『Parsimony, Phylogeny, and Genomics』

Viktor A. Albert (ed.)

(2005年,Oxford University Press, ISBN:0198564937



おお,Steve Farris に献呈されている! 系統学における最節約法だけの論文集だ.2002年の Hennig Society Meetings(ヘルシンキ)での講演をベースにしている.編者序文に,Farrisの開発した数量分岐学の理論の中で,とくに最節約法の離散数学的な部分に編者は感銘を受けたと書かれてある(p. v).確かに同意できるのだが,形質計量空間に関する〈Farris変換〉(Farris transform)と〈Gromov積〉との関係は,Semple and Steel『Phylogenetics』(2003年,Oxford University Press,ISBN:0198509421)の7.2節ですでに導出されているので,あえて Andreas Dress et al.「Δ additive and Δ ultra-additive maps, Gromov's trees, and the Farris transform」Discrete Applied Mathematics, 146: 51-73, 2005(→abstract)を参照するまでもないのではとぼくは考える.




【目次】
Dedication (Victor A. Albert) v
Preface (Victor A. Albert) vi
Contributors ix


1. Parsimony and phylogenetics in the genomic age (Victor A. Albert) 1


I: Philosophical aspects of parsimony analysis, including comparison with model-based approaches

2. What is the ratinale for 'Ockham's razor' (a. k. a. parsimony) in phylogenetic inference? (Arnold G. Kluge) 15

3. Parsimony and its presuppositions (Elliott Sober) 43


II: Parsimony, character analysis, and optimization of sequence characters

4. The logic of the data matrix in phylogenetic analysis (Brent D. Mishler) 57

5. Alignment, dynamic homology, and optimization (Ward C. Wheeler) 71

6. Parsimony and the problem of inapplicables in sequence data (Jan E. De Laet) 81


III: 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, and Damon P. Little) 119

8. Parsimony and Bayesian phylogenetics (Pablo A. Goloboff and Diego Pol) 148


IV: Mathematical attributes of parsimony

9. Maximum parsimony and the phylogenetic information in multistate characters (Mike Steel and David Penny) 163


V: Parsimony and genomics

10. Using phylogeny to understand genomic evolution (David A. Liberles) 181

11. Dollo parsimony and the reconstruction of genome evolution (Igor B. Rogozin, Yuri I. Wolf, Vladimir N. Babenko, and Eugene V. Koonin) 190


References 201
Index 218