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BK

First edition

Oxford : Oxford University Press, 2019

xvi, 310 stran : ilustrace (převážně barevné), mapy ; 25 cm

ISBN 978-0-19-883092-4 (brožováno)

Terminologický slovník

Obsahuje bibliografii na stranách 283-303 a rejstříky

001479038

Contents // 1 The foundations of evolutionary genetics 1 // 1.1 Concepts and ideas in a historical context 1 // 1.1.1 Evolutionary thoughts before Darwin 1 // 1.1.2 Evolution by natural selection—Darwin 2 // 1.1.3 Mendel and the origin of genetics 3 // 1.1.4 The mutation confusion 4 // 1.1.5 Theoretical population genetics 4 // 1.1.6 The modern synthesis of evolution 6 // 1.1.7 Toward molecular genetics 7 // 1.1.8 Diverging fields 10 // 1.2 Contemporary evolutionary genetics: toward a new synthesis 13 // 1.2.1 Molecular biology meets evolutionary genetics 13 // 1.2.2 The genotype-phenotype map: opportunities and challenges 14 // 1.3 Generating molecular genetic data 15 // 1.3.1 Gel electrophoresis 15 // 1.3.2 Polymerase chain reaction 15 // 1.3.3 Restriction enzyme digestion 16 // 1.3.4 Sanger sequencing 16 // 1.3.5 High-throughput sequencing 18 // 1.4 Analyzing genetic data 21 // 1.4.1 Statistics and bioinformatics 22 // 1.4.2 Internet resources 23 // Study questions 24 // 2 Genomes and the origin of genetic variation 25 // 2.1 Genome structure 25 // 2.1.1 Genome organization in bacteria, archaea, and eukarya 25 // 2.1.2 Structure of the eukaryote genome—functional elements 29 // 2.1.3 Structure of the eukaryote genome—parasitic and non-functional DNA 31 // 2.2 Mutations 35 // 2.2.1 Random mutations 35 // 2.2.2 Point mutations 35 // 2.2.3 Replication slippage 36 // xi // xii CONTENTS // 2.3 Recombination and associated mutations 38 // 2.3.1 Recombination and reshuffling

of alleles 38 // 2.3.2 Gene conversion 38 // 2.3.3 Unequal crossing over 38 // 2.3.4 Concerted evolution 42 // 2.4 Origin of new genes and protein functions 43 // 2.4.1 Gene and genome duplication 43 // 2.4.2 Exon shuffling 44 // 2.4.3 Protein moonlighting, RNA editing, and alternative splicing 45 // 2.5 External sources of genetic variation 46 // 2.5.1 Introgression 46 // 2.5.2 Horizontal gene transfer 47 // Study questions 47 // 3 Changes in allele and genotype frequency 49 // 3.1 The Hardy-Weinberg model 49 // 3.1.1 Assumptions 49 // 3.1.2 Testing for deviations from the Hardy-Weinberg expectation 51 // 3.2 Non-random mating 52 // 3.2.1 Inbreeding and outbreeding 52 // 3.2.2 Assortative and disassortative mating 54 // 3.2.3 Inbreeding/outbreeding versus assortative/disassortative mating 55 // 3.2.4 FIS—a coefficient for measuring within-population deviations // from HWE 55 // 3.3 Genetic drift—evolution in finite populations 56 // 3.3.1 Within-population effects of genetic drift 56 // 3.3.2 Effects of genetic drift in a structured metapopulation 58 // 3.3.3 FST—the fixation index 59 // 3.3.4 Empirical studies of population structure 60 // 3.4 Other deviations from the Hardy-Weinberg model 63 // 3.4.1 Selection and the Hardy-Weinberg model 63 // 3.4.2 Mutation and the Hardy-Weinberg model 63 // 3.4.3 Gene flow and the Hardy-Weinberg model 64 // 3.5 The gene pool 65 // 3.5.1 Hardy-Weinberg and real populations 65 // 3.5.2 Effective population size Ne 65 // Study questions

