title: Uncertain-tree: discriminating among competing approaches to the phylogenetic analysis of phenotype data.
abstract: Morphological data provide the only means of classifying the majority of life's history, but the choice between competing phylogenetic methods for the analysis of morphology is unclear. Traditionally, parsimony methods have been favoured but recent studies have shown that these approaches are less accurate than the Bayesian implementation of the Mk model. Here we expand on these findings in several ways: we assess the impact of tree shape and maximum-likelihood estimation using the Mk model, as well as analysing data composed of both binary and multistate characters. We find that all methods struggle to correctly resolve deep clades within asymmetric trees, and when analysing small character matrices. The Bayesian Mk model is the most accurate method for estimating topology, but with lower resolution than other methods. Equal weights parsimony is more accurate than implied weights parsimony, and maximum-likelihood estimation using the Mk model is the least accurate method. We conclude that the Bayesian implementation of the Mk model should be the default method for phylogenetic estimation from phenotype datasets, and we explore the implications of our simulations in reanalysing several empirical morphological character matrices. A consequence of our finding is that high levels of resolution or the ability to classify species or groups with much confidence should not be expected when using small datasets. It is now necessary to depart from the traditional parsimony paradigms of constructing character matrices, towards datasets constructed explicitly for Bayesian methods.
authors.affiliation: School of Earth Sciences, University of Bristol, Life Sciences Building, 24 Tyndall Avenue, Bristol BS8 1TQ, UK.|Department of Life Sciences, Natural History Museum, Cromwell Road, London SW7 5BD, UK.
authors.forename: Mark N
authors.identifier: 0000-0002-1011-3442
authors.initials: MN
authors.lastname: Puttick
authors.affiliation: School of Earth Sciences, University of Bristol, Life Sciences Building, 24 Tyndall Avenue, Bristol BS8 1TQ, UK.
authors.forename: Joseph E
authors.identifier: 0000-0001-9775-253X
authors.initials: JE
authors.lastname: O'Reilly
authors.affiliation: School of Biological Sciences, University of Bristol, Life Sciences Building, 24 Tyndall Avenue, Bristol BS8 1TQ, UK.
authors.forename: Alastair R
authors.initials: AR
authors.lastname: Tanner
authors.affiliation: School of Earth Sciences, University of Bristol, Life Sciences Building, 24 Tyndall Avenue, Bristol BS8 1TQ, UK.
authors.forename: James F
authors.initials: JF
authors.lastname: Fleming
authors.affiliation: School of Earth Sciences, University of Bristol, Life Sciences Building, 24 Tyndall Avenue, Bristol BS8 1TQ, UK.
authors.forename: James
authors.identifier: 0000-0003-2896-1631
authors.initials: J
authors.lastname: Clark
authors.affiliation: School of Earth Sciences, University of Bristol, Life Sciences Building, 24 Tyndall Avenue, Bristol BS8 1TQ, UK.
authors.forename: Lucy
authors.identifier: 0000-0003-1603-2296
authors.initials: L
authors.lastname: Holloway
authors.affiliation: School of Earth Sciences, University of Bristol, Life Sciences Building, 24 Tyndall Avenue, Bristol BS8 1TQ, UK.|School of Biological Sciences, University of Bristol, Life Sciences Building, 24 Tyndall Avenue, Bristol BS8 1TQ, UK.
authors.forename: Jesus
authors.identifier: 0000-0003-3597-1221
authors.initials: J
authors.lastname: Lozano-Fernandez
authors.affiliation: School of Earth Sciences, University of Bristol, Life Sciences Building, 24 Tyndall Avenue, Bristol BS8 1TQ, UK.
authors.forename: Luke A
authors.identifier: 0000-0002-3910-0346
authors.initials: LA
authors.lastname: Parry
authors.affiliation: School of Earth Sciences, University of Bristol, Life Sciences Building, 24 Tyndall Avenue, Bristol BS8 1TQ, UK.
authors.forename: James E
authors.initials: JE
authors.lastname: Tarver
authors.affiliation: School of Earth Sciences, University of Bristol, Life Sciences Building, 24 Tyndall Avenue, Bristol BS8 1TQ, UK davide.pisani@bristol.ac.uk.|School of Biological Sciences, University of Bristol, Life Sciences Building, 24 Tyndall Avenue, Bristol BS8 1TQ, UK.
authors.forename: Davide
authors.initials: D
authors.lastname: Pisani
authors.affiliation: School of Earth Sciences, University of Bristol, Life Sciences Building, 24 Tyndall Avenue, Bristol BS8 1TQ, UK phil.donoghue@bristol.ac.uk.
authors.forename: Philip C J
authors.identifier: 0000-0003-3116-7463
authors.initials: PC
authors.lastname: Donoghue
mesh_terms: D001499:Bayes Theorem; D016013:Likelihood Functions; D010641:Phenotype; D010802:Phylogeny; D035501:Uncertainty
keywords: Bayesian; cladistics; morphology; palaeontology; parsimony; phylogeny