UCE-based phylogeny and classification of Megachilini

Authors: PRAZ, CHRISTOPHE - University Of Neuchatel; GUENING, MORGAN - University Of Neuchatel; Branstetter, Michael; DORCHIN, ACHIK - University Of Mons-Hainaut; Griswold, Terry; PACKER, LAURENCE - York University; RISCH, STEPHEN - Non ARS Employee; LITMAN, JESSICA - Natural History Museum Neuchatel

Submitted to: Molecular Phylogenetics and Evolution
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/29/2026
Publication Date: 4/17/2026
Citation: Praz, C.J., Guening, M., Branstetter, M.G., Dorchin, A., Griswold, T.L., Packer, L., Risch, S., Litman, J. 2026. UCE-based phylogeny and classification of Megachilini. Molecular Phylogenetics and Evolution. https://doi.org/10.1016/j.ympev.2026.108701.
DOI: https://doi.org/10.1016/j.ympev.2026.108701

Interpretive Summary: Bees are essential pollinators in natural and agricultural ecosystems, with wild and managed bee species contributing significantly to food and seed production in the United States. USDA scientists and collaborators used advanced DNA data to study the evolutionary relationships of leafcutter bees and their close relatives, a group whose classification has long been confusing. Their results clearly show that these bees share a common ancestor and that parasitic behavior evolved only once within the group. The study also found that leafcutter bees form a natural group nested within other related bees, and that many previously named subgroups do not reflect true evolutionary history. To keep bee identification practical and useful for farmers, researchers, and conservationists, the scientists recommend keeping most of these important pollinators in the single, well-supported genus, currently named Megachile. These results will aid future research and communication about these important bees.

Technical Abstract: The generic-level classification of the bee tribe Megachilini (Megachilidae) has remained controversial due to poor phylogenetic resolution at the base of the group, particularly among the cleptoparasitic genera and the numerous dauber lineages. We present a phylogenomic analysis of Megachilini based on ultraconserved elements (UCEs), sampling 51 ingroup taxa with emphasis on the dauber lineages. We also present a combined UCE + six-gene analysis to improve taxon coverage, resulting in a 126-taxon dataset. Maximum likelihood, coalescent, and Bayesian analyses of multiple UCE matrices recover largely congruent topologies with substantially improved support relative to previous studies. Our results strongly support the monophyly of Megachilini, the early divergence of Noteriades and Gronoceras, and a single origin of cleptoparasitism. All remaining non-parasitic Megachilini form a moderately supported clade sister to the cleptoparasitic lineage. The leafcutter bees are monophyletic and nested among dauber lineages. Several major dauber clades are consistently recovered, including an exclusively Australian lineage corresponding to the Hackeriapis group of subgenera, while several recognized subgenera are paraphyletic. Divergence-time analyses place the crown age of Megachilini in the late Eocene to early Oligocene, with major extant lineages diversifying during the Miocene. Limited morphological diagnosability of several clades indicates that splitting non-parasitic lineages into numerous genera would result in an impractical classification that would widen the gap between taxonomists and non-specialists and exacerbate the taxonomic impediment in bees. We therefore advocate retaining a single genus Megachile for non-parasitic Megachilini (excluding Noteriades and Gronoceras), as the classification best supported by phylogenomic evidence and most robust to future taxon sampling.