Contents -- Numerical Examples -- 1 Molecular Basis of Evolution -- 1.1. Evolutionary Tree of Life -- 1.2. Mechanism of Evolution -- 1.3. Structure and Function of Genes -- 1.4. Mutational Changes of DNA Sequences -- 1.5. Codon Usage -- 2 Evolutionary Change of Amino Acid Sequences -- 2.1. Amino Acid Differences and Proportion of Different Amino Acids -- 2.2. Poisson Correction (PC) and Gamma Distances -- 2.3. Bootstrap Variances and Covariances -- 2.4. Amino Acid Substitution Matrix -- 2.5. Mutation Rate and Substitution Rate -- 3 Evolutionary Change of DNA Sequences -- 3.1. Nucleotide Differences Between Sequences -- 3.2. Estimation of the Number of Nucleotide Substitutions -- 3.3. Gamma Distances -- 3.4. Numerical Estimation of Evolutionary Distances -- 3.5. Alignment of Nucleotide Sequences -- 3.6. Handling of Sequence Gaps in the Estimation of Evolutionary Distances -- 4 Synonymous and Nonsynonymous Nucleotide Substitutions -- 4.1. Evolutionary Pathway Methods -- 4.2. Methods Based on Kimura's 2-Parameter Model -- 4.3. Nucleotide Substitutions at Different Codon Positions -- 4.4. Likelihood Methods with Codon Substitution Models -- 5 Phylogenetic Trees -- 5.1. Types of Phylogenetic Trees -- 5.2. Topological Differences -- 5.3. Tree-Building Methods -- 6 Phylogenetic Inference: Distance Methods -- 6.1. UPGMA -- 6.2. Least Squares (LS) Methods -- 6.3. Minimum Evolution (ME) Method -- 6.4. Neighbor Joining (NJ) Method -- 6.5. Distance Measures to Be Used for Phylogenetic Reconstruction -- 7 Phylogenetic Inference: Maximum Parsimony Methods -- 7.1. Finding Maximum Parsimony (MP) Trees -- 7.2. Strategies of Searching for MP Trees -- 7.3. Consensus Trees -- 7.4. Estimation of Branch Lengths -- 7.5. Weighted Parsimony -- 7.6. MP Methods for Protein Data -- 7.7. Shared Derived Characters -- 8 Phylogenetic Inference: Maximum Likelihood Methods.

8.1. Computational Procedure of ML Methods -- 8.2. Models of Nucleotide Substitution -- 8.3. Protein Likelihood Methods -- 8.4. Theoretical Foundation of ML Methods -- 8.5. Parameter Estimation for a Given Topology -- 9 Accuracies and Statistical Tests of Phylogenetic Trees -- 9.1. Optimization Principle and Topological Errors -- 9.2. Interior Branch Tests -- 9.3. Bootstrap Tests -- 9.4. Tests of Topological Differences -- 9.5. Advantages and Disadvantages of Different Tree-Building Methods -- 10 Molecular Clocks and Linearized Trees -- 10.1. Molecular Clock Hypothesis -- 10.2. Relative Rate Tests -- 10.3. Phylogenetic Tests -- 10.4. Linearized Trees -- 11 Ancestral Nucleotide and Amino Acid Sequences -- 11.1. Inference of Ancestral Sequences: Parsimony Approach -- 11.2. Inference of Ancestral Sequences: Bayesian Approach -- 11.3. Synonymous and Nonsynonymous Substitutions in Ancestral Branches -- 11.4. Convergent and Parallel Evolution -- 12 Genetic Polymorphism and Evolution -- 12.1. Evolutionary Significance of Genetic Polymorphism -- 12.2. Analysis of Allele Frequency Data -- 12.3. Genetic Variation in Subdivided Populations -- 12.4. Genetic Variation for Many Loci -- 12.5. DNA Polymorphism -- 12.6. Statistical Tests for Detecting Selection -- 13 Population Trees from Genetic Markers -- 13.1. Genetic Distance for Allele Frequency Data -- 13.2. Analysis of DNA Sequences by Restriction Enzymes -- 13.3. Analysis of RAPD Data -- 14 Perspectives -- 14.1. Statistical Methods -- 14.2. Genome Projects -- 14.3. Molecular Biology and Evolution -- Appendices -- A. Mathematical Symbols and Notations -- B. Geological Timescale -- C. Geological Events in the Cenozoic and Mesozoic Eras -- D. Organismal Evolution Based on the Fossil Record -- References -- Index -- A -- B -- C -- D -- E -- F -- G -- H -- I -- L -- M -- N -- O -- P -- R -- S -- T -- U -- V -- W.

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