A Systematist's Guide to Estimating Bayesian Phylogenies From Morphological Data

Abstract Phylogenetic trees are crucial to many aspects of taxonomic and comparative biology. Many researchers have adopted Bayesian methods to estimate their phylogenetic trees. In this family of methods, a model of morphological evolution is assumed to have generated the data observed by the researcher. These models make a variety of assumptions about the evolution of morphological characters, and these assumptions are translated into mathematics as parameters. The incorporation of prior distributions further allows researchers to quantify their prior beliefs about the value any one parameter can take. How to translate biological knowledge into mathematical language is difficult, and can be confusing to many biologists. This review aims to help systematics researchers understand the biological meaning of common models and assumptions. Using examples from the insect fossil record, I will demonstrate empirically what assumptions mean in concrete terms, and discuss how researchers can use and understand Bayesian methods for phylogenetic estimation.

• Publication year

  2019

• Venue

  Insect Systematics and Diversity

• Publication date

  2019-05-01

• Fields of study

  Biology, Mathematics, Medicine

• Identifiers
  DOI 10.1093/isd/ixz006PMID 31355348PMCID PMC6643758
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• PARAMO pipeline: reconstructing ancestral anatomies using ontologies and stochastic mapping

  2019cited by this paper
• Phylogenetic Comparative Methods: Learning From Trees

  2019cited by this paper
• Integration of Anatomy Ontologies and Evo-Devo Using Structured Markov Models Suggests a New Framework for Modeling Discrete Phenotypic Traits

  2019cited by this paper
• Neotropical frogs and mating songs: The evolution of advertisement calls in glassfrogs

  2018cited by this paper
• Morphological Data Sets Fit a Common Mechanism Much More Poorly than DNA Sequences and Call Into Question the Mkv Model

  2018cited by this paper
• Phylogenetic patterns of ant–fungus associations indicate that farming strategies, not only a superior fungal cultivar, explain the ecological success of leafcutter ants

  2018cited by this paper
• Bayesian Estimation of Species Divergence Times Using Correlated Quantitative Characters

  2018cited by this paper
• Bayesian placement of fossils on phylogenies using quantitative morphometric data

  2018cited by this paper
• Defensive traits exhibit an evolutionary trade‐off and drive diversification in ants

  2017cited by this paper
• Where Fossils Dare and Males Matter: combined morphological and molecular analysis untangles the evolutionary history of the spider ant genus Leptomyrmex Mayr (Hymenoptera : Dolichoderinae)

  2017cited by this paper
• Exploring phylogenetic relationships of Pteraspidiformes heterostracans (stem-gnathostomes) using continuous and discrete characters

  2017cited by this paper
• Use of Continuous Traits Can Improve Morphological Phylogenetics

  2017cited by this paper
• The Efficacy of Consensus Tree Methods for Summarizing Phylogenetic Relationships from a Posterior Sample of Trees Estimated from Morphological Data

  2017cited by this paper
• Dry habitats were crucibles of domestication in the evolution of agriculture in ants

  2017cited by this paper
• Rapid automated landmarking for morphometric analysis of three‐dimensional facial scans

  2017cited by this paper
• Phylogenetic Inference Using RevBayes

  2017cited by this paper
• Adaptive Radiation in Socially Advanced Stem-Group Ants from the Cretaceous.

  2016cited by this paper
• RevBayes: Bayesian Phylogenetic Inference Using Graphical Models and an Interactive Model-Specification Language

  2016cited by this paper
• Modeling Character Change Heterogeneity in Phylogenetic Analyses of Morphology through the Use of Priors.

  2016cited by this paper
• A cautionary note on the use of Ornstein Uhlenbeck models in macroevolutionary studies

  2015cited by this paper
• Crowdsourced geometric morphometrics enable rapid large-scale collection and analysis of phenotypic data

  2015cited by this paper
• Bayesian Total-Evidence Dating Reveals the Recent Crown Radiation of Penguins

  2015cited by this paper
• Automated Detection of 3D Landmarks for the Elimination of Non-Biological Variation in Geometric Morphometric Analyses

  2015cited by this paper
• Among-character rate variation distributions in phylogenetic analysis of discrete morphological characters.