67 // 4 The theory of natural selection 69 // 4.1 Fitness 69 // 4.1.1 Defining fitness 69 // 4.1.2 Absolute, relative, and marginal fitness 70 // 4.2 One-locus model of viability selection 71 // 4.2.1 The model 71 // 4.2.2 Finding all possible equilibria using ?? 72 // 4.2.3 Invasion fitness analysis 72 // 4.2.4 Adaptive landscapes 73 // CONTENTS xiii // 4.2.5 Directional selection 74 // 4.2.6 Overdominance and underdominance 77 // 4.3 Frequency-dependent selection 79 // 4.3.1 Negative and positive frequency-dependent selection 79 // 4.3.2 Relationship between balancing, disruptive, and // frequency-dependent selection 80 // 4.3.3 Evolutionary game theory 82 // 4.4 Mutation-selection balance 84 // 4.4.1 Approximating the mutation-selection equilibrium 84 // 4.4.2 Genetic load 87 // 4.5 Selection at other stages of the life cycle 87 // 4.5.1 Sexual selection 87 // 4.5.2 Fertility selection 88 // 4.5.3 Selection at the gametic level 89 // Study questions 90 // 5 The power of natural selection 92 // 5.1 The limits of natural selection 92 // 5.1.1 Genetic constraints 92 // 5.1.2 Historic and ontogenetic constraints 93 // 5.1.3 The problem of stasis in evolution 94 // 5.2 Level of selection 97 // 5.2.1 Level of sorting, adaptation, and immortal genes 97 // 5.2.2 Genetic conflict and gene level selection 98 // 5.2.3 Kin selection 99 // 5.2.4 Group selection 104 // 5.2.5 Individual adaptations to living in groups 105 // 5.3 Adaptation to a heterogeneous and unpredictable world 106

5.3.1 Phenotypic plasticity and learning 106 // 5.3.2 The paradox of sex 108 // 5.3.3 Sexual reproduction as an individual adaptation 109 // 5.3.4 Long-term advantages of sex and recombination 111 // 5.4 Evolving communities 113 // 5.4.1 Coevolution among mutualists 113 // 5.4.2 Coevolution among natural enemies 114 // 5.4.3 Coevolution between competitors 115 // Study questions 115 // 6 Multilocus evolution 117 // 6.1 The two-locus model 117 // 6.1.1 Linkage equilibrium and disequilibrium 117 // 6.1.2 Estimating haplotype frequencies from // genotype data 123 // 6.1.3 Factors that cause linkage disequilibrium 123 // 6.2 Multilocus selection 128 // 6.2.1 Additive and non-additive fitness 128 // 6.2.2 Epistasis and the evolutionary process 130 // xiv CONTENTS // 6.3 Quantitative genetics in the genomic era 132 // 6.3.1 The architecture of the genotype-phenotype map 132 // 6.3.2 Sources of phenotypic variance and the concept of heritability 132 // 6.3.3 Evolvability 135 // 6.3.4 Quantitative trait locus (QTL) analysis 136 // 6.3.5 Genome wide association study (GWAS) 141 // 6.3.6 The enigma of missing heritability 142 // Study questions 143 // 7 Inferring evolutionary processes from DNA sequence data 145 // 7.1 The neutral theory of molecular evolution 145 // 7.1.1 The neutral theory of molecular evolution 145 // 7.1.2 Mutation, genetic drift, and the molecular clock 146 // 7.1.3 The generation and population size problem 149 // 7.1.4 The value of the neutral theory as a null model

