The impact of fast radiation on the phylogeny ofBactrocerafruit flies

AbstractTrue fruit flies (Tephritidae) include several species that cause extensive damage to agriculture worldwide. Among them, species of the genusBactroceraare widely studied to understand the traits associated to their invasiveness and ecology. Comparative approaches based on a reliable phylogenetic framework are particularly effective, but, to date, molecular phylogenies ofBactroceraare still controversial. Here, we employed a comprehensive genomic dataset to infer a robust backbone phylogeny of eleven representativeBactroceraspecies and two outgroups. We further provide the first genome scaled inference of their divergence using calibrated relaxed clock. The results of our analyses support a closer relationship ofB. dorsalistoB. latifronsthan toB. tryoni, in contrast to all mitochondrial-based phylogenies. By comparing different evolutionary models, we show that this incongruence likely derives from the fast and recent radiation of these species that occurred around 2 million years ago, which may be associated with incomplete lineage sorting and possibly (ongoing) hybridization. These results can serve as basis for future comparative analyses and highlight the utility of using large datasets and efficient phylogenetic approaches to study the evolutionary history of species of economic importance.