Abstract:

Aims: Bees are ecologically and economically vital pollinators underpinning terrestrial ecosystems and food security. Genomic-scale datasets and phylogenomic methods have advanced reconstructions of bee relationships, yet the placement of several key clades remains unsettled, constraining inferences about origins, biogeography, and trait evolution. This review synthesizes recent progress in bee phylogenomics, while outlining key data types, analytical approaches, and representative results to reflect the traceability and value of relevant information. 

Methods: We systematically reviewed recent literatures on bee phylogenetics and phylogenomics, focusing on studies utilizing large-scale genomic datasets such as genomes, transcriptomes, and ultraconserved elements (UCEs). Meanwhile, we harmonized reporting standards, flagged low and unreported support, mapped cross-study conflicts, and compiled a fossil catalog for reference and traceability. 

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