Character Construction in Morphological Phylogenetics, and the Affinities of Turtles

314 Pages·2006·9.45 MB·English

by  Simon Harris

Character Construction in Morphological Phylogenetics,
and the Affinities of Turtles

Simon R. Harris

A dissertation submitted to the University of Bristol in accordance with the
requirements of the degree of PhD in the Faculty of Science, Department of Earth
Sciences.

Word Count: 78,043
For my mother and father, who have encouraged me throughout

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Abstract
Abstract
The process of character construction, by which morphological variation is
partitioned into discrete characters and character states and the taxa under investigation are
scored for those characters, is the most important process in any phylogenetic analysis of
morphological data. Currently, the number of cladistic analyses being carried out each year
is increasing dramatically, but little work has been done to try to improve the inherently
subjective character construction process.
Here it is shown that there is a problem of inconsistency in character construction
between workers in different fields of biology and between individual authors. Although
the infinite variability of morphological variation makes it impossible to describe a
definitive procedure for character construction, guidelines are presented for the best
available character construction in specific circumstances. The application of these
guidelines would be a start in improving the quality of data subjected to cladistic analysis
and increasing the consistency, and therefore repeatability and comparability, of
phylogenetic studies.
Analytical methods for identifying conflict in datasets are described, including two
new methods that improve upon those previously available. These methods, which are
implemented in a new computer program, Boildown, are utilised in an attempt to provide
new evidence in the debate over the affinities of turtles, which using conventional analysis
techniques has become deadlocked. Although this debate seemingly cannot be
satisfactorily resolved until new fossil evidence is unearthed, both the analytical methods
and a process of improving the character constructions and scorings in previously
published analyses of the group produced a diapsid placement for turtles, and this
combined evidence is compelling given the lack of other resolution to the debate.
In the light of the proliferation of the field of systematics in zoology, and the vital
importance of character construction in that field, the process deserves, and requires far
more attention in order to eliminate its image of a black box and to provide advice to those
attempting to construct phylogenies. Without more discussion of the problems involved in
character construction, morphological phylogenetics may never be thought of as an
objective, or scientifically rigorous process.
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Acknowledgements
Acknowledgements
First and foremost I would like to thank my PhD supervisors, Prof. Michael Benton,
Dr. Dave Gower, and Dr. Mark Wilkinson for all of their help during the production of this
dissertation. I would especially like to thank Mark and Dave for their input, allowing me to
raid their reference collections and for making me feel at home at the NHM.
I would also like to thank the many friends who have shared an office with me
during my PhD: Max Langer, Duncan Stewart and Kate Harcourt-Brown made me feel
comfortable when I nervously moved into their office four years ago. Kate especially made
me feel welcome, by giving me a crash course in PAUP (and Pacman). I must also mention
the coffee club members, Max Langer (the Brazilian), Davide Pisani (the Italian), Manu
Fara (the French), and Adam Yates (the Aussie) for teaching me a lot, although not always
about palaeontology. Davide particularly was of immense help with all of the cladistics
questions I confronted him, and also a great friend. I would also like to thank Simon
Loader in London for keeping me sane during my time in the museum, and to the late
Garth Underwood, who is a great loss to the scientific community. Returning to Bristol I
found my office inhabited by a new batch of PhD students, who also deserve my gratitude.
Keith DeBlanger has made me realise quite how many toys there are to be found on the
internet and Stewart Knott has suffered alongside me as we both struggled to write our
dissertations.
Finally, I would like to thank two people I’ve met through palaeontology who have
become two of my best friends and have taken the brunt of most of the complaining when
it all seemed too much. Erik Tetlie has inspired me against my will to gain an interest in
eurypterids, and Rachel Moore, who has suffered the most, and has progressed with me
through undergraduate and postgraduate years with surprisingly few arguments (I’ll get the
milk next time, honest!!!). And finally thanks to the many other friends I’ve made during
my time in Bristol and have not time or space to mention individually.
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Author’s Declaration
Author’s Declaration
I declare that the work in this dissertation was carried out in accordance with the
regulations of the University of Bristol. The work is original, except where indicated by
special reference in the text, and no part of the dissertation has been submitted for any
other degree. Any views expressed in the dissertation are those of the author.

