Molecular Evolution and Phylogenetics

Front Cover
Oxford University Press, 2000 - Medical - 333 pages
4 Reviews
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 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.
 

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User Review  - amarcobio - LibraryThing

Excellent. This compact book describes what phylogenetic is and how to put it into practice. I first learn myself phylogenetics with this text. It is a bit outdated, though (ML is barely covered and Bayesian analysis mostly omitted) Read full review

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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 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.
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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
References
301
Index
329
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Page 303 - D. 1998. Comparison of the complete protein sets of worm and yeast: Orthology and divergence. Science 282: 2022-2028.
Page 301 - Akashi, H (1995). Inferring weak selection from patterns of poly-morphism and divergence at "silent

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About the author (2000)

Masatoshi Nei is at Pennsylvania State University. Sudhir Kumar is at Arizona State University.

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