  2015cited by this paper
• An adaptive scheduling scheme for calculating Bayes factors with thermodynamic integration using Simpson’s rule

  2015cited by this paper
• Landmarking the Brain for Geometric Morphometric Analysis: An Error Study

  2014cited by this paper
• Bayesian Analysis Using a Simple Likelihood Model Outperforms Parsimony for Estimation of Phylogeny from Discrete Morphological Data

  2014cited by this paper
• BEAST 2: A Software Platform for Bayesian Evolutionary Analysis

  2014cited by this paper
• RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

  2014cited by this paper
• ANCESTRAL CHARACTER ESTIMATION UNDER THE THRESHOLD MODEL FROM QUANTITATIVE GENETICS

  2014cited by this paper
• Molecular Dynamics Study of the Opening Mechanism for DNA Polymerase I

  2014cited by this paper
• Geometric morphometric character suites as phylogenetic data: extracting phylogenetic signal from gastropod shells.

  2013cited by this paper
• Phylogenetic analysis using Lévy processes: finding jumps in the evolution of continuous traits.

  2013cited by this paper
• TESTING THE MUSEUM VERSUS CRADLE TROPICAL BIOLOGICAL DIVERSITY HYPOTHESIS: PHYLOGENY, DIVERSIFICATION, AND ANCESTRAL BIOGEOGRAPHIC RANGE EVOLUTION OF THE ANTS

  2013cited by this paper
• The fossilized birth–death process for coherent calibration of divergence-time estimates

  2013cited by this paper
• phytools: an R package for phylogenetic comparative biology (and other things)

  2012cited by this paper
• MODELING STABILIZING SELECTION: EXPANDING THE ORNSTEIN–UHLENBECK MODEL OF ADAPTIVE EVOLUTION

  2012cited by this paper
• Diversitree: comparative phylogenetic analyses of diversification in R

  2012cited by this paper
• The Theory That Would Not Die: How Bayes’ Rule Cracked the Enigma Code, Hunted Down Russian Submarines, and Emerged Triumphant from Two Centuries of Controversy

  2012cited by this paper
• Modelling rate distributions using character compatibility: implications for morphological evolution among fossil invertebrates

  2012cited by this paper
• A Total-Evidence Approach to Dating with Fossils, Applied to the Early Radiation of the Hymenoptera

  2012cited by this paper
• The metapleural gland of ants

  2011cited by this paper
• The Theory That Would Not Die: How Bayes' Rule Cracked the Enigma Code, Hunted Down Russian Submarines, and Emerged Triumphant from Two Centuries of Controversy

  2011cited by this paper
• A Comparative Method for Both Discrete and Continuous Characters Using the Threshold Model

  2011cited by this paper
• Improving marginal likelihood estimation for Bayesian phylogenetic model selection.

  2011cited by this paper
• The akaike information criterion will not choose the no common mechanism model.

  2010cited by this paper
• Estimating trait-dependent speciation and extinction rates from incompletely resolved phylogenies.

  2009cited by this paper
• Coding meristic characters for phylogenetic analysis: a comparison of step-matrix gap-weighting and generalized frequency coding.

  2008cited by this paper
• A Simple Method for Bracketing Absolute Divergence Times on Molecular Phylogenies Using Multiple Fossil Calibration Points

  2008cited by this paper
• TNT, a free program for phylogenetic analysis

  2008cited by this paper
• Mosaicism, modules, and the evolution of birds: results from a Bayesian approach to the study of morphological evolution using discrete character data.

  2008cited by this paper
• Convergent evolution of an ant-plant mutualism across plant families, continents and time

  2007cited by this paper
• Estimating a binary character's effect on speciation and extinction.

  2007cited by this paper
• The importance of data partitioning and the utility of Bayes factors in Bayesian phylogenetics.

  2007cited by this paper
• PAML 4: phylogenetic analysis by maximum likelihood.

  2007cited by this paper
• Phylogenetic comparative analysis of electric communication signals in ghost knifefishes (Gymnotiformes: Apteronotidae)

  2007cited by this paper
• REEXAMINING THE RELATIONSHIP BETWEEN BODY SIZE AND TONAL SIGNALS FREQUENCY IN WHALES: A COMPARATIVE APPROACH USING A NOVEL PHYLOGENY

  2007cited by this paper
• SIMMAP: Stochastic character mapping of discrete traits on phylogenies

  2006cited by this paper
• TESTING FOR DIFFERENT RATES OF CONTINUOUS TRAIT EVOLUTION USING LIKELIHOOD

  2006cited by this paper
• Computing Bayes factors using thermodynamic integration.

  2006cited by this paper
• The Posterior and the Prior in Bayesian Phylogenetics

  2006cited by this paper
• Phylogeny of the Ants: Diversification in the Age of Angiosperms

  2006cited by this paper
• Continuous characters analyzed as such

  2006cited by this paper
• Evolutionary trees from DNA sequences: A maximum likelihood approach

  2005cited by this paper
• Using the quantitative genetic threshold model for inferences between and within species

  2005cited by this paper
• Dating of the human-ape splitting by a molecular clock of mitochondrial DNA

  2005cited by this paper
• Model Selection in Phylogenetics

  2005cited by this paper
• Models for Estimating Bayes Factors with Applications to Phylogeny and Tests of Monophyly

  2005cited by this paper
• Frequentist properties of Bayesian posterior probabilities of phylogenetic trees under simple and complex substitution models.

