Evolutionary genetics: concepts, analysis, and practice
Gespeichert in:
| Hauptverfasser: | , |
|---|---|
| Format: | Buch |
| Sprache: | English |
| Veröffentlicht: |
Oxford
Oxford University Press
2019
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| Ausgabe: | First edition |
| Schlagworte: | |
| Online-Zugang: | Inhaltsverzeichnis |
| Beschreibung: | xvi, 310 Seiten Illustrationen, Diagramme, Karten |
| ISBN: | 9780198830924 9780198830917 |
Internformat
MARC
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Datensatz im Suchindex
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| adam_text | Contents 1 2 The foundations of evolutionary genetics 1 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: opportunitiesandchallenges 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 1 1 2 3 4 4 6 7 10 13 13 14 15 15 15 16 16 18 21 22 23 24 Genomes and the origin of genetic variation 25 2.1 Genome structure 2.1.1 Genome organization in bacteria, archaea, andeukarya 2.1.2 Structure of the eukaryote genome—functional elements 2.1.3 Structure of the eukaryote genome—parasitic and non-functional DNA 2.2 Mutations 2.2.1 Random mutations 2.2.2 Point mutations 2.2.3 Replication slippage 25 25 29 31 35 35 35 36 XI
xii CONTENTS 3 4 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 38 38 38 38 42 43 43 44 45 46 46 47 47 Changes in allele and genotype frequency 49 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 FJS—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 49 49 51 52 52 54 55 55 56 56 58 59 60 63 63 63 64 65 65 65 67 The theory of natural selection 69 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 model 4.2.2 Finding ah possible equilibria using Др 4.2.3 Invasion fitness analysis 4.2.4 Adaptive landscapes 69 69 70 71 71 72 72 73
CONTENTS 5 6 xiii 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 74 77 79 79 80 82 84 84 87 87 87 88 89 90 The power of natural selection 92 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 92 92 93 94 97 97 98 99 104 105 106 106 108 109 111 113 113 114 115 115 Multilocus evolution 117 6.1 The two-locus model 6.1.1 Linkage equilibrium and disequilibrium 6.1.2 Estimating haplotype frequencies from genotype data 6.1.3
Factors that cause linkage disequilibrium 6.2 Multilocus selection 6.2.1 Additive and non-additive fitness 6.2.2 Epistasis and the evolutionary process 117 117 123 123 128 128 130
XIV CONTENTS 7 8 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 132 132 132 135 136 141 142 143 Inferring evolutionary processes from DNA sequence data 145 7.1 The neutral theory of molecular evolution 7.1.1 The neutral theory of molecular evolution 7.1.2 Mutation, genetic drift, and the molecular clock 7.1.3 The generation and population size problem 7.1.4 The value of the neutral theory as a null model 7.2 Describing and interpreting variation in DNA sequences 7.2.1 DNA sequence versus allelic data 7.2.2 Descriptive statistics of DNA sequence variation 7.2.3 Coalescent theory and the expected pattern of sequence variation 7.2.4 Tajima s D test 7.2.5 Natural selection and the sign of Tajima s D 7.2.6 Demographic changes and the sign of Tajima s D 7.2.7 Descriptive statistics for sequence divergence between populations 7.3 Neutrality tests 7.3.1 The HKA test(Hudson-Kreitman-Aguadé test) 7.3.2 The McDonald-Kreitman (MK) test and 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 145 145 146 149 149 150 150 152 153 155 156 157 159 159 159 160 163 163 164 167 170 172 Genetics and genomics of spéciation 173 8.1 Species concepts 8.1.1 What are species? 8.1.2
Typological species definitions 8.1.3 Species concepts that rely on biological properties 8.1.4 Species concepts that seek to incorporate the historical dimension of spéciation 8.2 Evolution of barriers to gene exchange 8.2.1 Classifying barriers to gene exchange 8.2.2 Ecological incompatibilities 8.2.3 Assortative mating 8.2.4 Sexual incompatibility 173 173 174 175 178 181 181 182 183 187
