Molecular population genetics and evolution, v. 40.

General preface . . . . . . . . . . . . . . . . . . . . . . . Foreword . . . . . . . . . . . . . . . . . . . . . . . . . . Preface . . . . . . . . . . . . . . . . . . . . . . . . . . . Chapter 1. Introduction . . . . . . . . . . . . . . . . . . . Chapter 2 . Evolutionury history o f life . . . . . . . . . . . . . 2.1 Evidence from paleontology and comparative morphology . . . . . . . 2.2 Evidence from molecular biology . . . . . . . . . . . . . . . . 2.3 Biochemical unity of life . . . . . . . . . . . . . . . . . . . Chapter 3. Mututiou . . . . . . . . . . . . . . . . . . . . 3.1 The basic process of gene action . . . . . . . . . . . . . . . . 3.2 Types of changes in DNA . . . . . . . . . . . . . . . . . . . 3.3 Mutations and amino acid substitutions . . . . . . . . . . . . . . 3.4 Effects on fitness . . . . . . . . . . . . . . . . . . . . . . 3.5 Rate of spontaneous mutation . . . . . . . . . . . . . . . . . Chapter 4. Natural selection ulld its eflects . . . . . . . . . . . 4.1 Natural selection and mathematical models 4.2 Growth and regulation of populations . . 4.2.1 Continuous time niodel . . . . . 4.2.2 Discrete generation model . . . . 4.3 Natural selection with constant fitness . . 4.3.1 Selection with a single locus . . . 4.3.2 Selection with multiple loci . . . . 4.4 Competitive selection . . . . . . . . 4.4.1 Haploid model . . . . . . . . 4.4.2 Diploid model . . . . . . . . 4.4.3 Selection with rliultiple loci . . . . 4.5 Fertility excess required for gene substitution . . . . . . . . . . . . 4.6 Equilibrium gene frequencies . . . . . . . . . . . . . . . . . . 4.6.1 Mutation-selection balance for deleterious genes . . . . . . . . 4.6.2 Balancing selection . . . . . . . . . . . . . . . . . . . Chapter 5. Mutant genes in . finite populations . . . . . . . . . . 5.1 Stochastic change of gene frequency: discrete processes . . . . . . . . 5.1.1 Markov chain methods . . . . . . . . . . . . . . . . . 5.1.2 Variance of gene frequencies and heterozygosity . . . . . . . . 5.1.3 Effective population size . . . . . . . . . . . . . . . . . 5.2 Diffusion approximations . . . . . . . . . . . . . . . . . . . 5.2.1 Basic equations in diffusion processes . . . . . . . . . . . . 5.2.2 Transient distribution of gene frequencies . . . . . . . . . . . 5.3 Gene substitution in populations . . . . . . . . . . . . . . . . 5.3.1 Probability of fixation of mutant genes . . . . . . . . . . . 5.3.2 Rate of gene substitution and average substitution time . . . . . 5.3.3 Fixation time and extinction time of mutant genes . . . . . . . 5.3.4 First arrival time and age of a mutant gene . . . . . . . . . . 5.4 Stationary distribution of gene frequencies . . . . . . . . . . . . . 5.4.1 General formula . . . . . . . . . . . . . . . . . . . . 5.4.2 Neutral genes with migration . . . . . . . . . . . . . . . 5.4.3 Mutation and selection . . . . . . . . . . . . . . . . . 5.4.4 Neutral mutations . . . . . . . . . . . . . . . . . . . 5.4.5 Distribution under irreversible mutation . . . . . . . . . . . 5.5 Genetic differentiation of populations . . . . . . . . . . . . . . 5.5.1 Differentiation with migration . . . . . . . . . . . . . . 5.5.2 Gene differentiation under complete isolation . . . . . . . . . Chapter 6. Genetic variability in nuturalpopulations . . . . . . . 6.1 Introductory remarks . . . . . . . . . . . . 6.2 Measures of genic variation . . . . . . . . . . 6.3 Gene diversity within populations . . . . . . . . 6.3.1 Enzyme and protein loci . . . . . . . . . 6.3.2 Blood groups and other loci . . . . . . . . 6.4 Gene diversity in subdivided populations . . . . . 6.5 Mechanisms of maintenance of protein polyniorphisnis 6.5.1 Overdoniinalice hypothesis . . . . . . . . 6.5.2 Other types of balancing selection . . . . . 6.5.3 Neutral mutations . . . . . . . . . . . 6.5.4 Transient polyniorphism due to selection . . . Chapter 7. Difirenticrtion qfpop~/lutionsa nt1 spec*icrtio~.l . . . . . 7.1 Measures of gcnetic distance . . . . . . . . . . . . . . . . . . 7.2 Gene dilrcrcntiation among populations: a general theory . 7.2.1 Complcte isolation . . . . . . . . . . . . . . . . . . . 179 7.2.2 Efkcts of migration . . . . . . . . . . . . . . . . . . 182 7.3 Interracial and intcrspecific gcnc tiifli.rcnccs . . . . . . . . . . . . 182 7.4 Phylogeny of closcly rclatcci organisms . . . . . . . . . . . . . . 191 7.4.1 Evolution;iry timc . . . . . . . . . . . . . . . . . . . 192 7.4.2 Phylogcnetic trccs . . . . . . . . . . . . . . . . . . . 197 7.5 Mechanism of speciation . . . . . . . . . . . . . . . . . . . 202 7.5.1 Classification of isolation mechanisms . . . . . . . . . . . . 202 7.5.2 Evolution of rcproductivc isolation . . . . . . . . . . . . . 204 7.5.3 How fast is rcproductivc isolation established? . . . . . . . . . 207 Chapter 8. Long-ter~ne solut io~.~ . . . . . . . . . . . . . . . 211 8.1 Evolutionary change of DNA . . . . . . . . . . . . . . . . . 211 8.1.1 DNA content . . . . . . . . . . . . . . . . . . . . . 211 8.1.2 Evolutionary mechanisms of increase in DNA content . . . . . . 213 8.1.3 Formation of new genes . . . . . . . . . . . . . . . . . 214 8.1.4 Repeated DNA . . . . . . . . . . . . . . . . . . . . 219 8.1.5 Nonfunctional DNA . . . . . . . . . . . . . . . . . . 222 8.2 Nucleotide substitution in DNA . . . . . . . . . . . . . . . . 224 8.2.1 Some theoretical backgrounds . . . . . . . . . . . . . . . 224 8.2.2 DNA hybridization . . . . . . . . . . . . . . . . . . . 226 8.3 Amino acid substitution in proteins . . . . . . . . . . . . . . . 230 8.3.1 Rate of amino acid substitution . . . . . . . . . . . . . . 230 8.3.2 Differences among proteins . . . . . . . . . . . . . . . . 232 8.3.3 Is the rate of amino acid substitution constant in a given protein? . . 233 8.4 Phylogenetic trees . . . . . . . . . . . . . . . . . . . . . . 240 8.4.1 Codon or nucleotide substitution data . . . . . . . . . . . . 240 8.4.2 Immunological data . . . . . . . . . . . . . . . . . . 242 8.4.3 Phylogenics of hon~ologousp roteins . . . . . . . . . . . . 243 8.5 Adaptive and nonadaptive evolution . . . . . . . . . . . . . . . 246 8.5.1 Mechanisms of molecular evolution . . . . . . . . . . . . 246 8.5.2 Polyn~orphisma s a phase of evolution . . . . . . . . . . . . 250 8.5.3 Molecular evolution and morphological change . . . . . . . . 251 References . . . . . . . . . . . . . . . .