  2004cited by this paper
• Phylogenetic Comparative Analysis: A Modeling Approach for Adaptive Evolution

  2004cited by this paper
• Bayesian phylogenetic analysis of combined data.

  2004cited by this paper
• TESTING FOR PHYLOGENETIC SIGNAL IN COMPARATIVE DATA: BEHAVIORAL TRAITS ARE MORE LABILE

  2003cited by this paper
• Mapping mutations on phylogenies.

  2002cited by this paper
• Phylogenetic Systematics

  2002cited by this paper
• Character analysis in morphological phylogenetics: problems and solutions.

  2001cited by this paper
• MRBAYES: Bayesian inference of phylogenetic trees

  2001cited by this paper
• Exploring among-site rate variation models in a maximum likelihood framework using empirical data: effects of model assumptions on estimates of topology, branch lengths, and bootstrap support.

  2001cited by this paper
• A likelihood approach to estimating phylogeny from discrete morphological character data.

  2001cited by this paper
• PAUP* Phylogenetic analysis using parsimony (*and other methods) Version 4

  2000cited by this paper
• The Maximum Likelihood Approach to Reconstructing Ancestral Character States of Discrete Characters on Phylogenies

  1999cited by this paper
• Bayesian Phylogenetic Inference via Markov Chain Monte Carlo Methods

  1999cited by this paper
• Step matrices and the interpretation of homoplasy.

  1998cited by this paper
• Testing Phylogenetic Methods with Tree Congruence: Phylogenetic Analysis of Polymorphic Morphological Characters in Phrynosomatid Lizards

  1998cited by this paper
• Links between maximum likelihood and maximum parsimony under a simple model of site substitution.

  1997cited by this paper
• Phylogenetic Inference for Binary Data on Dendograms Using Markov Chain Monte Carlo

  1997cited by this paper
• Links between maximum likelihood and maximum parsimony under a simple model of site substitution

  1997cited by this paper
• The effect of topology on estimates of among-site rate variation

  1996cited by this paper
• Probability distribution of molecular evolutionary trees: A new method of phylogenetic inference

  1996cited by this paper
• Among-site rate variation and its impact on phylogenetic analyses.

  1996cited by this paper
• Bayes factors

  1995cited by this paper
• THE BEHAVIOUR OF GOLOBOFF'S TREE FITNESS MEASURE F

  1995cited by this paper
• Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: Approximate methods

  1994cited by this paper
• Is there something wrong with the bootstrap on phylogenies? A reply to Hillis and Bull

  1993cited by this paper
• THE HOLY GRAIL OF THE PERFECT CHARACTER: THE CLADISTIC TREATMENT OF MORPHOMETRIC DATA

  1993cited by this paper
• An Empirical Test of Bootstrapping as a Method for Assessing Confidence in Phylogenetic Analysis

  1993cited by this paper
• ESTIMATING CHARACTER WEIGHTS DURING TREE SEARCH

  1993cited by this paper
• Squared-Change Parsimony Reconstructions of Ancestral States for Continuous-Valued Characters on a Phylogenetic Tree

  1991cited by this paper
• Character States, Morphological Variation, and Phylogenetic Analysis: A Review

  1991cited by this paper
• Phylogenies and quantitative characters

  1988cited by this paper
• Some probabilistic and statistical problems in the analysis of DNA sequences

  1986cited by this paper

• Comparative Morphology of the Stingless Bees (Apidae, Meliponini) and Its Phylogenetic Relevance

  2026cites this paper
• From fossils to phylogenies: exploring the integration of paleontological data into Bayesian phylogenetic inference

  2025cites this paper
• Is additive coding useful for morphological phylogenetic analyses? An empirical evaluation

  2025cites this paper
• Incorporating continuous characters in joint estimation of dicynodont phylogeny

  2025cites this paper
• Integrating Deep Learning Derived Morphological Traits and Molecular Data for Total-Evidence Phylogenetics: Lessons from Digitized Collections

  2025cites this paper
• Phylogeochemistry: exploring evolutionary constraints on belemnite rostrum element composition

  2025influential citation
• Assessing the impact of character evolution models on phylogenetic and macroevolutionary inferences from fossil data

  2025influential citation
• Distinguishing punctuated and continuous-time models of character evolution for discrete characters and the implications for macroevolutionary theory

  2025cites this paper
• Phylogeny of Athyridida (Brachiopoda): a comparison of methods of inference

  2025cites this paper
• Practical Guide and Review of Fossil Tip-Dating in Phylogenetics

  2025influential citation
• Reevaluating the phylogenetic relationships of zosterophylls with a comprehensively sampled dataset and a combination of traditional and new alternative methods.

