Table Of ContentRefining Phylogenetic
Analyses
Species and Systematics
The Species and Systematics series will investigate the theory and practice of sys-
tematics, phylogenetics, and taxonomy and explore their importance to biology in a
series of comprehensive volumes aimed at students and researchers in biology and in
the history and philosophy of biology. The book series will examine the role of bio-
logical diversity studies at all levels of organization and focus on the philosophical
and theoretical underpinnings of research in biodiversity dynamics. The philosoph-
ical consequences of classification, integrative taxonomy, and future implications of
rapidly expanding data and technologies will be among the themes explored by this
series. Approaches to topics in Species and Systematics may include detailed studies
of systematic methods, empirical studies of exemplar taxonomic groups, and histor-
ical treatises on central concepts in systematics.
Editor in Chief: Kipling Will (University of California, Berkeley)
Editorial Board
Sandra Carlson (University of California, Davis, USA)
Marcelo R. de Carvalho (University of Sao Paulo, Brazil)
Darren Curnoe (University of New South Wales, Australia)
Malte C. Ebach (University of New South Wales, Australia)
Anthony C. Gill (Smithsonian Institution, USA)
Mark S. Harvey (Western Australian Museum, Australia)
David R. Maddison (Oregon State University, Corvallis, USA)
Ellinor Michel (The Natural History Museum, London)
Olivier Rieppel (The Field Museum, Chicago, USA)
Sonal Singhal (California State University, Dominguez Hills)
Catharine Sole (University of Pretoria)
Felix Sperling (Strickland Museum of Entomology, Edmonton, Alberta, Canada)
Christiane Weirauch (University of California, Riverside)
David M. Williams (The Natural History Museum, London, UK)
René Zaragüeta i Bagils (University of Paris 6, France)
Science Publisher:
Charles R. Crumly, CRC Press/Taylor and Francis
For more information visit:
www.crcpress.com/Species-and-Systematics/book-series/CRCSPEANDSYS
Species and Systematics
Phylogenetic Systematics: Haeckel To Hennig, by Olivier Rieppel
Evolution By Natural Selection: Confidence, Evidence and the Gap, by Michaelis
Michael
The Evolution of Phylogenetic Systematics, edited by Andrew Hamilton
Molecular Panbiogeography on the Tropics, by Michael Heads
Beyond Cladistics, edited by David M. Williams and Sandra Knapp
Comparative Biogeography: Discovering and Classifying Bio-Geographical
Patterns of a Dynamic Earth, by Lynee R. Parenti and Malte C. Ebach
Species: A History of the Idea, by John S. Wilkins
What Species Mean: Understanding the Units of Biodiversity, by Julia Sigwart
What, if anything, are species? by Brent D. Mishler
Biological Systematics, by Igor Ya. Pavlinov
Species Problems and Beyond: Contemporary Issues in Philosophy and Practice,
by John S. Wilkins, Frank E. Zachos, Igor Ya. Pavlinov
From Observations to Optimal Phylogenetic Trees: Phylogenetic Analysis of
Morphological Data: Volume 1, by Pablo Goloboff
Refining Phylogenetic Analyses: Phylogenetic Analysis of Morphological Data:
Volume 2, by Pablo Goloboff
For more information about this series, please visit:
www.crcpress.com/Species-and-Systematics/book-series/CRCSPEANDSYS
Refining Phylogenetic
Analyses
Phylogenetic Analysis of
Morphological Data: Volume 2
Pablo A. Goloboff
First edition published 2022
by CRC Press
6000 Broken Sound Parkway NW, Suite 300, Boca Raton, FL 33487–2742
and by CRC Press
4 Park Square, Milton Park, Abingdon, Oxon, OX14 4RN
CRC Press is an imprint of Taylor & Francis Group, LLC
© 2022 Taylor & Francis Group, LLC
Reasonable efforts have been made to publish reliable data and information, but the author and
publisher cannot assume responsibility for the validity of all materials or the consequences of
their use. The authors and publishers have attempted to trace the copyright holders of all material
reproduced in this publication and apologize to copyright holders if permission to publish in this
form has not been obtained. If any copyright material has not been acknowledged please write and
let us know so we may rectify in any future reprint.
