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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 aims to demonstrate the potential that this powerful hierarchial data summarisation method also has for both structural and functional comparative genomic research.
Preface; 1. Parsimony and phylogenetics in the genomic age; THE PHILOSOPHY OF PARSIMONY ANALYSIS, INCLUDING COMPARISON WITH MODEL-BASED APPROACHES; 2. What is the rationale for 'Ockham's Razor' (a.k.a. parsimony) in phylogenetic inference?; 3. Parsimony and its presuppositions; PARSIMONY, CHARACTER ANALYSIS, AND OPTIMIZATION OF SEQUENCE CHARACTERS; 4. The logic of the data matrix in phylogenetic analysis; 5. Alignment, dynamic homology, and optimization; 6. Parsimony and the problem of inapplicables in sequence data; COMPUTATIONAL LIMITS OF PARSIMONY ANALYSIS: FROM HISTORICAL ASPECTS TO COMPETITION WITH FAST MODEL-BASED APPROACHES; 7. The limits of conventional cladistic analysis; 8. Parsimony and Bayesian phylogenetics; MATHEMATICAL ATTRIBUTES OF PARSIMONY; 9. Maximum parsimony and the phylogenetic information in multi-state characters; PARSIMONY AND GENOMICS; 10. Using phylogeny to understand genomic evolution; 11. Dollo parsimony and reconstruction of genome evolution; References; Index
There is a lot to consider in the book for practicing systematists, mostly issues of molecular systematics, ranging from DNA sequence alignment problems to those of the practicality of analysis of the enormous and ever increasing data sets that are generated by genomic approaches to phylogeny reconstruction. Olivier Rieppel, Biology and Philosophy (2007), 22:141-144 All in all, this is an interesting conribution to the genre. The production quality of the book is mostly very good. Staunch devotees of parsimony will find this to be an essential reference, while everyone else will find much that is of interest. Systematic Biology, 56(1): 147-149, 2007 ... a cogent, comprehensive overview ... of parsimony and its role in genomics. Rob DeSalle, Quarterly Review of Biology, Vol 82, June 2007 ...this is the book to consult if you want to know more about the role that parsimony analysis has to play in phylogenetics today and what it might be used for in the future. Systematic Biology, 56(1): 147-149, 2007