  2025cites this paper
• Accuracy of phylogenetic reconstructions from continuous characters analyzed under parsimony and its parametric correlates

  2024cites this paper
• Patagomaia could be a gondwanatherian

  2024cites this paper
• Assessing the Adequacy of Morphological Models using Posterior Predictive Simulations.

  2024cites this paper
• A macroevolutionary analysis of European Late Upper Palaeolithic stone tool shape using a Bayesian phylodynamic framework

  2024cites this paper
• Assessing the Adequacy of Morphological Models used in Palaeobiology

  2024cites this paper
• Mesozoic stem-group zoroasterid sea stars imply a delayed radiation of the crown group and adaptation to the deep seas

  2023cites this paper
• Practical guidelines for Bayesian phylogenetic inference using Markov chain Monte Carlo (MCMC)

  2023cites this paper
• Phylogenetic analysis of the Belostoma plebejum group sensu Nieser (Insecta, Hemiptera, Belostomatidae): the effect of adding continuous characters on its accuracy

  2023cites this paper
• Twenty-five well-justified fossil calibrations for primate divergences

  2023cites this paper
• rphenoscate: An R package for semantic-aware evolutionary analyses of anatomical traits

  2023cites this paper
• First representative of the odonatan superfamily Triassolestoidea (Odonatoptera: Parazygoptera) from the Upper Triassic of the Korean Peninsula

  2022cites this paper
• New opabiniid diversifies the weirdest wonders of the euarthropod stem group

  2022cites this paper
• Phylogenetic analysis of Middle-Late Miocene apes.

  2022cites this paper
• Early cephalopod evolution clarified through Bayesian phylogenetic inference

  2022cites this paper
• The Occurrence Birth–Death Process for Combined-Evidence Analysis in Macroevolution and Epidemiology

  2022cites this paper
• Developing a bioinformatics pipeline for comparative protein classification analysis

  2022cites this paper
• Permian parallelisms: Reanalysis of †Tshekardocoleidae sheds light on the earliest evolution of the Coleoptera

  2022cites this paper
• Evaluating the Impact of Anatomical Partitioning on Summary Topologies Obtained with Bayesian Phylogenetic Analyses of Morphological Data.

  2022cites this paper
• Design Space Constraints and the Cultural Taxonomy of European Final Palaeolithic Large Tanged Points: A Comparison of Typological, Landmark-Based and Whole-Outline Geometric Morphometric Approaches

  2021cites this paper
• New opabiniid diversifies the weirdest wonders of the euarthropod lower stem group

  2021cites this paper
• Permian–Triassic phylogenetic and morphologic evolution of rhynchonellide brachiopods

  2021cites this paper
• Updated diagnoses for the cricket family Trigonidiidae (Insecta: Orthoptera: Grylloidea) and its subfamilies (Trigonidiinae, Nemobiinae), with a review of the fossil record

  2021cites this paper
• Evolution: Morphological saturation and release in mammals

  2021cites this paper
• Revising dating estimates and the antiquity of eusociality in termites using the fossilized birth–death process

  2021cites this paper
• Investigating Morphological Complexes Using Informational Dissonance and Bayes Factors: A Case Study in Corbiculate Bees

  2020cites this paper
• Reproduction strategies in a marine protist : A modelling approach

  2020cites this paper
• The molecular clock as a tool for understanding host-parasite evolution

  2020cites this paper
• Phylogenetic Comparative Methods: A User's Guide for Paleontologists

  2020cites this paper
• Phylogeny and biogeography of some Cretaceous spatangoid echinoids with special emphasis on taxa from the Western Interior Seaway

  2020cites this paper
• Understanding the Tripartite Approach to Bayesian Divergence Time Estimation

  2020cites this paper
• A skyline birth-death process for inferring the population size from a reconstructed tree with occurrences

  2020cites this paper
• A relictual troglomorphic harvestman discovered in a volcanic cave of western Argentina: Otilioleptes marcelae, new genus, new species, and Otilioleptidae, new family (Arachnida, Opiliones, Gonyleptoidea)

  2019cites this paper
• Toward Phylomics in Entomology: Current Systematic and Evolutionary Morphology

  2019cites this paper
• Estimating the phylogeny of geoemydid turtles (Cryptodira) from landmark data: an assessment of different methods

  2019cites this paper