CONTENTS 8.2.5 Developmental incompatibility 8.2.6 Haldane s rule and the larger X/Z effect 8.3 Modes of spéciation 8.3.1 Population structure and allelic models of divergence and spéciation 8.3.2 Non-allopatric spéciation 8.3.3 Genomic islands of spéciation and the divergence hitchhiking hypothesis 8.3.4 Allopatric and non-allopatric divergence and the studyof hybrid zones 8.3.5 The fate of hybridizing populations 8.3.6 Reinforcement and coupling of barriers to gene exchange 8.4 The role of hybridization in spéciation 8.4.1 Polyploid hybrid spéciation 8.4.2 Homoploid hybrid spéciation 8.4.3 Hybridization and adaptive radiation Study questions 9 xv 190 193 194 194 195 199 202 203 205 208 208 209 211 212 Reconstructing the past 214 9.1 Phylogenetics and phylogenomics 9.1.1 The origins of tree thinking 9.1.2 Trees, phytogenies, and evolutionary relationships 9.1.3 The basis of phylogenetic inference 9.1.4 Alignment and models of sequence evolution 9.1.5 Building trees using distance and 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 time and space 9.2.1 Phylogeography and its link to modern population genetics 9.2.2 Phylogeography and biogeography 9.2.3 Detecting spatial population structure with genomic data 9.2.4 Testing demographic models and evolutionary scenarios 9.2.5 Ancient DNA—a direct insight to the past 9.2.6 Human origins: insights from genomic data 9.2.7 Using the four-population test to infer gene flow
and introgression Study questions 214 214 216 218 220 222 224 225 227 229 233 233 234 236 239 242 244 246 248 10 Sequencing the genome and beyond 10.1 Assembling and building on the genome 10.1.1 Reference genomes and genome assembly 10.1.2 Genome annotation, gene expression, and gene interactions 10.1.3 Proteomics—bridging the gap between gene expression and the phenotype 10.1.4 DNA méthylation, chromatin binding, and epigenomics 10.1.5 The 3D structure of the genome 250 250 250 254 256 257 258
XVI CONTENTS 10.2 Manipulating the genome 10.2.1 From candidate genes to an understanding of function 10.2.2 CRISPR/Cas9 and the future of genetic manipulation 10.2.3 Prospects for genome editing in evolutionary genetics 10.3 The future of evolutionary genetics? Study questions Glossary References Index Species index 259 259 262 264 266 267 269 283 305 309
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| spelling | Sætre, Glenn-Peter Verfasser (DE-588)1188623834 aut Evolutionary genetics concepts, analysis, and practice Glenn-Peter Sætre and Mark Ravinet First edition Oxford Oxford University Press 2019 xvi, 310 Seiten Illustrationen, Diagramme, Karten txt rdacontent n rdamedia nc rdacarrier Populationsgenetik (DE-588)4046804-5 gnd rswk-swf Genetik (DE-588)4071711-2 gnd rswk-swf Genom (DE-588)4156640-3 gnd rswk-swf Genetik (DE-588)4071711-2 s Genom (DE-588)4156640-3 s Populationsgenetik (DE-588)4046804-5 s DE-604 Ravinet, Mark Verfasser (DE-588)1188623958 aut Digitalisierung UB Regensburg - ADAM Catalogue Enrichment application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=030847721&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Sætre, Glenn-Peter Ravinet, Mark Evolutionary genetics concepts, analysis, and practice Populationsgenetik (DE-588)4046804-5 gnd Genetik (DE-588)4071711-2 gnd Genom (DE-588)4156640-3 gnd |
| subject_GND | (DE-588)4046804-5 (DE-588)4071711-2 (DE-588)4156640-3 |
| title | Evolutionary genetics concepts, analysis, and practice |
| title_auth | Evolutionary genetics concepts, analysis, and practice |
| title_exact_search | Evolutionary genetics concepts, analysis, and practice |
| title_full | Evolutionary genetics concepts, analysis, and practice Glenn-Peter Sætre and Mark Ravinet |
| title_fullStr | Evolutionary genetics concepts, analysis, and practice Glenn-Peter Sætre and Mark Ravinet |
| title_full_unstemmed | Evolutionary genetics concepts, analysis, and practice Glenn-Peter Sætre and Mark Ravinet |
| title_short | Evolutionary genetics |
| title_sort | evolutionary genetics concepts analysis and practice |
| title_sub | concepts, analysis, and practice |
| topic | Populationsgenetik (DE-588)4046804-5 gnd Genetik (DE-588)4071711-2 gnd Genom (DE-588)4156640-3 gnd |
| topic_facet | Populationsgenetik Genetik Genom |
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