Submitted to: Systematic Entomology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/19/2025
Publication Date: 9/3/2025
Citation: Norrbom, A.L., Rodriquez, E.J., Steck, G.J., Cassel, B.K., Ruiz-Arce, R., Muller, A., Gangadin, A., Savaris, M., Nolazco, A.N., Troya, H., Rodriquez, P., Madriz Picado, J., Rodriquez, C.P., Moore, M.R., Branham, M., Cattle, E., Wiegmann, B. 2025. A new phylogeny of Anastrepha (Diptera Tephritidae) based on nuclear loci obtained by phylogenomic methods. Systematic Entomology. Article e10.5061. https://doi.org/10.5061/dryad.7d7wm3864.
DOI: https://doi.org/10.5061/dryad.7d7wm3864

Interpretive Summary: The true fruit fly genus Anastrepha is the largest and most agriculturally important in the American tropics and subtropics. It includes 325 currently recognized species and numerous additional unnamed species. Some are major pests of a wide variety of commercial crops such as citrus, mango and apple. Although a few species occur in southern Texas or Florida, most of the pest species are exotic and are a significant threat to US agriculture if introduced. This publication provides an analysis of the evolutionary relationships among these flies based on the most comprehensive data set of genetic sequences ever produced, comprising 295 DNA regions for 728 Anastrepha individuals representing 237 species. Our results provide a useful framework for all types of future comparative biological studies. The massive data set in this publication should lead to more rapid and reliable identification methods for all life stages of these flies, particularly for the fraterculus pest species complex, information critical to APHIS-PPQ and other action agencies charged with preventing the entry of invasive pest species into the USA, as well as other scientists concerned with the biology or control of pest fruit flies.

Technical Abstract: With 325 currently recognized species, Anastrepha (Diptera Tephritidae) is the largest genus of fruit flies within the American tropics and subtropics. It also includes the most economically important pest species in the region, some that have invaded the US and others that remain serious threats to U.S. agriculture. As part of a large collaborative effort to better understand Anastrepha species diversity and interrelationships and to address the need for new genetic data for integrated identification systems, we developed a new phylogenetic tree of Anastrepha species and species groups from anchored hybrid enrichment phylogenomics to serve as a reference system and diagnostic data resource. We captured and analyzed 293 orthologous nuclear loci for 728 Anastrepha individuals representing 237 species, as well as from seven outgroup Tephritidae. These data strongly support the monophyly of most of the previously recognized Anastrepha species groups, but also reveal new support for previously unknown relationships for unplaced taxa and species of uncertain affinities as well as relationships among the species groups. Our results confirm that the fraterculus complex is polyphyletic and indicate that the cryptic species of the complex and the other most similar Anastrepha species are generally not each other’s closest relatives. Our analyses delimit 7-8 lineages, not all of which match the current morph concepts, and suggest that the Mexican morph and Anastrepha zenildae Zucchi are conspecific. Our results provide a useful framework for understanding the history of this major radiation of fruit infesting flies, indicate the closest relatives of the pest species to give new perspective on their biology and behavior, and provide a large genome wide nuclear gene resource for potential use as identification markers and phylogenetic placement loci for pest and other species and populations.