Cladistics Theory and Practice of Parsimony Analysis

by Kitching, Ian; Forey, Peter; Humphries, Christopher; Williams, David

• ISBN13: 9780198501398
• ISBN10: 0198501390
• Edition: 2nd
• Format: Hardcover
• Copyright: 1998-09-10
• Publisher: Oxford University Press

Summary

Cladistics aims to reconstruct genealogies based on common ancestry, thus revealing the phylogenetic relationships between taxa. Its applications vary from linguistic analysis to the study of conservation and biodiversity, and it has become a method of choice for comparative studies in all fields of biiology. This new edition of Cladistics --first published in 1992--reflects the many changes and developments which have taken place in the field over the last five years, while retaining the clarity and readability that made the first edition so successful. For all students interested in the systematic relationships among organisms, this book provides a state-of-the-art account of the techniques and methods of modern cladistics, and how to put them into practice.

Table of Contents

List of authors	xiii
1. Introduction to cladistic concepts	1	(18)
1.1 Definition of relationship	1	(1)
1.2 Types of characters	2	(3)
1.3 Parsimony	5	(5)
1.4 Groups	10	(5)
1.5 Cladograms and trees	15	(2)
1.6 Tree terminology	17	(1)
1.7 Chapter summary	18	(1)
2. Characters and character coding	19	(19)
2.1 Introduction	19	(1)
2.1.1 Filters	19	(1)
2.2 Kinds of characters	20	(3)
2.2.1 Qualitative and quantitative variables	20	(1)
2.2.2 Discrete and continuous variables	21	(1)
2.2.3 Overlapping and non-overlapping characters	22	(1)
2.3 Cladistic characters	23	(4)
2.3.1 Diagnostic and systematic characters	23	(2)
2.3.2 Character transformations	25	(1)
2.3.3 Characters and character states	25	(1)
2.3.4 Homology	26	(1)
2.4 Character coding for discrete variables	27	(6)
2.4.1 Multistate characters-character linkage during analysis	29	(1)
2.4.2 Binary characters-character linkage during analysis	29	(1)
2.4.3 Hierarchical character linkage	30	(1)
2.4.4 Transformation between character states: order and polarity	30	(1)
2.4.5 Missing values and coding	31	(1)
2.4.6 Information content and the congruence test	32	(1)
2.5 Morphometric data in cladistic analysis	33	(2)
2.5.1 Coding morphometric data	33	(1)
2.5.2 Gap-weighting	33	(2)
2.6 Discussion: character discovery and coding	35	(2)
2.6.1 Choice of characters	35	(1)
2.6.2 Coding	36	(1)
2.7 Chapter summary	37	(1)
3. Cladogram construction, character polarity and rooting	38	(32)
3.1 Discovering the most parsimonious cladograms	38	(10)
3.1.1 Hennigian argumentation	38	(1)
3.1.2 Exact methods	39	(3)
3.1.3 Heuristic methods	42	(1)
Stepwise addition	43	(2)
Branch-swapping	45	(3)
3.2 Character polarity and rooting	48	(20)
3.2.1 Outgroup comparison	49	(5)
3.2.2 The ontogenetic criterion	54	(5)
3.2.3 Ontogenetic criterion or outgroup comparison-which is superior?	59	(1)
3.2.4 A priori models of character state change	60	(1)
Ingroup commonality	60	(1)
Stratigraphy	61	(1)
Biogeography	61	(1)
Function/adaptive value	62	(1)
Underlying synapomorphy	62	(2)
3.2.5 Polarity and rooting a posteriori	64	(4)
3.3 Chapter summary	68	(2)
4. Optimization and the effects of missing values	70	(22)
