PARAMO pipeline: reconstructing ancestral anatomies using ontologies and stochastic mapping

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 (Phylogenetic Ancestral Reconstruction of Anatomy by Mapping Ontologies) 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.

[1]  Andrea L. Cirranello,et al.  The Placental Mammal Ancestor and the Post–K-Pg Radiation of Placentals , 2013, Science.

[2]  Hilmar Lapp,et al.  Annotation of phenotypes using ontologies: a gold standard for the training and evaluation of natural language processing systems , 2018, bioRxiv.

[3]  Alexandros Stamatakis,et al.  The evolutionary history of holometabolous insects inferred from transcriptome-based phylogeny and comprehensive morphological data , 2014, BMC Evolutionary Biology.

[4]  R Core Team,et al.  R: A language and environment for statistical computing. , 2014 .

[5]  William J. L. Felts Ph. D.,et al.  Gross Anatomy , 1987, Oklahoma Notes.

[6]  M. Pagel.  Detecting correlated evolution on phylogenies: a general method for the comparative analysis of discrete characters , 1994, Proceedings of the Royal Society of London. Series B: Biological Sciences.

[7]  Seth Kaufman,et al.  MorphoBank: phylophenomics in the “cloud” , 2011, Cladistics : the international journal of the Willi Hennig Society.

[8]  W. Wheeler,et al.  Phylogenetic relationships among superfamilies of Hymenoptera , 2012, Cladistics : the international journal of the Willi Hennig Society.

[9]  D. Maddison,et al.  Mesquite: a modular system for evolutionary analysis. Version 2.6 , 2009 .

[10]  Paula M. Mabee,et al.  Annotation of phenotypes using ontologies: a Gold Standard for the training and evaluation of natural language processing systems , 2018, bioRxiv.

[11]  Ernest Turro,et al.  ontologyX: a suite of R packages for working with ontological data , 2016, Bioinform..

[12]  M. Ramírez,et al.  Calculating structural complexity in phylogenies using ancestral ontologies , 2014, Cladistics : the international journal of the Willi Hennig Society.

[13]  Paula M. Mabee,et al.  500,000 fish phenotypes: The new informatics landscape for evolutionary and developmental biology of the vertebrate skeleton , 2012, Zeitschrift fur angewandte Ichthyologie = Journal of applied ichthyology.

[14]  M. Pagel.  The Maximum Likelihood Approach to Reconstructing Ancestral Character States of Discrete Characters on Phylogenies , 1999 .

[15]  Paula M. Mabee,et al.  Phenex: Ontological Annotation of Phenotypic Diversity , 2010, PloS one.

[16]  Michael J. Landis,et al.  RevBayes: Bayesian Phylogenetic Inference Using Graphical Models and an Interactive Model-Specification Language , 2016, Systematic biology.

[17]  M. Donoghue,et al.  Identifying hidden rate changes in the evolution of a binary morphological character: the evolution of plant habit in campanulid angiosperms. , 2013, Systematic biology.

[18]  José L. V. Mejino,et al.  CARO - The Common Anatomy Reference Ontology , 2008, Anatomy Ontologies for Bioinformatics.

[19]  Jonathan P. Bollback,et al.  Stochastic mapping of morphological characters. , 2003, Systematic biology.

[20]  S. Tarasov.  Integration of Anatomy Ontologies and Evo-Devo Using Structured Markov Models Suggests a New Framework for Modeling Discrete Phenotypic Traits , 2019, Systematic biology.

[21]  F. Ronquist,et al.  The Hymenopteran Tree of Life: Evidence from Protein-Coding Genes and Objectively Aligned Ribosomal Data , 2013, PLoS ONE.

[22]  Katja C. Seltmann,et al.  A Gross Anatomy Ontology for Hymenoptera , 2010, PloS one.

[23]  Charles S. P. Foster,et al.  The ancestral flower of angiosperms and its early diversification , 2017, Nature Communications.

[24]  Paula M. Mabee,et al.  Toward Synthesizing Our Knowledge of Morphology: Using Ontologies and Machine Reasoning to Extract Presence/Absence Evolutionary Phenotypes across Studies , 2015, Systematic biology.

[25]  James P. Balhoff,et al.  A Semantic Model for Species Description Applied to the Ensign Wasps (Hymenoptera: Evaniidae) of New Caledonia , 2013, Systematic biology.

[26]  Bertram Ludäscher,et al.  Introducing Explorer of Taxon Concepts with a case study on spider measurement matrix building , 2016, BMC Bioinformatics.

[27]  G. Slater,et al.  Hierarchy in adaptive radiation: A case study using the Carnivora (Mammalia) , 2019, Evolution; international journal of organic evolution.

[28]  Sergei Tarasov,et al.  The Invariant Nature of a Morphological Character and Character State: Insights from Gene Regulatory Networks , 2018, bioRxiv.