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Leaf-mining flies (Diptera: Agromyzidae) are a diverse clade of phytophagous Diptera known largely for their economic impact as leaf- or stem-miners on vegetable and ornamental plants. Higher-level phylogenetic relationships of Agromyzidae have remained uncertain because of challenges in sampling of both taxa and characters for morphology and PCR-based Sanger-era molecular systematics. Here, we used hundreds of orthologous single-copy nuclear loci obtained from anchored hybrid enrichment (AHE) to reconstruct phylogenetic relationships among the major lineages of leaf-mining flies. Resulting phylogenetictrees are highly congruent and well-supported, except for a few deep nodes, when using different molecular data types and phylogenetic methods. Based on divergence time dating using a relaxed clock and model-based historical biogeography analysis, leaf-mining flies are shown to have originated in the Nearctic Region at approximately 64.47 million years ago. Diversification and speciation rates in Agromyzidae increased rapidly during the Miocene, a pattern which may be attributable to vicariance events associated with the disjunction of North American and Eurasian plates, and with numerous host plant shifts in multiple agromyzid lineages. Our study not only reveals a revised classification system of leaf-mining flies, but also provides a new phylogenetic framework to understand their macroevolution. |