Except as permitted under U.S. Copyright Law, no part of this book may be reprinted, reproduced,
transmitted, or utilized in any form by any electronic, mechanical, or other means, now known or
hereafter invented, including photocopying, microfilming, and recording, or in any information
storage or retrieval system, without written permission from the publishers.
For permission to photocopy or use material electronically from this work, access www.
copyright.com or contact the Copyright Clearance Center, Inc. (CCC), 222 Rosewood Drive,
Danvers, MA 01923, 978–750–8400. For works that are not available on CCC please contact
[email protected]
Trademark notice: Product or corporate names may be trademarks or registered trademarks and are
used only for identification and explanation without intent to infringe.
Library of Congress Cataloging‑in‑Publication Data
Names: Goloboff, Pablo A., author.
Title: Refining phylogenetic analyses. Volume 2, Phylogenetic analysis of morphological data /
Pablo Goloboff.
Other titles: Phylogenetic analysis of morphological data
Description: First edition. | Boca Raton, FL : CRC Press, 2022. | Includes bibliographical
references and index.
Identifiers: LCCN 2021061922 (print) | LCCN 2021061923 (ebook) | ISBN 9780367420277
(hardback) | ISBN 9781032274676 (paperback) | ISBN 9780367823412 (ebook)
Subjects: LCSH: Phylogeny. | Morphology.
Classification: LCC QH351 .G65 2022 (print) | LCC QH351 (ebook) | DDC 576.8/8—dc23/
eng/20220228
LC record available at https://lccn.loc.gov/2021061922
LC ebook record available at https://lccn.loc.gov/2021061923
ISBN: 978-0-36742-027-7 (hbk)
ISBN: 978-1-03227-467-6 (pbk)
ISBN: 978-0-36782-341-2 (ebk)
DOI: 10.1201/9780367823412
Typeset in Times
by Apex CoVantage, LLC
Contents
Preface .....................................................................................................................xiii
Author Biography ..................................................................................................xvii
Abbreviations ..........................................................................................................xix
Chapter 6 Summarizing and comparing phylogenetic trees .................................1
6.1 Consensus methods ...................................................................2
6.1.1 Cluster-based methods ................................................3
6.1.1.1 Strict consensus trees..................................3
6.1.1.2 Majority rule consensus trees .....................4
6.1.1.3 Combinable components consensus ...........6
6.1.1.4 Frequency difference consensus .................8
6.1.2 Methods not based on clusters ....................................8
6.1.2.1 Adams consensus .......................................8
6.1.2.2 Rough recovery consensus .........................8
6.1.2.3 Median trees ...............................................9
6.2 Taxonomic congruence vs. total evidence ...............................10
6.3 Pruned (=reduced) consensus and identification of
unstable taxa ............................................................................13
6.3.1 Maximum agreement subtrees (MAST) .....................15
6.3.2 Brute-force methods ..................................................15
6.3.3 Triplet-based methods ...............................................16
6.3.4 Improving majority rule or frequency
difference consensus .................................................17
6.3.5 Swap and record moves .............................................19
6.3.6 Improving prune sets with an optimality
criterion .....................................................................20
6.4 Zero-length branches and ambiguity .......................................21
6.4.1 Identification of zero-length branches and
collapsing rules..........................................................21
6.4.2 Consensus under different collapsing rules ...............24
6.4.3 Numbers of trees, search effort .................................24
6.4.4 Temporary collapsing ................................................26
6.5 Supertrees ................................................................................26
6.5.1 Semi-strict supertrees ................................................29
6.5.2 Matrix representation with parsimony (MRP) ..........30
6.5.3 Other methods based on matrix
representation ............................................................31
6.5.4 Majority rule supertrees ............................................31
6.6 Anticonsensus ..........................................................................32
vii
viii Contents
6.7 Tree distances ..........................................................................32
6.7.1 Robinson-Foulds distances (RF), and
derivatives ..................................................................34
6.7.2 Group similarity (rough recovery) ............................36
6.7.3 Rearrangement distances ...........................................37
6.7.4 Distortion coefficient (DC)........................................37
6.7.5 Triplets and quartets ..................................................38
6.8 Implementation in TNT ...........................................................39
6.8.1 Consensus trees .........................................................39
6.8.2 Temporary collapsing of zero-length
