analysis; WGA is therefore likely to be tractable for other similar studies that seek to randomly sample markers across the genome in small organisms.