Preface ........................................................ ix
1 Selectionism and Mutationism ................................. 1
1.1 Darwin's Theory of Evolution ............................ 1
1.2 Criticisms of Darwin's Theory ........................... 2
1.3 Evolution by Discontinuous Variation .................... 3
1.4 Mutationism ............................................. 6
1.5 Neo-Darwinism ........................................... 7
1.6 Neomutationism or Mutation-Driven Evolution ............. 9
1.7 Survival of the Fittest and Survival of the Niche-
Filling Variants ........................................ 9
2 Neo-Darwinism and Panselectionism ........................... 13
2.1 Backgrounds ............................................ 13
2.2 Allele Frequency Changes as the Basic Process of
Evolution .............................................. 14
Mutation ............................................... 14
Natural Selection with Constant Fitness ................ 15
Mutation-Selection Balance ............................. 17
Balanced Polymorphism .................................. 18
Natural Selection for Multiple Loci .................... 19
2.3 Difficulties of Defining and Estimating Selection
Coefficients ........................................... 20
Estimates of Selection Coefficients and their
Reliability ............................................ 20
Fluctuation of Selection Coefficients .................. 22
General Considerations ................................. 23
2.4 Stochastic Changes of Allele Frequencies ............... 24
Probability of Fixation of Mutant Alleles .............. 25
Equilibrium Distribution of Allele Frequencies ......... 25
Effective Population Size and Sampling Errors of
Allele Frequencies ..................................... 28
Random Errors Caused by Fluctuation of Selection
Coefficients ........................................... 29
2.5 Mutation and Standing Genetic Variation ................ 31
Artificial and Natural Selection in Quantitative
Characters ............................................. 31
Evolution of Drug Resistance ........................... 34
2.6 Classical and Balance Theories of Maintenance of
Genetic Variation ...................................... 34
Genetic Load ........................................... 35
Number of Alleles that can be Maintained in Finite
Populations ............................................ 36
2.7 Natural Selection as a Creative Force .................. 37
2.8 Summary ................................................ 39
3 Evolutionary Theories in the Neo-Darwinian Era .............. 41
3.1 Modifier Genes ......................................... 41
Evolution of Dominance ................................. 42
Modification of Linkage Intensity ...................... 43
3.2 Fisher's Fundamental Theorem of Natural Selection ...... 44
3.3 Cost of Natural Selection and Fertility Excess
Required ............................................... 46
3.4 Shifting Balance Theory of Evolution ................... 48
3.5 Accumulation of Nonfunctional and Deleterious
Mutations .............................................. 50
Y Chromosomes .......................................... 50
Nonfunctional Mutations in Duplicate Genes ............. 52
Deleterious Mutations and Muller's Ratchet ............. 52
3.6 Bottleneck Effects and Genetic Variability ............. 53
3.7 Beanbag Genetics and Evolution ......................... 56
3.8 Summary ................................................ 58
4 Molecular Evolution ......................................... 59
4.1 Early Studies of Molecular Evolution ................... 59
4.2 Neutral Evolution at the Protein Level ................. 60
Cost of Natural Selection and Neutral Theory ........... 60
Definition of Neutral Mutations ........................ 61
King and Jukes's View .................................. 63
Definition of Neutral Theory ........................... 64
4.3 Molecular Clocks ....................................... 65
Evolutionary Rate under Purifying Selection ............ 65
Evolutionary Rate and Generation Time .................. 65
Functional Constraints of Proteins ..................... 66
Variation in Mutation Rate ............................. 67
Molecular Clocks and Neutral Theory .................... 68
4.4 Evolution of Protein-Coding Genes ...................... 69
General Properties of Evolution of Protein-Coding
Genes .................................................. 69
Fast-Evolving Genes .................................... 70
4.5 Protein Polymorphism ................................... 70
4.6 Neutral Evolution at the DNA Level ..................... 72
Synonymous and Nonsynonymous Nucleotide Substitutions .. 72
Pseudogenes as a Paradigm of Neutral Evolution ......... 72
Slightly Deleterious or Nearly Neutral Mutations ....... 73
4.7 Advantageous Mutations ................................. 74
Evolution of New Protein Function ...................... 74
Immune System Genes .................................... 78
Trans-Species Polymorphism ............................. 79
4.8 Recent Statistical Studies for Detecting Positive
Selection .............................................. 81
Bayesian Methods for Identifying Positively-Selected
Codon Sites ............................................ 81
MK Test and its Extensions ............................. 82
Extended Haplotype Homozygosity and FST Tests .......... 84
Statistical Studies and Biochemical Verification ....... 86
Frequency Distributions of Mutant Nucleotides .......... 87
4.9 Summary ................................................ 87
5 Gene Duplication, Multigene Families, and Repetitive DNA
Sequences ................................................... 89
5.1 New Genes Generated by Gene Duplication ................ 89
Increase in the Number of Genes by Gene Duplication .... 90
Genome Size and Number of Genes ........................ 91
Gene Numbers and Phenotypic Complexity ................. 92
5.2 Evolution of Multigene Families ........................ 94
5.3 Concerted Evolution .................................... 95
Unequal Crossover, Gene Conversion, and Purifying
Selection .............................................. 95
Tandemly Arrayed Histone Genes ......................... 96
5.4 Birth-and-Death Evolution .............................. 97
MHC Genes .............................................. 97
Immunoglobulins and other Immune Systems Genes ......... 99
Olfactory and other Chemosensory Receptor Genes ....... 101
Birth-and-Death Evolution with Strong Purifying
Selection ............................................. 102
5.5 Multigene Families and Evolution of New Genetic