149 // 7.2 Describing and interpreting variation in DNA sequences 150 // 7.2.1 DNA sequence versus allelic data 150 // 7.2.2 Descriptive statistics of DNA sequence variation 152 // 7.2.3 Coalescent theory and the expected pattern of sequence variation 153 // 7.2.4 Tajima’s D test 155 // 7.2.5 Natural selection and the sign of Tajima’s D 156 // 7.2.6 Demographic changes and the sign of Tajima’s D 157 // 7.2.7 Descriptive statistics for sequence divergence between populations 159 // 7.3 Neutrality tests 159 // 7.3.1 The HKA test (Hudson-Kreitman-Aguadé test) 159 // 7.3.2 The McDonald-Kreitman (MK) test and its extensions 160 // 7.4 Genome scans 163 // 7.4.1 The logic of genome scans 163 // 7.4.2 Sliding window genome scans 164 // 7.4.3 Haplotype tests and selective sweeps 167 // 7.4.4 Limits to genome scans 170 // Study questions 172 // 8 Genetics and genomics of speciation 173 // 8.1 Species concepts 173 // 8.1.1 What are species? 173 // 8.1.2 Typological species definitions 174 // 8.1.3 Species concepts that rely on biological properties 175 // 8.1.4 Species concepts that seek to incorporate the historical // dimension of speciation 178 // 8.2 Evolution of barriers to gene exchange 181 // 8.2.1 Classifying barriers to gene exchange 181 // 8.2.2 Ecological incompatibilities 182 // 8.2.3 Assortative mating 183 // 8.2.4 Sexual incompatibility 187 // CONTENTS XV // 8.2.5 Developmental incompatibility 190 // 8.2.6 Haldane’s rule and the larger X/Z effect 193 // 8.3 Modes of speciation

194 // 8.3.1 Population structure and allelic models of divergence and speciation 194 // 8.3.2 Non-allopatric speciation 195 // 8.3.3 Genomic "islands of speciation" and the divergence // hitchhiking hypothesis 199 // 8.3.4 Allopatric and non-allopatric divergence and the study of hybrid zones 202 // 8.3.5 The fate of hybridizing populations 203 // 8.3.6 Reinforcement and coupling of barriers to gene exchange 205 // 8.4 The role of hybridization in speciation 208 // 8.4.1 Polyploid hybrid speciation 208 // 8.4.2 Homoploid hybrid speciation 209 // 8.4.3 Hybridization and adaptive radiation 211 // Study questions 212 // 9 Reconstructing the past 214 // 9.1 Phylogenetics and phylogenomics 214 // 9.1.1 The origins of tree thinking 214 // 9.1.2 Trees, phylogenies, and evolutionary relationships 216 // 9.1.3 The basis of phylogenetic inference 218 // 9.1.4 Alignment and models of sequence evolution 220 // 9.1.5 Building trees using distance and character data 222 // 9.1.6 Maximum likelihood tree estimation 224 // 9.1.7 Bayesian phylogenetic inference 225 // 9.1.8 Gene tree and species tree discordance 227 // 9.1.9 Phylogenetics at the genomic scale 229 // 9.2 Phylogeography—genes in time and space 233 // 9.2.1 Phylogeography and its link to modern population genetics 233 // 9.2.2 Phylogeography and biogeography 234 // 9.2.3 Detecting spatial population structure with genomic data 236 // 9.2.4 Testing demographic models and evolutionary scenarios 239 // 9.2.5 Ancient DNA—a direct

insight to the past 242 // 9.2.6 Human origins: insights from genomic data 244 // 9.2.7 Using the four-population test to infer gene flow and introgression 246 // Study questions 248 // 10 Sequencing the genome and beyond 250 // 10.1 Assembling and building on the genome 250 // 10.1.1 Reference genomes and genome assembly 250 // 10.1.2 Genome annotation, gene expression, and gene interactions 254 // 10.1.3 Proteomics—bridging the gap between gene expression and // the phenotype 256 // 10.1.4 DNA methylation, chromatin binding, and epigenomics 257 // 10.1.5 The 3D structure of the genome 258 // xvi CONTENTS // 10.2 Manipulating the genome 259 // 10.2.1 From candidate genes to an understanding of function 259 // 10.2.2 CRISPR/Cas9 and the future of genetic manipulation 262 // 10.2.3 Prospects for genome editing in evolutionary genetics 264 // 10.3 The future of evolutionary genetics? 266 // Study questions 267 // Glossary 269 // References > 283 // index 305 // Species index 309