Abstract:

Background: Bees are ecologically and economically vital pollinators that underpin terrestrial ecosystems and global food security. Genomic-scale datasets and phylogenomic methods have greatly advanced reconstructions of bee relationships, yet the placement of several key clades remains unsettled, constraining inferences about the origins, biogeography, and evolution of key traits. Here we synthesize recent progress in bee phylogenomics, with particular emphasis on major genomic data types (genomes, transcriptomes and ultraconserved elements), commonly used analytical pipelines and representative phylogenetic results. We harmonize reporting standards across studies, flag nodes with low or unreported support, map cross-study topological conflicts and compile an updated fossil catalogue, in order to enhance the traceability, comparability and reuse of existing phylogenomic evidence.

Review results: Phylogenomics corroborates family-level monophyly and has clarified many higher-level relationships and deep nodes. Temporal frameworks across studies commonly support a Cretaceous origin with subsequent radiations coincident with angiosperm diversification. However, instable clustering remain in several smaller or sparsely sampled lineages, with topological conflicts tied to heterogeneous matrices, analytical choices, and low or unreported support.

Conclusions: Bee phylogenomics has made substantial advances in reconstructing the evolutionary history of this ecologically vital group, but major challenges remain. To improve phylogenetic resolution and evolutionary inference, we recommend expanding taxon and gene sampling, standardizing fossil calibration practices, and integrating morphological and ecological data. Future research should also prioritize linking phylogenetic frameworks to questions in trait evolution, species diversification, and biogeography. A well-resolved bee phylogeny will serve as a robust foundation for understanding ecological functions, conservation priorities, and co-evolutionary dynamics, ultimately advancing biodiversity science and ecosystem sustainability on a global scale.

Key words: Apoidea, bees, phylogenomics, high-throughput data, functional trait