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ОбложкаNei M. Mutation - driven evolution. - Oxford: Oxford university press, 2014. - xi, 244 p., [2] l. of plates: ill., tab. - Bibliogr.: p.207-231. - Auth. ind.: p.233-237. - Sub. ind.: p.238-244. - ISBN 978-0-19-872410-0
Шифр: (И/Е0-N35) 02
 

Место хранения: 02 | Отделение ГПНТБ СО РАН | Новосибирск

Оглавление / Contents
 
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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