Grass fly evolution unlocked: phylogenomics and classificationof worldwide Chloropidae (Diptera)

Chloropidae, commonly known as grass flies, is a hyperdiverse family of true flies thriving in terrestrial ecosystems around the world with importance to conservation and economy. However, true grass fly diversity and evolutionary affinities are still largely unknown leading to an obscure classification at varied taxonomic levels. The massive lack of data on grass fly evolution hampers studies ranging from species discovery to diversification and provision of ecological services. To overcome this issue, we provide the first comprehensive phylogeny of worldwide Chloropidae using whole-genome shotgun sequencing to retrieve mitochondrial genes, ultraconserved elements and single-copy orthologs. With this, we generated genomic resources from all subfamilies, 95% of the tribes and 48% of the chloropid genera from all biogeographic regions which provides an invaluable resource for biodiversity studies worldwide. Overall, our results provide novel genomic data of over 100 fly species. We implemented dramatic changes in grass fly classification system that redefine one subfamily, propose three new tribes, reassign the tribal position of 59 genera, and synonymize four suprageneric taxa. In addition, we reveal a novel synapomorphy for the family, elucidate grass fly sister-group, and assess the utility of the mitochondrial genome alone to recover evolutionary relationships of a recent lineages of flies. This study is fundamental to mitigate the neglect associated with grass flies through an unprecedented source of genomic data, ultimately providing a novel framework for understanding the rapid evolution of the last and most species-rich radiation of flies.