Signed: ........................................................... Date: ..................................
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Contents
Contents
Chapter 1: Introduction........................................................................................1
1.1 The Origins of Classification.....................................................................1
1.2 Cladistics.....................................................................................................1
1.3 Homology and the Character Concept......................................................4
1.3.1 Homology, What’s in a Word?..........................................................................4
1.3.2 The Bat Wing Bird Wing Problem.....................................................................6
1.3.3 Homology ≠ Synapomorphy..............................................................................7
1.3.4 The Opposite of Homology: Analogy, Homoplasy or Nonhomology?.............11
1.3.5 Types of Homology.........................................................................................12
1.3.6 Homology Assessment for Phylogenetic Analyses...........................................13
1.3.7 The Character Concept....................................................................................14
1.4 Aims of This Study...................................................................................16
1.5 Glossary....................................................................................................17
Chapter 2: A Survey of Character Construction Methods..............................22
2.1 Introduction...............................................................................................22
2.2 Conventional coding................................................................................22
2.3 Unconventional Coding Methods............................................................23
2.3.1 Composite Coding...........................................................................................23
2.3.2 Conjunction Coding........................................................................................23
2.3.3 Inapplicable Data Coding................................................................................24
2.3.4 Logically Related Coding................................................................................25
2.3.5 Nominal Variable Coding................................................................................25
2.3.6 Positional Coding............................................................................................26
2.3.7 Ratio Coding...................................................................................................27
2.3.8 Unifying Coding.............................................................................................28
2.3.9 Unspecified Homologue Coding......................................................................28
2.3.10 Extent Coding...............................................................................................29
2.3.11 Repetition Coding.........................................................................................29
2.3.12 Behavioural, Developmental and Landmark Coding......................................30
2.3.13 Mixed Coding...............................................................................................30
2.4 Methods.....................................................................................................30
2.5 Results.......................................................................................................31
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Contents
2.5.1 Neontological Versus Palaeontological Analyses.............................................37
2.5.2 Invertebrate Versus Vertebrate Analyses.........................................................37
2.6 Discussion.................................................................................................38
2.6.1 Palaeontology Versus Neontology...................................................................40
2.6.2 Inapplicable Data Characters...........................................................................42
2.7 Conclusions..............................................................................................46
Chapter 3: Character Construction and the Phylogeny of Aetosaurian
Archosaurs (Reptilia, Diapsida)........................................................................49
3.1 Introduction...............................................................................................49
3.1.1 Aetosaurs........................................................................................................50
3.2 Materials and Methods.............................................................................51
3.3 Results.......................................................................................................53
3.3.1 A review of aetosaurian phylogenetics............................................................53
3.3.2 Parrish (1994)..................................................................................................53
3.3.2.1 Review......................................................................................................53
3.3.2.2 Reanalysis................................................................................................55
3.3.2.3 Support.....................................................................................................56
3.3.3 Heckert, Hunt and Lucas (1996)......................................................................57
3.3.3.1 Review......................................................................................................57
3.3.3.2 Reanalysis................................................................................................58
3.3.3.3 Support.....................................................................................................59
3.3.3.4 Characters................................................................................................60
3.3.4 Heckert and Lucas (1999)................................................................................63
3.3.4.1 Review......................................................................................................63
3.3.4.2 Reanalysis................................................................................................63
3.3.4.3 Support.....................................................................................................65
3.3.4.4 Characters................................................................................................66
3.3.5 Combined Matrix............................................................................................67
3.4 Discussion.................................................................................................72
3.4.1 Aetosaurian phylogeny....................................................................................72
3.4.2 Intraorganismal Homology, Character Independence and Character Construction
................................................................................................................................72
Chapter 4: Compatibility Methods and Their Uses.........................................79
4.1 Introduction...............................................................................................79
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Contents
4.2 Compatibility.............................................................................................79
4.2.1 Fuzzy compatibility.........................................................................................84
4.2.2 Uses of Compatibility......................................................................................87
4.2.2.1 The Coefficient of Character State Randomness (CCSR)...........................89
4.2.2.2 The Normal Deviate (NDev).....................................................................89
4.2.2.3 Le Quesne Probability (LQP)...................................................................90
4.2.2.4 Clique Analysis.........................................................................................91
4.2.2.5 Boildown..................................................................................................91
4.2.2.6 Boildown Bootstrap..................................................................................93
4.3 Potential Problems with Compatibility Methods....................................95
4.3.1 Uncertainty and Polymorphism Within Leaves................................................95
4.3.2 Logical linkage and Inapplicable data..............................................................97
4.3.3 Tree Balance...................................................................................................98
4.3.3.1 Bias Towards Unbalanced Trees in Compatibility..................................106
Chapter 5: The Boildown Computer Program................................................108
5.1 Introduction.............................................................................................108
5.2 Specifications.........................................................................................109
5.3 Users Manual..........................................................................................110
