Phylogenetic and Divergence Time Estimation of Muscomorpha with Low-Coverage Whole-Genome Sequencing of Syrphidae (Diptera: Brachycera)

Muscomorpha is one of the most diverse groups in Brachycera, yet its higher-level phylogenetic relationships remain controversial, primarily concerning the monophyly and placement of Syrphoidea, the position of Platypezoidea, internal relationships in Calyptratae and Acalyptratae, and the non-monophyly of Eristalinae in Syrphidae. This study utilized 81 Muscomorpha species, including 22 newly sequenced Syrphidae species, and reconstructed their phylogeny with multiple datasets and models. The results confirmed monophyly of most superfamilies except Syrphoidea, with Platypezoidea as sister to the remaining Muscomorpha. Oestroidea was sister to Muscoidea. Within Syrphidae, Syrphinae monophyly and Syrphini relationships were strongly supported, while Eristalinae was non-monophyletic. Milesiini, Eristalini, Volucellini, Brachyopini, and Rhingiini were monophyletic. Divergence time estimation using MCMCTree indicated that Muscomorpha originated in the Middle Jurassic at approximately 171.66 Mya, with Syrphoidea diverging in the Late Jurassic at 151.05 Mya, Acalyptratae in the Early Cretaceous at 117.50 Mya, Calyptratae in the Late Cretaceous at 84.66 Mya, and Syrphidae at 103.44 Mya. These findings provide a robust phylogenomic framework for Muscomorpha evolution.