A new phylogeny of Anastrepha (Diptera: Tephritidae) based on nuclear loci obtained by phylogenomic methods

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 analysed 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, while also revealing new support for previously unknown relationships among species, some previously unassigned, and species groups. Our results confirm that the fraterculus cryptic species complex is polyphyletic and delimit 7–8 lineages, not all of which match the current morph concepts. They also 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 and indicate the closest relatives of the pest species to give new perspective on their biology and behaviour. They also provide a large genome‐wide nuclear gene resource for potential use as identification markers and phylogenetic placement loci for pest and non‐pest species and populations.