Molecular Evolution and PhylogeneticsDuring 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 analysis of 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 numerical examples using the computer program MEGA2 that is provided. |
Contents
1 Molecular Basis of Evolution | 3 |
12 Mechanism of Evolution | 4 |
13 Structure and Function of Genes | 5 |
14 Mutational Changes of DNA Sequences | 9 |
15 Codon Usage | 11 |
2 Evolutionary Change of Amino Acid Sequences | 17 |
22 Poisson Correction PC and Gamma Distances | 19 |
23 Bootstrap Variances and Covariances | 25 |
Maximum Likelihood Methods | 147 |
82 Models of Nucleotide Substitution | 152 |
83 Protein Likelihood Methods | 159 |
84 Theoretical Foundation of ML Methods | 162 |
85 Parameter Estimation for a Given Topology | 163 |
Accuracies and Statistical Tests of Phylogenetic Trees | 165 |
92 Interior Branch Tests | 168 |
93 Bootstrap Tests | 171 |
24 Amino Acid Substitution Matrix | 27 |
25 Mutation Rate and Substitution Rate | 29 |
3 Evolutionary Change of DMA Sequences | 33 |
32 Estimation of the Number of Nucleotide Substitutions | 35 |
33 Gamma Distances | 43 |
34 Numerical Estimation of Evolutionary Distances | 45 |
35 Alignment of Nucleotide Sequences | 46 |
36 Handling of Sequence Gaps in the Estimation of Evolutionary Distances | 49 |
Synonymous and Nonsynonymous Nucleotide Substitutions | 51 |
41 Evolutionary Pathway Methods | 52 |
42 Methods Based on Kimuras 2Parameter Model | 62 |
43 Nucleotide Substitutions at Different Codon Positions | 67 |
44 Likelihood Methods with Codon Substitution Models | 69 |
5 Phylogenetic Trees | 73 |
52 Topological Differences | 81 |
53 TreeBuilding Methods | 83 |
Distance Methods | 87 |
62 Least Squares LS Methods | 92 |
63 Minimum Evolution ME Method | 99 |
64 Neighbor oining N Method | 103 |
65 Distance Measures to Be Used for Phylogenetic Reconstruction | 111 |
Maximum Parsimony Methods | 115 |
71 Finding Maximum Parsimony MP Trees | 116 |
72 Strategies of Searching for MP Trees | 122 |
73 Consensus Trees | 130 |
74 Estimation of Branch Lengths | 131 |
75 Weighted Parsimony | 133 |
76 MP Methods for Protein Data | 137 |
77 Shared Derived Characters | 140 |
94 Tests of Topological Differences | 175 |
95 Advantages and Disadvantages of Different TreeBuilding Methods | 178 |
101 Molecular Clock Hypothesis | 187 |
102 Relative Rate Tests | 191 |
103 Phylogenetic Tests | 196 |
104 Linearized Trees | 203 |
11 Ancestral Nucleotide and Amino Acid Sequences | 207 |
Bayesian Approach | 208 |
113 Synonymous and Nonsynonymous Substitutions in Ancestral Branches | 216 |
114 Convergent and Parallel Evolution | 221 |
121 Evolutionary Significance of Genetic Polymorphism | 231 |
122 Analysis of Allele Frequency Data | 233 |
123 Genetic Variation in Subdivided Populations | 236 |
124 Genetic Variation for Many Loci | 244 |
125 DNA Polymorphism | 250 |
126 Statistical Tests for Detecting Selection | 258 |
13 Population Trees from Genetic Markers | 265 |
132 Analysis of DNA Sequences by Restriction Enzymes | 275 |
133 Analysis of RAPD Data | 285 |
14 Perspectives | 291 |
142 Genome Projects | 292 |
143 Molecular Biology and Evolution | 294 |
A Mathematical Symbols and Notations | 297 |
B Geological Timescale | 298 |
C Geological Events in the Cenozoic and Mesozoic Eras | 299 |
| 301 | |
| 329 | |
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Common terms and phrases
algorithm allele frequencies amino acid sequences amino acid substitution assumption b₁ Biol bootstrap bootstrap test branch length estimates chimpanzees cleotide codon usage bias computer simulation consensus tree constructed correct topology data set Dayhoff distance measures DNA sequences Drosophila enzymes Equation Evol evolutionary example expected number Figure gamma distance genetic genome given heterozygosity human i-th interior branch Jukes-Cantor large number lineages loci locus lysozyme matrix maximum likelihood maximum parsimony mitochondrial ML method model tree molecular clock MP tree mutation Natl NJ tree node nucleotide or amino nucleotide sequences nucleotide substitution null hypothesis number of amino number of nucleotide number of sequences number of substitutions numbers of synonymous pair parameters parsimony phylogenetic trees phylogeny polymorphism population protein quences realized tree Rzhetsky sequence data species substitution matrix substitution model synonymous substitutions Takezaki taxa taxon tion topology total number tree obtained tree topology tree-building methods true tree UPGMA variance