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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]

Organismal anatomy is a hierarchical system of anatomical entities often imposing dependencies among multiple morphological characters. Ontologies provide a formal and computable framework for incorporating prior biological knowledge about anatomical dependencies in models of trait evolution. They also offer new opportunities for working with semantic representations of morphological data.In this work, we present a new R package—rphenoscate—that enables incorporating ontological knowledge in evolutionary analyses and exploring semantic patterns of morphological data. In conjunction with rphenoscape, it allows for assembling synthetic phylogenetic character matrices from semantic phenotypes of morphological data. We showcase the package functionality with data sets from bees and fishes.We demonstrate that ontologies can be employed to automatically set up evolutionary models accounting for trait dependencies in stochastic character mapping. We also demonstrate how ontology annotations can be explored to interrogate patterns of morphological evolution. Finally, we demonstrate that synthetic character matrices assembled from semantic phenotypes retain most of the phylogenetic information from their original data sets.Ontologies will become important tools for integrating anatomical knowledge into phylogenetic methods and making morphological data FAIR compliant—a critical step of the ongoing 'phenomics' revolution. Our new package offers key advancements towards this goal. [ABSTRACT FROM AUTHOR]

Morphology remains a primary source of phylogenetic information for many groups of organisms, and the only one for most fossil taxa. Organismal anatomy is not a collection of randomly assembled and independent "parts", but instead a set of dependent and hierarchically nested entities resulting from ontogeny and phylogeny. How do we make sense of these dependent and at times redundant characters? One promising approach is using ontologies—structured controlled vocabularies that summarize knowledge about different properties of anatomical entities, including developmental and structural dependencies. Here, we assess whether evolutionary patterns can explain the proximity of ontology-annotated characters within an ontology. To do so, we measure phylogenetic information across characters and evaluate if it matches the hierarchical structure given by ontological knowledge—in much the same way as across-species diversity structure is given by phylogeny. We implement an approach to evaluate the Bayesian phylogenetic information (BPI) content and phylogenetic dissonance among ontology-annotated anatomical data subsets. We applied this to data sets representing two disparate animal groups: bees (Hexapoda: Hymenoptera: Apoidea, 209 chars) and characiform fishes (Actinopterygii: Ostariophysi: Characiformes, 463 chars). For bees, we find that BPI is not substantially explained by anatomy since dissonance is often high among morphologically related anatomical entities. For fishes, we find substantial information for two clusters of anatomical entities instantiating concepts from the jaws and branchial arch bones, but among-subset information decreases and dissonance increases substantially moving to higher-level subsets in the ontology. We further applied our approach to address particular evolutionary hypotheses with an example of morphological evolution in miniature fishes. While we show that phylogenetic information does match ontology structure for some anatomical entities, additional relationships and processes, such as convergence, likely play a substantial role in explaining BPI and dissonance, and merit future investigation. Our work demonstrates how complex morphological data sets can be interrogated with ontologies by allowing one to access how information is spread hierarchically across anatomical concepts, how congruent this information is, and what sorts of processes may play a role in explaining it: phylogeny, development, or convergence. [Apidae; Bayesian phylogenetic information; Ostariophysi; Phenoscape; phylogenetic dissonance; semantic similarity.] [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]

Phylogenetic relationships of corbiculate bees have been a well-known focus of controversies over the past 30 years. The majority of the morphological datasets support the monophyly of Apina + Meliponina, whereas molecular datasets recover Meliponina as sister to Bombina. This issue is especially critical to the proper understanding of the evolution of clusters of traits that define the corbiculate eusocial behaviour. This work provides a description and discussion on characters of the head capsule, mandibles and sitophore of bees. Thirty-three characters are proposed and optimized within concurrent phylogenetic hypotheses for corbiculate bees, which results in seven derived character-states supporting the monophyly of the Apina + Meliponina + Bombina and nine supporting the Apina + Meliponina clades. Although some striking synapomorphies (e.g. tentorial bridge, pleurostomal condyle, hypopharyngeal lobe) support the former clade, most characters supporting the latter (i.e. Apina + Meliponina) were losses/reductions. Moreover, two previously undescribed character transformations on hypostoma and sitophore favour the Bombina + Meliponina clade. Internal head capsule characters are useful for phylogenetic analysis in comparative studies of bees, and corbiculate bees in particular, when efforts are made to solve the 'corbiculate controversy'. An attempt is made to standardize the current terminology used for bees and for other Hymenoptera. [ABSTRACT FROM AUTHOR]