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Reconstructing ancestral states for discrete characters is essential for understanding trait evolution in organisms. However, most existing methods are limited to individual characters and often overlook the hierarchical and interactive nature of traits. Recent advances in phylogenetics now offer the possibility of integrating knowledge from anatomy ontologies to reconstruct multiple discrete character histories. Nonetheless, practical applications that fully harness the potential of these new approaches are still lacking.This paper introduces ontophylo, an R package that extends the PARAMO pipeline to address these limitations. Ontophylo enables the reconstruction of phenotypic entities composed of amalgamated characters, such as anatomical regions or entire phenomes. It offers three new applications: (1) reconstruction of evolutionary rates of amalgamated characters using phylogenetic non‐homogeneous Poisson process (pNHPP) that allows modelling rate variation across tree branches and time; (2) reconstruction of morphospace dynamics; and (3) visualization of evolutionary rates on vector images of organisms. Ontophylo incorporates ontological knowledge to facilitate these applications.Benchmarking confirms the accuracy of pNHPP in estimating character rates under different evolutionary scenarios, and example applications demonstrate the utility of ontophylo in studying morphological evolution in Hymenoptera using simulated data.Ontophylo can be easily integrated with other ontology‐oriented and general‐purpose R packages and offers new opportunities to examine morphological evolution on a phenomic scale using new and legacy data. [ABSTRACT FROM AUTHOR]

Complex internal skeletal structures, despite their potential as rich sources of phylogenetic information, are still poorly described and used in comparative studies of insects in general, and bees in particular. In this study we present the results of a comprehensive investigation of the internal structures of the mesosoma of bees (e.g. prosternum, propleuron, mesofurca/metafurca and mesophragma); a comparative study was undertaken for bees in general with special emphasis on the tribe Apini. Phylogenetically informative characters are defined and the morphological terminology used for bees is standardized to that used for other Hymenoptera. The potential of these morphological complexes as sources of phylogenetic information was evaluated contrasting the data obtained here with alternative scenarios for corbiculate phylogeny and a phylogenetic analysis was performed. The prosternum possessed the largest number of unambiguous character state changes - nine transformations in the most parsimonious scenario. The changes include the produced lateral processes of the prosternum, absence of the profurcal pit, constriction between the basisternum and the furcasternum, and absence of pubescence on the surface of the basisternum. On the other hand, considerable homoplasy was observed particularly for the characters from the propleuron and mesofurca/metafurca. This may be the consequence of a long morphological branch separating Apini from the remaining apids or a rapid diversification of the corbiculate lineages. In this context, the inclusion of fossil information and use of new technologies for phenotypic studies can open new windows for future comparative morphological studies in bees. [ABSTRACT FROM AUTHOR]