The Impact of Fast Radiation on the Phylogeny of Fruit Flies As Revealed by Multiple Evolutionary Models and Mutation Rate-Calibrated Clock

Several true fruit flies (Tephritidae) cause major damage to agriculture worldwide. Among them, species of the genus are extensively studied to understand the traits associated with their invasiveness and ecology. Comparative approaches based on a reliable phylogenetic framework are particularly effective, but several nodes of the phylogeny are still controversial, especially concerning the reciprocal affinities of the two major pests and . Here, we analyzed a newly assembled genomic-scaled dataset using different models of evolution to infer a phylogenomic backbone of ten representative species and two outgroups. We further provide the first genome-scaled inference of their divergence by calibrating the clock using fossil records and the spontaneous mutation rate. The results reveal a closer relationship of with than to , contrary to what was previously supported by mitochondrial-based phylogenies. By employing coalescent-aware and heterogeneous evolutionary models, we show that this incongruence likely derives from a hitherto undetected systematic error, exacerbated by incomplete lineage sorting and possibly hybridization. This agrees with our clock analysis, which supports a rapid and recent radiation of the clade to which , and belong. These results provide a new picture of phylogeny that can serve as the basis for future comparative analyses.