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Mutation-Driven Evolution PDF

261 Pages·2013·2.525 MB·English
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Mutation-Driven Evolution Masatoshi Nei Pennsylvania State University 1 Mutation-Driven Evalution. First Edition. Masatoshi Nei. © Masatoshi Nei 2013. Published 2013 by Oxford University Press. 3 Great Clarendon Street, Oxford, OX2 6DP, United Kingdom Oxford University Press is a department of the University of Oxford. It furthers the University’s objective of excellence in research, scholarship, and education by publishing worldwide. Oxford is a registered trade mark of Oxford University Press in the UK and in certain other countries © Masatoshi Nei 2013 The moral rights of the author have been asserted First published 2013 Impression: 1 All rights reserved. No part of this publication may be reproduced, stored in a retrieval system, or transmitted, in any form or by any means, without the prior permission in writing of Oxford University Press, or as expressly permitted by law, by licence or under terms agreed with the appropriate reprographics rights organization. Enquiries concerning reproduction outside the scope of the above should be sent to the Rights Department, Oxford University Press, at the address above You must not circulate this work in any other form and you must impose this same condition on any acquirer British Library Cataloguing in Publication Data Data available ISBN 978–0–19–966173–2 Printed and bound by CPI Group (UK) Ltd, Croydon, CR0 4YY Links to third party websites are provided by Oxford in good faith and for information only. Oxford disclaims any responsibility for the materials contained in any third party website referenced in this work. 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 1 3 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 Diffi culties of Defi ning and Estimating Selection Coeffi cients 20 Estimates of Selection Coeffi cients and their Reliability 20 Fluctuation of Selection Coeffi cients 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 Coeffi cients 29 2.5 Mutation and Standing Genetic Variation 31 Artifi cial 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 iii iv CONTENTS 3 E volutionary Theories in the Neo-Darwinian Era 41 3.1 Modifi er Genes 41 Evolution of Dominance 42 Modifi cation 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 5 9 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 Defi nition of Neutral Mutations 61 King and Jukes’s View 63 Defi nition 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 F Tests 84 ST Statistical Studies and Biochemical Verifi cation 86 Frequency Distributions of Mutant Nucleotides 87 4.9 Summary 87 CONTENTS v 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 Defi nition 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 E volutionary Change of MicroRNAs 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 vi CONTENTS 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 Specifi c Characters 156 Evolution of Eyes and Photoreceptors 156 Evolution of Caste Systems in Honeybees and some other Insects 157 Evolution of Asymmetric Morphology in Flatfi sh, 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 Selfi sh Gene Theory of Evolution 174 Molecular Studies of Behavioral Genes 175 8.7 Summary 177 CONTENTS vii 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 Conclusion 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 Infi nite-Site Model 202 C. Temporal Fluctuation of Selection Coeffi cients 202 General Comments 202 D. Artifi cial 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 This page intentionally left blank Preface I started my career with theoretical population approach of studying evolution was integrated with genetics in the 1960s after a short period of fi eld population genetics theory in the latter half of the work experience concerning quantitative genetics. 1960s and in the 1970s. This integration transformed At that time evolutionary studies were conducted the study of evolution profoundly. First, we could primarily by comparing phenotypic characters now identify homologous genes in different species among individuals within and between species. and study long-term evolution of genes by compar- These studies did not give clear insights into the ing the nucleotide or amino acid sequences from cause and the effect of evolution, because the genetic different species. Second, molecular data on the basis of phenotypic characters was not well evolutionary change of genes soon indicated the understood. importance of mutation in evolution. Third, com- In theoretical population genetics, we could con- parison of the DNA contents of different species sider a set of alleles at one or a few loci and study suggested that gene or genome duplication occurred the theoretical changes of genotype frequencies due frequently in the process of evolution. Because gene to mutation, natural selection, and genetic drift. or genome duplication is a form of mutation in the These studies gave only possible evolutionary broad sense, I realized that mutation is the driving changes of populations, but they were still much force of evolution. Yet, this view was regarded as a better than intuitive arguments. For this reason, a heresy at the time when neo-Darwinism dominated large body of mathematical theories of evolution the fi eld. In the meantime the neutral theory of was developed. These theories depended on many molecular evolution was proposed to explain the simplifying assumptions about the breeding sys- evolution of genes and proteins. This theory clearly tem, population structure, selection coeffi cients, showed that the evolution of nucleotide sequences gene interaction, etc., and different assumptions has occurred mainly by random fi xation of neutral about these factors often generated very different mutations. However, most neo-Darwinians did not predictions of evolutionary changes. This resulted pay much attention to this discovery, because they in many controversies which could not be resolved believed that neutral evolution has nothing to do easily because of the diffi culty of doing experimen- with phenotypic evolution, in which most evolu- tal studies. At that time, population genetics was tionists are interested. In fact, even the proponents dominated by neo-Darwinism with the idea of per- of the neutral theory of molecular evolution stated vasive natural selection, and I was working within that phenotypic evolution occurs mostly by natural the framework of neo-Darwinism. Furthermore, selection, as will be mentioned later. because it was diffi cult to identify the homologous By the early 1970s, I came to believe that the prin- genes between different species, population genet- ciple of phenotypic evolution must be the same as ics studies were primarily concerned with the gene that of molecular evolution because both types of frequency changes within species. evolution are controlled by mutation at the DNA In the early 1960s a number of molecular biolo- level. I briefl y presented this idea in my 1975 book gists were working on the evolutionary changes of Molecular Population Genetics and Evolution . However, genes and proteins at the molecular level, and this few people paid attention to this view. I elaborated ix

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