Systems ............................................... 103
Adaptive Immune System ................................ 103
Homeobox Genes Involved in Animal and Plant
Development ........................................... 104
Multigene Families and Flower Development in Plants ... 105
5.6 Genomic Drift and Copy Number Variation ............... 105
5.7 Noncoding DNA and Transposable Genetic Elements ....... 107
Exons and Introns ..................................... 108
Transposable Genetic Elements ......................... 109
Tandem Repetitive Sequences ........................... 110
5.8 Summary ............................................... 110
6 Evolution of Phenotypic Characters ......................... 113
6.1 Changing Concepts of the Gene and Gene Expression ..... 113
Definition of a Gene .................................. 113
Protein-Coding and Regulatory Regions of Genes ........ 115
Gene Regulatory Networks .............................. 116
Small RNAs that Control the Level of Gene Expression .. 116
Methylation and Epigenetics ........................... 117
Signaling Pathways and Gene Interaction ............... 118
6.2 Evolution of Physiological and Morphological
Characters ............................................ 120
Changes in the Protein-Coding Regions of Genes ........ 120
Gene Regulation Hypothesis ............................ 122
Major Gene Effect Hypothesis .......................... 126
Gene Regulatory Networks and Morphological Evolution .. 128
6.3 Evolution of Gene Regulatory Systems .................. 129
Cis-Regulatory Elements ............................... 129
Evolutionary Change ofMicroRNAs and other Small RNAs
Controlling Gene Expression ........................... 130
6.4 Epigenetics and Phenotypic Evolution .................. 131
Environmental Sex Determination ....................... 131
Evolution of Temperature-Dependent Sex Determination .. 132
Vernalization and Flowering in Plants ................. 132
6.5 Gene Co-Option and Horizontal Gene Transfer ........... 133
Gene Co-Option ........................................ 133
Horizontal Gene Transfer .............................. 134
Photosynthetic Animals ................................ 135
6.6 Summary ............................................... 136
7 Mutation and Selection in Speciation ....................... 137
7.1 Speciation by Chromosomal Mutations ................... 138
Formation of New Species by Polyploidization .......... 138
Changes of Genomic Structures and Speciation .......... 139
Chromosomal Rearrangements and Speciation ............. 140
7.2 Evolution of Reproductive Isolation by Genic
Mutation .............................................. 141
Oka Model of Speciation by Duplicate Gene Mutations ... 141
Dobzhansky-Muller (DM) Model of Evolution of
Reproductive Isolation ................................ 143
Multiallelic Complementary Genes Model ................ 146
Single-Locus Speciation ............................... 148
7.3 Reproductive Isolation by Complex Genetic Systems ..... 149
Segregation Distorters and Speciation ................. 149
Heterochromatin-Associated Hybrid Incapacity .......... 150
7.4 Other Mechanisms of Evolution of Reproductive
Isolation ............................................. 150
7.5 Speciation by Bottleneck Effects ...................... 151
7.6 Hybrid Sterility Generated by Passive Process of
Phenotypic Evolution .................................. 152
7.7 Summary ............................................... 153
8 Adaptation and Evolution ................................... 155
8.1 Adaptation by Mutation ................................ 155
8.2 Evolution of Some Specific Characters ................. 156
Evolution of Eyes and Photoreceptors .................. 156
Evolution of Caste Systems in Honeybees and some
other Insects ......................................... 157
Evolution of Asymmetric Morphology in Flatfish,
Snails, and other Organisms ........................... 161
8.3 Regressive Evolution and Pseudogenes .................. 162
Universality of Vestigial Characters .................. 162
Molecular Basis of Regressive Evolution ............... 162
Parasitic Organisms and their Genomic Changes ......... 165
8.4 Evolution of Sex-Determination Mechanisms ............. 166
Sex Determination in Vertebrates ...................... 167
Sex Determination in Invertebrates .................... 169
8.5 Degeneration of the Y (W) Chromosome .................. 171
Y Degeneration and Dosage Compensation ................ 171
Molecular Basis of X-Chromosome Dosage Compensation ... 172
Evolution by Sexually Antagonistic Mutations .......... 173
8.6 Evolution of Behavioral Characters .................... 174
Selfish Gene Theory of Evolution ...................... 174
Molecular Studies of Behavioral Genes ................. 175
8.7 Summary ............................................... 177
9 Mutation and Selection in Evolution ........................ 179
9.1 Distinct Processes of Mutation and Selection .......... 179
9.2 Random Factors and Gene Co-Option in Evolution ........ 181
9.3 Retrospective and Prospective Studies of Evolution .... 182
9.4 Genomic Constraints and Constraint-Breaking
Evolution ............................................. 183
Progressive Evolution ................................. 183
Origin of Life Without Purpose ........................ 183
Constraint-Breaking Evolution ......................... 184
9.5 Genetic Variation within Species ...................... 185
9.6 Niche-Filling Evolution ............................... 186
10 General Summary and Conclusions ............................ 189
Appendix: Mathematical Notes .................................. 201
A. Allele Frequency Changes Due to Natural Selection .......... 201
Deterministic Models for Allele Frequency Changes .......... 201
Equilibrium Frequencies Due to Mutation and Selection ...... 201
B. Allele Frequency Distributions under the Infinite-Site
Model ...................................................... 202
C. Temporal Fluctuation of Selection Coefficients ............. 202
General Comments ........................................... 202
D. Artificial Selection for Quantitative Characters ........... 203
E. Genetic Load ............................................... 203
Mutation Load .............................................. 204
Segregation Load ........................................... 204
F. Bayesian Method of Detecting Positively Selected Codons .... 204
References ................................................. 207
Author Index .................................................. 233
Subject Index ................................................. 238
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