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Numerical Examples xiii
Molecular Basis of Evolution 3 (14)
Evolutionary Tree of Life 3 (1)
Mechanism of Evolution 4 (1)
Structure and Function of Genes 5 (4)
Mutational Changes of DNA Sequences 9 (2)
Codon Usage 11 (6)
Evolutionary Change of Amino Acid Sequences 17 (16)
Amino Acid Differences and Proportion of 17 (2)
Different Amino Acids
Poisson Correction (PC) and Gamma Distances 19 (6)
Bootstrap Variances and Covariances 25 (2)
Amino Acid Substitution Matrix 27 (2)
Mutation Rate and Substitution Rate 29 (4)
Evolutionary Change of DNA Sequences 33 (18)
Nucleotide Differences Between Sequences 33 (2)
Estimation of the Number of Nucleotide 35 (8)
Substitutions
Gamma Distances 43 (2)
Numerical Estimation of Evolutionary 45 (1)
Distances
Alignment of Nucleotide Sequences 46 (3)
Handling of Sequence Gaps in the Estimation 49 (2)
of Evolutionary Distances
Synonymous and Nonsynonymous Nucleotide 51 (22)
Substitutions
Evolutionary Pathway Methods 52 (10)
Methods Based on Kimura's 2-Parameter Model 62 (5)
Nucleotide Substitutions at Different Codon 67 (2)
Positions
Likelihood Methods with Codon Substitution 69 (4)
Models
Phylogenetic Trees 73 (14)
Types of Phylogenetic Trees 73 (8)
Topological Differences 81 (2)
Tree-Building Methods 83 (4)
Phylogenetic Inference: Distance Methods 87 (28)
UPGMA 87 (5)
Least Squares (LS) Methods 92 (7)
Minimum Evolution (ME) Method 99 (4)
Neighbor Joining (NJ) Method 103 (8)
Distance Measures to Be Used for 111 (4)
Phylogenetic Reconstruction
Phylogenetic Inference: Maximum Parsimony 115 (32)
Methods
Finding Maximum Parsimony (MP) Trees 116 (6)
Strategies of Searching for MP Trees 122 (8)
Consensus Trees 130 (1)
Estimation of Branch Lengths 131 (2)
Weighted Parsimony 133 (5)
MP Methods for Protein Data 138 (2)
Shared Derived Characters 140 (7)
Phylogenetic Inference: Maximum Likelihood 147 (18)
Methods
Computational Procedure of ML Methods 147 (5)
Models of Nucleotide Substitution 152 (7)
Protein Likelihood Methods 159 (3)
Theoretical Foundation of ML Methods 162 (1)
Parameter Estimation for a Given Topology 163 (2)
Accuracies and Statistical Tests of 165 (22)
Phylogenetic Trees
Optimization Principle and Topological 165 (3)
Errors
Interior Branch Tests 168 (3)
Bootstrap Tests 171 (4)
Tests of Topological Differences 175 (3)
Advantages and Disadvantages of Different 178 (9)
Tree-Building Methods
Molecular Clocks and Linearized Trees 187 (20)
Molecular Clock Hypothesis 187 (4)
Relative Rate Tests 191 (5)
Phylogenetic Tests 196 (7)
Linearized Trees 203 (4)
Ancestral Nucleotide and Amino Acid Sequences 207 (24)
Inference of Ancestral Sequences: Parsimony 207 (1)
Approach
Inference of Ancestral Sequences: Bayesian 208 (8)
Approach
Synonymous and Nonsynonymous Substitutions 216 (5)
in Ancestral Branches
Convergent and Parallel Evolution 221 (10)
Genetic Polymorphism and Evolution 231 (34)
Evolutionary Significance of Genetic 231 (2)
Polymorphism
Analysis of Allele Frequency Data 233 (3)
Genetic Variation in Subdivided Populations 236 (8)
Genetic Variation for Many Loci 244 (6)
DNA Polymorphism 250 (8)
Statistical Tests for Detecting Selection 258 (7)
Population Trees from Genetic Markers 265 (26)
Genetic Distance for Allele Frequency Data 265 (10)
Analysis of DNA Sequences by Restriction 275 (10)
Enzymes
Analysis of RAPD Data 285 (6)
Perspectives 291 (14)
Statistical Methods 291 (1)
Genome Projects 292 (2)
Molecular Biology and Evolution 294 (3)
Appendices
A. Mathematical Symbols and Notations 297 (2)
B. Geological Timescale 299 (2)
C. Geological Events in the Cenozoic and 301 (2)
Mesozoic Eras
D. Organismal Evolution Based on the Fossil 303 (2)
Record
References 305 (24)
Index 329

During the last ten years, remarkable progress has occurred in the study of molecular evolution. Among the most important factors that are responsible for this progress are the development of new statistical methods and advances in computational technology. In particular, phylogenetic analysisof DNA or protein sequences has become a powerful tool for studying molecular evolution. Along with this developing technology, the application of the new statistical and computational methods has become more complicated and there is no comprehensive volume that treats these methods in depth.Molecular Evolution and Phylogenetics fills this gap and present various statistical methods that are easily accessible to general biologists as well as biochemists, bioinformatists and graduate students. The text covers measurement of sequence divergence, construction of phylogenetic trees,statistical tests for detection of positive Darwinian selection, inference of ancestral amino acid sequences, construction of linearized trees, and analysis of allele frequency data. Emphasis is given to practical methods of data analysis, and methods can be learned by working through numericalexamples using the computer program MEGA2 that is provided.