5.3.1 The File Menu...............................................................................................110
5.3.1.1 New........................................................................................................110
5.3.1.2 Edit.........................................................................................................110
5.3.1.3 Execute...................................................................................................110
5.3.1.4 Close......................................................................................................113
5.3.1.5 Save, Save As..........................................................................................113
5.3.1.6 Revert.....................................................................................................113
5.3.1.7 Page Setup..............................................................................................113
5.3.1.8 Print.......................................................................................................113
5.3.2 The Edit Menu..............................................................................................113
5.3.2.1 Undo......................................................................................................113
5.3.2.2 Redo.......................................................................................................113
5.3.2.3 Cut, Copy...............................................................................................114
5.3.2.4 Paste......................................................................................................114
5.3.2.5 Delete.....................................................................................................114
5.3.2.6 Select All................................................................................................114
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Contents
5.3.2.7 Clear Log...............................................................................................114
5.3.3 The Analyses Menu.......................................................................................114
5.3.3.1 Compatibility Analysis............................................................................114
5.3.3.2 Boildown Analysis..................................................................................116
5.3.3.3 Boildown Bootstrap Analysis..................................................................117
5.3.3.4 Taxon Jacknife Analysis..........................................................................120
5.3.3.5 Show Results...........................................................................................122
Chapter 6: The Stagnation of Phylogenetic Debates and the Affinities of
Turtles...............................................................................................................123
6.1 Introduction.............................................................................................123
6.2 A Case Study: The Origin of Turtles.....................................................124
6.2.1 History of the Debate....................................................................................125
6.2.2 Data Exploration Methods.............................................................................136
6.2.2.1 Consensus Matrix...................................................................................138
6.2.2.2 Compatibility Methods............................................................................140
6.3 Results.....................................................................................................140
6.3.1 Rieppel and Reisz (1999)..............................................................................140
6.3.1.1 Reanalysis..............................................................................................140
6.3.1.2 Sequential Sister-Group Removal...........................................................142
6.3.1.3 RSACW...................................................................................................143
6.3.1.4 Compatibility Methods............................................................................144
6.3.1.4.1 Taxon Jacknife Analysis...................................................................144
6.3.1.4.2 Compatibility Analysis.....................................................................146
6.3.1.4.3 Boildown Analysis...........................................................................150
6.3.1.4.4 Fuzzy Compatibility.........................................................................151
6.3.2 Lee (2001).....................................................................................................154
6.3.2.1 Reanalysis..............................................................................................154
6.3.2.2 Sequential Sister-Group Removal...........................................................155
6.3.2.3 RSACW...................................................................................................155
6.3.2.4 Compatibility Methods............................................................................156
6.3.2.4.1 Taxon Jacknife Analysis...................................................................156
6.3.2.4.2 Compatibility Analysis.....................................................................157
6.3.2.4.3 Boildown Analysis...........................................................................162
6.3.2.4.4 Fuzzy Compatibility.........................................................................162
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Contents
6.3.3 Consensus Matrix..........................................................................................165
6.3.3.1 Sequential Sister-Group Removal...........................................................166
6.3.3.2 RSACW...................................................................................................167
6.3.3.3 Compatibility Analysis............................................................................169
6.3.3.3.1 Taxon Jacknife Analysis...................................................................169
6.3.3.3.2 Compatibility Analysis.....................................................................170
6.3.3.3.3 Boildown Analysis...........................................................................175
6.3.3.3.4 Fuzzy Compatibility.........................................................................175
6.4 Discussion...............................................................................................178
6.4.1 Locating the Disagreement: The Consensus Matrix.......................................178
6.4.2 Identification of Problematic Taxa.................................................................181
6.4.3 Identification of Competing Signals..............................................................183
6.4.4 Compatibility as an Alternative to Parsimony................................................183
6.4.5 Ending the Boildown.....................................................................................188
6.4.6 Boildowns and the turtle debate.....................................................................189
6.4.7 Why All the Confusion?................................................................................193
6.4.8 The Utility of Alternatives to Parsimony.......................................................196
6.5 Conclusions............................................................................................197
Chapter 7: A Closer Look at Turtle Morphology............................................198
7.1 Aims.........................................................................................................198
7.2 Methods...................................................................................................198
7.3 Character Examination...........................................................................198
7.3.1 Debated Scorings..........................................................................................220
7.3.2 Taxon Sampling............................................................................................222
7.4 Analyses..................................................................................................226
7.4.1 Coding Methods and Character Strength.......................................................226
7.4.2 Phylogenetic Analysis of the New Matrix......................................................226
7.4.3 Taxon Jacknife..............................................................................................229
7.4.4 Boildown Analysis........................................................................................233
7.5 Discussion...............................................................................................233
7.5.1 Weak Character Coding Types......................................................................234
7.5.2 The Phylogeny..............................................................................................234
7.6 Conclusions: Anapsid or Diapsid?.......................................................242
7.7 Future Work.............................................................................................243
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