A demonstration of phylogenetic placement-based identification of agriculturally-significant fruit flies (Diptera: Tephritidae)

The fruit fly genus Anastrepha (Diptera: Tephritidae) contains many agriculturally important pest species, including several already-invasive Neotropical fruit and seed borers in the United States. Monitoring and management of Anastrepha species present in agricultural systems and imported produce relies on timely identification of both adults and larvae, which currently depends on a small handful of experienced specialists with limited time. On top of this bottleneck, the most distinct characters of high-risk species can be difficult to view, let alone distinguish, as shown in the taxonomic difficulties surrounding the Anastrepha fraterculus cryptic species complex. In the absence of distinct morphological characters, molecular data is key to delineation of species. Informative differences between select molecular sequences can be assessed using phylogenetic methods, showing the potential relationship between specimens in the context of a chosen sampling. Phylogenetic trees grow more computationally expensive to build with the inclusion of more terminals, making comprehensive trees difficult to build as sampling increases. This expense of time and computing resources can be circumvented with the use of phylogenetic placement, allowing new samples from multiple loci to be compared to the genetic sequence data used to create a static reference tree in comparatively little time. Given the right primers, phylogenetic placement could therefore be used for effective and efficient molecular identification of these difficult-to-delimit and crucial-to-identify fruit flies.