Molecular Evolution and Phylogenetics

by Nei, Masatoshi; Kumar, Sudhir

• ISBN13: 9780195135848
• ISBN10: 0195135849
• Format: Hardcover
• Copyright: 2000-07-27
• Publisher: Oxford University Press

Summary

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.

Table of Contents

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 Different Amino Acids	17	(2)
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 Substitutions	35	(8)
Gamma Distances	43	(2)
Numerical Estimation of Evolutionary Distances	45	(1)
Alignment of Nucleotide Sequences	46	(3)
Handling of Sequence Gaps in the Estimation of Evolutionary Distances	49	(2)
Synonymous and Nonsynonymous Nucleotide Substitutions	51	(22)
Evolutionary Pathway Methods	52	(10)
Methods Based on Kimura's 2-Parameter Model	62	(5)
Nucleotide Substitutions at Different Codon Positions	67	(2)
Likelihood Methods with Codon Substitution Models	69	(4)
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 Phylogenetic Reconstruction	111	(4)
Phylogenetic Inference: Maximum Parsimony Methods	115	(32)
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 Methods	147	(18)
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 Phylogenetic Trees	165	(22)
Optimization Principle and Topological Errors	165	(3)
Interior Branch Tests	168	(3)
Bootstrap Tests	171	(4)
Tests of Topological Differences	175	(3)
Advantages and Disadvantages of Different Tree-Building Methods	178	(9)
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 Approach	207	(1)
Inference of Ancestral Sequences: Bayesian Approach	208	(8)
Synonymous and Nonsynonymous Substitutions in Ancestral Branches	216	(5)
Convergent and Parallel Evolution	221	(10)
Genetic Polymorphism and Evolution	231	(34)
Evolutionary Significance of Genetic Polymorphism	231	(2)
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 Enzymes	275	(10)
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 Mesozoic Eras	301	(2)
D. Organismal Evolution Based on the Fossil Record	303	(2)
References	305	(24)
Index	329