Data from: Assessing bayesian phylogenetic information content of morphological data using knowledge from anatomy ontologies

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
the proximity of ontology-annotated characters within an ontology predicts
evolutionary patterns. To do so, we measure phylogenetic information
across characters and evaluate if it is hierarchically structured by
ontological knowledge—in much the same way as phylogeny structures
across-species diversity. 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 datasets 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 structured 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 ontology
does indeed structure phylogenetic information, 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 datasets 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 structure it: phylogeny,
development, or convergence.