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 Benchmarking confirms the accuracy of pNHPP in estimating character rates under different evolutionary scenarios, and example applications demonstrate the utility of
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— 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.
- NSF-PAR ID:
- 10467602
- Publisher / Repository:
- Wiley-Blackwell
- Date Published:
- Journal Name:
- Methods in Ecology and Evolution
- Volume:
- 14
- Issue:
- 10
- ISSN:
- 2041-210X
- Format(s):
- Medium: X Size: p. 2531-2540
- Size(s):
- ["p. 2531-2540"]
- Sponsoring Org:
- National Science Foundation
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