The phylogeny and divergence times of leaf-mining flies (Diptera: Agromyzidae) from anchored phylogenomics

• Published in: Molecular phylogenetics and evolution Vol. 184; p. 107778
• Main Authors: Xuan, Jing-Li, Scheffer, Sonja J., Lewis, Matt, Cassel, Brian K., Liu, Wan-Xue, Wiegmann, Brian M.
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 01.07.2023
• Subjects: Animals; Diptera; Diptera - genetics; Divergence times; Genetic Loci; Genomics; Leaf-miner; Likelihood Functions; Phylogenomics; Phylogeny; Divergence times; Leaf-miner; Diptera; Phylogenomics
• ISSN: 1055-7903; 1095-9513
• DOI: 10.1016/j.ympev.2023.107778

[Display omitted] •The phylogeny of leaf-mining flies is reconstructed using anchored phylogenomics.•A new subfamily clade is proposed, Ophiomyiinae.•Divergence times for leaf-mining fly lineages are inferred from molecular data. 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. The resulting phylogenetic trees 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 model-based analysis, leaf-mining flies are shown to have diversified in multiple lineages since the early Paleocene, approximately 65 million years ago. Our study not only reveals a revised classification system of leaf-mining flies, but also provides a new phylogenetic framework to understand their macroevolution.