4.1 Optimality criteria and character optimization	70	(9)
4.1.1 Wagner optimization	70	(3)
4.1.2 Fitch optimization	73	(2)
4.1.3 Dollo optimization	75	(2)
4.1.4 Camin-Sokal optimization	77	(1)
4.1.5 Generalized optimization	78	(1)
4.2 Missing values	79	(12)
4.3 Chapter summary	91	(1)
5. Measures of character fit and character weighting	92	(26)
5.1 Measures of character fit	92	(7)
5.1.1 Cladogram length	92	(3)
5.1.2 Consistency index(ci)	95	(1)
5.1.3 Ensemble consistency index (CI)	95	(1)
5.1.4 Problems with the consistency index	96	(1)
5.1.5 Retention index (ri)	97	(2)
5.1.6 Ensemble retention index (RI)	99	(1)
5.2 Character weighting	99	(17)
5.2.1 Types of character weighting	100	(1)
5.2.2 A priori weighting	100	(1)
Character analysis	100	(1)
Morphological data	101	(1)
Molecular data	102	(6)
Compatibility analysis	108	(2)
5.2.3 A posteriori weighting	110	(1)
Cladistic consistency	110	(1)
Successive weighting	111	(1)
Implied weighting	112	(3)
5.2.4 Prospects	115	(1)
5.3 Chapter summary	116	(2)
6. Support and confidence statistics for cladograms and groups	118	(21)
6.1 Introduction	118	(1)
6.2 Randomization procedures applied to the whole cladogram	118	(8)
6.2.1 Data decisiveness	119	(1)
6.2.2 Distribution of cladogram lengths (DCL)	120	(2)
6.2.3 Permutation tail probability (PTP)	122	(4)
6.3 Support for individual clades on a cladogram	126	(9)
6.3.1 Bremer support	127	(2)
6.3.2 Randomization procedures	129	(1)
Bootstrap	129	(2)
Jackknife	131	(2)
Clade stability index	133	(1)
Topology-dependent permutation tail probability (T-PTP)	134	(1)
6.4 Summary	135	(1)
6.5 Chapter summary	136	(3)
7. Consensus trees	139	(12)
7.1 Introduction	139	(2)
7.2 Strict consensus trees	141	(2)
7.3 Combinable components or semi-strict consensus	143	(2)
7.4 Majority-rule and median consensus trees	145	(1)
7.5 Nelson consensus	146	(1)
7.6 Adams consensus	147	(1)
7.7 Agreement subtrees or common pruned trees	147	(1)
7.8 Conclusions	148	(1)
7.9 Chapter summary	149	(2)
8. Simultaneous and partitioned analysis	151	(17)
8.1 Introduction	151	(4)
8.2 Theoretical issues	155	(2)
8.3 Partitioned analysis (taxonomic congruence)	157	(3)
8.3.1 Independence of data sets	157	(2)
8.3.2 Cladogram support	159	(1)
8.3.3 Different sized data sets	159	(1)
8.4 Simultaneous analysis	160	(2)
8.4.1 Resolution	160	(1)
8.4.2 Arbitrary consensus	161	(1)
8.5 Conditional data combination	162	(2)
8.6 Operational difficulties	164	(1)
8.7 Conclusions	165	(1)
8.8 Chapter summary	166	(2)
9. Three-item statements analysis	168	(19)
9.1 Introduction	168	(1)
9.2 Coding	168	(2)
9.3 Implementation	170	(10)
9.3.1 Binary characters	170	(1)
9.3.2 Multistate characters	171	(1)
9.3.3 Representation of three-item statements for analysis with current parsimony programs	171	(1)
9.3.4 Cladogram length and three-item statements	172	(1)
9.3.5 Uniform and fractional weighting	173	(4)
9.3.6 Minimal cladograms	177	(1)
9.3.7 Optimization	178	(1)
9.3.8 Information measures: CI and RI	179	(1)
9.3.9 Summary of implementation procedures	180	(1)
9.4 Precision	180	(5)
9.5 Chapter summary	185	(2)
References	187	(9)
Suggestions for further reading	196	(3)
Glossary	199	(22)
Appendix: Computer programs	221	(2)
Index	223