Evolutionary genetics : concepts, analysis, and practice

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Cover Evolutionary Genetics: Concepts, Analysis, and Practice Copyright Dedication Preface Acknowledgments Contents CHAPTER 1: The foundations of evolutionary genetics 1.1 Concepts and ideas in a historical context 1.1.1 Evolutionary thoughts before Darwin 1.1.2 Evolution by natural selection—Darwin 1.1.3 Mendel and the origin of genetics 1.1.4 The mutation confusion 1.1.5 Theoretical population genetics 1.1.6 The modern synthesis of evolution 1.1.7 Toward molecular genetics 1.1.8 Diverging fields 1.2 Contemporary evolutionary genetics: toward a new synthesis 1.2.1 Molecular biology meets evolutionary genetics 1.2.2 The genotype–phenotype: map:opportunities and challenges 1.3 Generating molecular genetic data 1.3.1 Gel electrophoresis 1.3.2 Polymerase chain reaction 1.3.3 Restriction enzyme digestion 1.3.4 Sanger sequencing 1.3.5 High-throughput sequencing 1.4 Analyzing genetic data 1.4.1 Statistics and bioinformatics 1.4.2 Internet resources Study questions CHAPTER 2: Genomes and the origin of genetic variation 2.1 Genome structure 2.1.1 Genome organization in bacteria, archaea, and eukarya Genomes of bacteria Genomes of archaea Genomes of eukaryotes 2.1.2 Structure of the eukaryote genome—functional elements Protein coding genes RNA genes Non-transcribed functional DNA 2.1.3 Structure of the eukaryote genome—parasitic and non-functional DNA Parasitic DNA Nonfunctional DNA derived from transposition Origin of introns Other sources of nonfunctional DNA 2.2 Mutations 2.2.1 Random mutations 2.2.2 Point mutations 2.2.3 Replication slippage 2.3 Recombination and associated mutations 2.3.1 Recombination and reshuffling of alleles 2.3.2 Gene conversion 2.3.3 Unequal crossing over 2.3.4 Concerted evolution 2.4 Origin of new genes and protein functions 2.4.1 Gene and genome duplication 2.4.2 Exon shuffling 2.4.3 Protein moonlighting, RNA editing, and alternative splicing 2.5 External sources of genetic variation 2.5.1 Introgression 2.5.2 Horizontal gene transfer Study questions CHAPTER 3: Changes in allele and genotype frequency 3.1 The Hardy–Weinberg model 3.1.1 Assumptions 3.1.2 Testing for deviations from the Hardy–Weinberg expectation 3.2 Non-random mating 3.2.1 Inbreeding and outbreeding 3.2.2 Assortative and disassortative mating 3.2.3 Inbreeding/outbreeding versus assortative/disassortative mating 3.2.4 FIS—a coefficient for measuring within-population deviations from HWE 3.3 Genetic drift—evolution in finite populations 3.3.1 Within-population effects of genetic drift 3.3.2 Effects of genetic drift in a structured metapopulation 3.3.3 FST—the fixation index 3.3.4 Empirical studies of population structure 3.4 Other deviations from the Hardy–Weinberg model 3.4.1 Selection and the Hardy–Weinberg model 3.4.2 Mutation and the Hardy–Weinberg model 3.4.3 Gene flow and the Hardy–Weinberg model 3.5 The gene pool 3.5.1 Hardy–Weinberg and real populations 3.5.2 Effective population size Ne Study questions CHAPTER 4: The theory of natural selection 4.1 Fitness 4.1.1 Defining fitness 4.1.2 Absolute, relative, and marginal fitness 4.2 One-locus model of viability selection 4.2.1 The mode 4.2.2 Finding all possible equilibria using Δp 4.2.3 Invasion fitness analysis 4.2.4 Adaptive landscapes 4.2.5 Directional selection 4.2.6 Overdominance and underdominance 4.3 Frequency-dependent selection 4.3.1 Negative and positive frequency-dependent selection 4.3.2 Relationship between balancing, disruptive, and frequency-dependent selection 4.3.3 Evolutionary game theory 4.4 Mutation–selection balance 4.4.1 Approximating the mutation–selection equilibrium 4.4.2 Genetic load 4.5 Selection at other stages of the life cycle 4.5.1 Sexual selection 4.5.2 Fertility selection 4.5.3 Selection at the gametic level Study questions CHAPTER 5: The power of natural selection 5.1 The limits of natural selection 5.1.1 Genetic constraints 5.1.2 Historic and ontogenetic constraints 5.1.3 The problem of stasis in evolution 5.2 Level of selection 5.2.1 Level of sorting, adaptation, and immortal genes 5.2.2 Genetic conflict and gene level selection 5.2.3 Kin selection 5.2.4 Group selection 5.2.5 Individual adaptations to living in groups 5.3 Adaptation to a heterogeneous and unpredictable world 5.3.1 Phenotypic plasticity and learning 5.3.2 The paradox of sex 5.3.3 Sexual reproduction as an individual adaptation 5.3.4 Long-term advantages of sex and recombination 5.4 Evolving communities 5.4.1 Coevolution among mutualists 