Parsimony analysis (cladistics) has long been one of the most widely used methods of phylogenetic inference in the fields of systematic and evolutionary biology. Moreover it has mathematical attributes that lend itself for use with complex, genomic-scale data sets. This book demonstrates the potential that this powerful hierarchical data summarization method also has for both structural and functional comparative genomic research.
Author(s): Ioannis P. Stavroulakis, Stepan A. Tersian
Publisher: Oxford University Press, USA
Year: 2005
Language: English
Pages: 240
Contents......Page 8
Contributors......Page 10
1 Parsimony and phylogenetics in the genomic age......Page 12
I: Philosophical aspects of parsimony analysis, including comparison with model-based approaches......Page 24
2 What is the rationale for ‘Ockham’s razor’ (a.k.a. parsimony) in phylogenetic inference?......Page 26
3 Parsimony and its presuppositions......Page 54
II: Parsimony, character analysis, and optimization of sequence characters......Page 66
4 The logic of the data matrix in phylogenetic analysis......Page 68
5 Alignment, dynamic homology, and optimization......Page 82
6 Parsimony and the problem of inapplicables in sequence data......Page 92
III: Computational limits of parsimony analysis: from historical aspects to competition with fast model-based approaches......Page 128
7 The limits of conventional cladistic analysis......Page 130
8 Parsimony and Bayesian phylogenetics......Page 159
IV: Mathematical attributes of parsimony......Page 172
9 Maximum parsimony and the phylogenetic information in multistate characters......Page 174
V: Parsimony and genomics......Page 190
10 Using phylogeny to understand genomic evolution......Page 192
11 Dollo parsimony and the reconstruction of genome evolution......Page 201
References......Page 212
B......Page 229
C......Page 230
F......Page 231
H......Page 232
J......Page 233
M......Page 234
O......Page 235
P......Page 236
Q......Page 237
S......Page 238
T......Page 239
Z......Page 240