branches, unshared taxa ............................................41
6.8.3 Tree comparisons and manipulations ........................43
6.8.4 Identifying unstable taxa ...........................................45
6.8.5 Supertrees ..................................................................49
6.8.6 Measures of tree distance ..........................................50
Chapter 7 Character weighting ...........................................................................53
7.1 Generalities ..............................................................................55
7.2 General arguments for weighting ............................................58
7.2.1 Homoplasy and reliability .........................................60
7.3 Successive approximations weighting (SAW) ..........................60
7.3.1 Weighting and functions of homoplasy .....................62
7.3.2 Problems with SAW ..................................................65
7.3.3 Potential solutions .....................................................68
7.4 Implied weighting (IW) ...........................................................68
7.4.1 Weighting functions ..................................................70
7.4.1.1 Weighting strength ...................................71
7.4.1.2 Maximization of weights and
self-consistency ........................................74
7.4.2 Binary recoding, step-matrix characters ...................75
7.4.3 Tree searches .............................................................76
7.4.4 Prior weights .............................................................76
7.4.5 IW and compatibility .................................................76
7.5 Weighting strength, sensitivity, and conservativeness .............78
7.6 Practical consequences of application of IW ...........................80
7.7 Problematic methods for evaluating data quality ....................82
7.7.1 Tree-independent .......................................................82
7.7.2 Probability-based.......................................................82
7.8 Improvements to IW ................................................................84
7.8.1 Influence of missing entries ......................................84
7.8.2 Uniform and average weighting of
molecular partitions ...................................................87
7.8.3 Self-weighted optimization and state
transformations ..........................................................87
7.8.4 Weights changing in different branches ....................92
Contents ix
7.9 Implied weights and likelihood ...............................................93
7.10 To weight or not to weight, that is the question. . . ..................98
7.10.1 Criticisms of IW based on simulations ......................98
7.10.2 Support and character reliability .............................103
7.10.3 Weighting, predictivity, and stability ......................106
7.10.4 Convergence between results of IW and
equal weights ...........................................................107
7.10.5 Weighting in morphology vs molecules ..................109
7.11 Implementation in TNT .........................................................111
7.11.1 Self-weighted optimization .....................................112
7.11.2 Extended implied weighting ...................................113
7.11.2.1 Missing entries .......................................114
7.11.2.2 Uniform weighting of characters
or sets ......................................................115
Chapter 8 Measuring degree of group support ..................................................119
8.1 The difficulty of measuring group supports ..........................119
8.2 Bremer supports: definitions ..................................................122
8.2.1 Variants of Bremer supports ....................................123
8.2.1.1 Relative Bremer supports (RBS) .............123
8.2.1.2 Combined Bremer supports ....................125
8.2.1.3 Relative explanatory power ....................127
8.2.1.4 Site concordance factors (sCF)
and group supports .................................129
8.2.1.5 Partitioned Bremer supports ...................131
8.3 Bremer supports in practice ...................................................134
8.3.1 Performing searches under reverse constraints .......135
8.3.2 Searching suboptimal trees .....................................135
8.3.3 Recording score differences during TBR
branch-swapping .....................................................137
8.3.3.1 The ALRT and aBayes methods .............138
8.3.4 Calculating average differences in length ...............139
8.4 Resampling methods .............................................................140
8.4.1 Plotting group supports ...........................................143
8.4.2 Different resampling methods .................................144
8.4.2.1 Bootstrapping .........................................144
8.4.2.2 Jackknifing .............................................145
8.4.2.3 Symmetric resampling ............................146
8.4.2.4 No-zero-weight resampling ....................147
8.4.2.5 Influence of number of
pseudoreplicates .....................................149
8.4.3 Final summary of results .........................................151
8.4.3.1 Frequency-within-replicates (FWR)
or strict consensus ..................................151
