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It is widely recognized that different regions of a genome often have different evolutionary histories and that ignoring this variation when estimating phylogenies can be misleading. However, the extent to which this is also true for morphological data is still largely unknown. Discordance among morphological traits might plausibly arise due to either variable convergent selection pressures or else phenomena such as hemiplasy. Here, we investigate patterns of discordance among 282 morphological characters, which we scored for 50 bee species particularly targeting corbiculate bees, a group that includes the well-known eusocial honeybees and bumblebees. As a starting point for selecting the most meaningful partitions in the data, we grouped characters as morphological modules, highly integrated trait complexes that as a result of developmental constraints or coordinated selection we expect to share an evolutionary history and trajectory. In order to assess conflict and coherence across and within these morphological modules, we used recently developed approaches for computing Bayesian phylogenetic information allied with model comparisons using Bayes factors. We found that despite considerable conflict among morphological complexes, accounting for among-character and among-partition rate variation with individual gamma distributions, rate multipliers, and linked branch lengths can lead to coherent phylogenetic inference using morphological data. We suggest that evaluating information content and dissonance among partitions is a useful step in estimating phylogenies from morphological data, just as it is with molecular data. Furthermore, we argue that adopting emerging approaches for investigating dissonance in genomic datasets may provide new insights into the integration and evolution of anatomical complexes. [Apidae; entropy; morphological modules; phenotypic integration; phylogenetic information.]., (© The Author(s) 2020. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved. For permissions, please email: journals.permissions@oup.com.)

The pharyngeal plate is a morphological complex with extensive anatomical variation among bees and, therefore, potential as a source of phylogenetic information. The pharyngeal plate of bees is divided into four morphologically distinct regions: sitophore, hypopharyngeal lobe, pharyngeal rods, and median oral plate. In this work we illustrate and document in detail for the first time the pharyngeal plate of 43 bee species, providing descriptions of the morphological variation and contrasting these findings with representatives of apoid wasps (Crabronidae and Sphecidae). We evaluate and discuss the potential of this structure as a rich source of morphological information in the context of bee phylogeny and any research potentially impacted by comparative morphological data. The shape of the hypopharyngeal lobe is highly variable among suprageneric taxa of bees and can be readily employed to characterise taxa at various levels. We argue that the global patterns in the variation of the pharyngeal plate can provide information for phylogenetic inference within bees and constructed and coded 10 characters that encompass the most noticeable morphological differences discussed herein., (Copyright © 2019 Elsevier Ltd. All rights reserved.)

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.].

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]

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]

Bees are the most significant pollinators of flowering plants. This partnership began ca. 120 million years ago, but the uncertainty of how and when bees spread across the planet has greatly obscured investigations of this key mutualism. We present a novel analysis of bee biogeography using extensive new genomic and fossil data to demonstrate that bees originated in Western Gondwana (Africa and South America). Bees likely originated in the Early Cretaceous, shortly before the breakup of Western Gondwana, and the early evolution of any major bee lineage is associated with either the South American or African land masses. Subsequently, bees colonized northern continents via a complex history of vicariance and dispersal. The notable early absences from large landmasses, particularly in Australia and India, have important implications for understanding the assembly of local floras and diverse modes of pollination. How bees spread around the world from their hypothesized Southern Hemisphere origin parallels the histories of numerous flowering plant clades, providing an essential step to studying the evolution of angiosperm pollination syndromes in space and time. • Bees likely originated in Gondwana before the breakup of Africa and South America • The geological history of southern continents impacted early bee diversification • Northward range expansions in the Tertiary impacted modern bee distribution • Southern Hemisphere origin of bees parallels the histories of many plant groups Almeida, Bossert, et al. combine phylogenomics and the fossil record to propose a comprehensive hypothesis of bee biogeography. Bees originated in Gondwana and later colonized all continents through a series of events that parallel the histories of numerous flowering plants, offering opportunities to interpret the evolution of pollination in space. [ABSTRACT FROM AUTHOR]