LAUSR

The agromyzid leafminer Liriomyza trifolii (Burgess) is an important polyphagous pest of vegetable crops and ornamental plants. It is native to the Americas but has spread throughout the world over the past 50 years. Previous molecular research has indicated that this species contains highly distinct mitochondrial lineages suggestive of cryptic species. To better interpret the mitochondrial divergence, we used anchored hybrid enrichment datasets in order to conduct genome‐wide phylogenetic analyses. We found that individuals of L. trifolii from pepper and tomatillo populations form a monophyletic group (“PT group”) distinct from the remaining L. trifolii (“non‐PT group”). These results corroborate previous mitochondrial and nuclear datasets and indicate an absence of gene flow between the PT and non‐PT groups. This is consistent with previous work on reproductive isolation and oviposition preferences, and provides substantial evidence that the PT group represents a distinct and previously unrecognized species. The presence of two species within a nominally single pest species has important implications for management. Although there was only weak genetic differentiation between geographically disparate groups of non‐PT L. trifolii, a monophyletic group of Chinese specimens was found in a coalescent‐based analysis that is concordant with the history of invasions in Asia. Our study provides important new insight into geographic and host‐associated structure in L. trifolii.