5.4.2 Coevolution among natural enemies 5.4.3 Coevolution between competitors Study questions CHAPTER 6: Multilocus evolution 6.1 The two-locus model 6.1.1 Linkage equilibrium and disequilibrium Defining linkage equilibrium and disequilibrium Decay of linkage disequilibrium by recombination 6.1.2 Estimating haplotype frequencies from genotype data 6.1.3 Factors that cause linkage disequilibrium Non-random mating Genetic drift Natural selection Mutations Gene flow 6.2 Multilocus selection 6.2.1 Additive and non-additive fitness 6.2.2 Epistasis and the evolutionary process 6.3 Quantitative genetics in the genomic era 6.3.1 The architecture of the genotype–phenotype map 6.3.2 Sources of phenotypic variance and the concept of heritability 6.3.3 Evolvability 6.3.4 Quantitative trait locus (QTL) analysis 6.3.5 Genome wide association study (GWAS) 6.3.6 The enigma of missing heritability Study questions CHAPTER 7: Inferring evolutionary processesfrom DNA sequence data 7.1 The neutral theory of molecularevolution 7.1.2 Mutation, genetic drift, and themolecular clock 7.1.3 The generation and populationsize problem 7.1.4 The value of the neutral theoryas a null model 7.2 Describing and interpreting variationin DNA sequences 7.2.1 DNA sequence versus allelic data 7.2.2 Descriptive statistics of DNA sequencevariation 7.2.3 Coalescent theory and the expectedpattern of sequence variation 7.2.4 Tajima’s D test 7.2.5 Natural selection and the signof Tajima’s D 7.2.6 Demographic changes and the signof Tajima’s D 7.2.7 Descriptive statistics for sequencedivergence between populations 7.3 Neutrality tests 7.3.1 The HKA test (Hudson–Kreitman–Aguadé test) 7.3.2 The McDonald–Kreitman (MK) testand its extensions 7.4 Genome scans 7.4.1 The logic of genome scans 7.4.2 Sliding window genome scans 7.4.3 Haplotype tests and selective sweeps 7.4.4 Limits to genome scans Study questions CHAPTER 8 :Genetics and genomics of speciation 8.1 Species concepts8.1.1 What are species? 8.1.2 Typological species definitions 8.1.3 Species concepts that rely on biologicalproperties 8.1.4 Species concepts that seek to incorporatethe historical dimension of speciation 8.2 Evolution of barriers to geneexchange8.2.1 Classifying barriers to gene exchange 8.2.2 Ecological incompatibilities 8.2.3 Assortative mating 8.2.4 Sexual incompatibility 8.2.5 Developmental incompatibility 8.2.6 Haldane’s rule and the larger X/Z effect 8.3 Modes of speciation 8.3.1 Population structure and allelic models ofdivergence and speciation 8.3.2 Non-allopatric speciation 8.3.3 Genomic “islands of speciation” and thedivergence hitchhiking hypothesis 8.3.4 Allopatric and non-allopatric divergenceand the study of hybrid zones 8.3.5 The fate of hybridizing populations 8.3.6 Reinforcement and coupling of barriers togene exchange 8.4 The role of hybridization inspeciation 8.4.1 Polyploid hybrid speciation 8.4.2 Homoploid hybrid speciation 8.4.3 Hybridization and adaptive radiation Study questions CHAPTER 9 : Reconstructing the past 9.1 Phylogenetics and phylogenomics 9.1.1 The origins of tree thinking 9.1.2 Trees, phylogenies, and evolutionaryrelationships 9.1.3 The basis of phylogenetic inference 9.1.4 Alignment and models of sequenceevolution 9.1.5 Building trees using distanceand character data 9.1.6 Maximum likelihood tree estimation 9.1.7 Bayesian phylogenetic inference 9.1.8 Gene tree and species tree discordance 9.1.9 Phylogenetics at the genomic scale 9.2 Phylogeography—genes in timeand space 9.2.1 Phylogeography and its link to modernpopulation genetics 9.2.2 Phylogeography and biogeography 9.2.3 Detecting spatial population structurewith genomic data 9.2.4 Testing demographic models andevolutionary scenarios 9.2.5 Ancient DNA—a direct insight to the past 9.2.6 Human origins: insights fromgenomic data 9.2.7 Using the four-population test to infergene flow and introgression Study questions CHAPTER 10 : Sequencing the genome and beyond 10.1 Assembling and building on thegenome 10.1.1 Reference genomes and genomeassembly 10.1.2 Genome annotation, gene expression,and gene interactions 10.1.3 Proteomics—bridging the gap betweengene expression and the phenotype 10.1.4 DNA methylation, chromatin binding,and epigenomics 10.1.5 The 3D structure of the genome 10.2 Manipulating the genome 10.2.1 From candidate genes to anunderstanding of function 10.2.2 CRISPR/Cas9 and the future of geneticmanipulation 10.2.3 Prospects for genome editingin evolutionary genetics 10.3 The future of evolutionary genetics? Study questions Glossary References Index Species index