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.

Preface 1. Parsimony and phylogenetics in the genomic age, Victor A. Albert 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?, Arnold G. Kluge 3. Parsimony and its presuppositions, Elliott Sober Parsimony, character analysis, and optimization of sequence characters 4. The logic of the data matrix in phylogenetic analysis, Brent D. Mishler 5. Alignment, dynamic homology, and optimization, Ward C. Wheeler 6. Parsimony and the problem of inapplicables in sequence data, Jan De Laet Computational limits of parsimony analysis: from historical aspects to competition with fast model-based approaches 7. The limits of conventional cladistic analysis, Jerrold I. Davis, Kevin C. Nixon, Damon P. Little 8. Parsimony and Bayesian phylogenetics, Pablo A. Goloboff, Diego Pol Mathematical attributes of parsimony 9. Maximum parsimony and the phylogenetic information in multi-state characters, Mike Steel and David Penny Parsimony and genomics 10. Using phylogeny to understand genomic evolution, David A. Liberles 11. Dollo parsimony and reconstruction of genome evolution, Igor Rogozin et al. References Index