PARAMO pipeline: reconstructing ancestral anatomies using ontologies and stochastic mapping

ABSTRACT Comparative phylogenetics has been largely lacking a method for reconstructing the evolution of phenotypic entities that consist of ensembles of multiple discrete traits – entire organismal anatomies or organismal body regions. In this study, we provide a new approach named PARAMO ( P hylogenetic A ncestral R econstruction of A natomy by M apping O ntologies ) that appropriately models anatomical dependencies and uses ontology-informed amalgamation of stochastic maps to reconstruct phenotypic evolution at different levels of anatomical hierarchy including entire phenotypes. This approach provides new opportunities for tracking phenotypic radiations and evolution of organismal anatomies.