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Author:   Matthew Hamilton
Publisher:   John Wiley and Sons Ltd
Imprint:   Wiley-Blackwell (an imprint of John Wiley & Sons Ltd)
Dimensions:   Width: 21.00cm , Height: 2.60cm , Length: 28.70cm
Weight:   1.324kg
ISBN:  

9781405132770

ISBN 10:   1405132779
Pages:   424
Publication Date:   20 March 2009
Audience:   Professional and scholarly ,  Professional & Vocational
Format:   Hardback
Publisher's Status:   Unknown
Availability:   In Print  
Limited stock is available. It will be ordered for you and shipped pending supplier's limited stock.

Table of Contents

Preface and acknowledgments xi 1 Thinking like a population geneticist 1 1.1 Expectations 1 Parameters and parameter estimates 2 Inductive and deductive reasoning 3 1.2 Theory and assumptions 4 1.3 Simulation 6 Interact box 1.1 The textbook website 7 Chapter 1 review 8 Further reading 8 2 Genotype frequencies 9 2.1 Mendel’s model of particulate genetics 9 2.2 Hardy–Weinberg expected genotype frequencies 13 Interact box 2.1 Genotype frequencies 14 2.3 Why does Hardy–Weinberg work? 17 2.4 Applications of Hardy–Weinberg 19 Forensic DNA profiling 19 Problem box 2.1 The expected genotype frequency for a DNA profile 22 Testing for Hardy–Weinberg 22 Box 2.1 DNA profiling 22 Interact box 2.2 χ2 test 26 Assuming Hardy–Weinberg to test alternative models of inheritance 26 Problem box 2.2 Proving allele frequencies are obtained from expected genotype frequencies 27 Problem box 2.3 Inheritance for corn kernel phenotypes 28 2.5 The fixation index and heterozygosity 28 Interact box 2.3 Assortative mating and genotype frequencies 29 Box 2.2 Protein locus or allozyme genotyping 32 2.6 Mating among relatives 33 Impacts of inbreeding on genotype and allele frequencies 33 Inbreeding coefficient and autozygosity in a pedigree 34 Phenotypic consequences of inbreeding 37 The many meanings of inbreeding 40 2.7 Gametic disequilibrium 41 Interact box 2.4 Decay of gametic disequilibrium and a χ2 test 44 Physical linkage 45 Natural selection 46 Interact box 2.5 Gametic disequilibrium under both recombination and natural selection 46 Mutation 47 Mixing of diverged populations 47 Mating system 48 Chance 48 Interact box 2.6 Estimating genotypic disequilibrium 49 Chapter 2 review 50 Further reading 50 Problem box answers 51 3 Genetic drift and effective population size 53 3.1 The effects of sampling lead to genetic drift 53 Interact box 3.1 Genetic drift 58 3.2 Models of genetic drift 58 The binomial probability distribution 58 Problem box 3.1 Applying the binomial formula 60 Math box 3.1 Variance of a binomial variable 62 Markov chains 62 Interact box 3.2 Genetic drift simulated with a Markov chain model 65 Problem box 3.2 Constructing a transition probability matrix 66 The diffusion approximation of genetic drift 67 3.3 Effective population size 73 Problem box 3.3 Estimating Ne from information about N 77 3.4 Parallelism between drift and inbreeding 78 3.5 Estimating effective population size 80 Interact box 3.3 Heterozygosity,and inbreeding over time in finite populations 81 Different types of effective population size 82 Problem box 3.4 Estimating Ne from observed heterozygosity over time 85 Breeding effective population size 85 Effective population sizes of different genomes 87 3.6 Gene genealogies and the coalescent model 87 Math box 3.2 Approximating the probability of a coalescent event with the exponential distribution 93 Interact box 3.4 Build your own coalescent genealogies 94 3.7 Effective population size in the coalescent model 96 Interact box 3.5 Simulating gene genealogies in populations with different effective sizes 97 Coalescent genealogies and population bottlenecks 98 Coalescent genealogies in growing and shrinking populations 99 Interact box 3.6 Coalescent genealogies in populations with changing size 101 Chapter 3 review 101 Further reading 102 Problem box answers 103 4 Population structure and gene flow 105 4.1 Genetic populations 105 Method box 4.1 Are allele frequencies random or clumped in two dimensions? 110 4.2 Direct measures of gene flow 111 Problem box 4.1 Calculate the probability of a random haplotype match and the exclusion probability 117 Interact box 4.1 Average exclusion probability for a locus 117 4.3 Fixation indices to measure the pattern of population subdivision 118 Problem box 4.2 Compute FIS  FST,and FIT 122 Method box 4.2 Estimating fixation indices 124 4.4 Population subdivision and the Wahlund effect 124 Interact box 4.2 Simulating the Wahlund effect 127 Problem box 4.3 Account for population structure in a DNA-profile match probability 130 4.5 Models of population structure 131 Continent-island model 131 Interact box 4.3 Continent-island model of gene flow 134 Two-island model 134 Infinite island model 135 Interact box 4.4 Two-island model of gene flow 136 Math box 4.1 The expected value of FST in the infinite island model 138 Problem box 4.4 Expected levels of FST for Y-chromosome and organelle loci 139 Interact box 4.5 Finite island model of gene flow 139 Stepping-stone and metapopulation models 141 4.6 The impact of population structure on genealogical branching 142 Combining coalescent and migration events 143 The average length of a genealogy with migration 144 Interact box 4.6 Coalescent events in two demes 145 Math box 4.2 Solving two equations with two unknowns for average coalescence times 148 Chapter 4 review 149 Further reading 150 Problem box answers 151 5 Mutation 154 5.1 The source of all genetic variation 154 5.2 The fate of a new mutation 160 Chance a mutation is lost due to Mendelian segregation 160 Fate of a new mutation in a finite population 162 Interact box 5.1 Frequency of neutral mutations in a finite population 163 Geometric model of mutations fixed by natural selection 164 Muller’s Ratchet and the fixation of deleterious mutations 166 Interact box 5.2 Muller’s Ratchet 168 5.3 Mutation models 168 Mutation models for discrete alleles 169 Interact box 5.3 RST and FST as examples of the consequences of different mutation models 172 Mutation models for DNA sequences 172 5.4 The influence of mutation on allele frequency and autozygosity 173 Math box 5.1 Equilibrium allele frequency with two-way mutation 176 Interact box 5.4 Simulating irreversible and bi-directional mutation 177 5.5 The coalescent model with mutation 178 Interact box 5.5 Build your own coalescent genealogies with mutation 181 Chapter 5 review 183 Further reading 183 6 Fundamentals of natural selection 185 6.1 Natural selection 185 Natural selection with clonal reproduction 185 Problem box 6.1 Relative fitness of HIV genotypes 189 Natural selection with sexual reproduction 189 6.2 General results for natural selection on a diallelic locus 193 Math box 6.1 The change in allele frequency each generation under natural selection 194 Selection against a recessive phenotype 195 Selection against a dominant phenotype 196 General dominance 197 Heterozygote disadvantage 198 Heterozygote advantage 198 The strength of natural selection 199 Math box 6.2 Equilibrium allele frequency with overdominance 200 6.3 How natural selection works to increase average fitness 200 Average fitness and rate of change in allele frequency 201 Problem box 6.2 Mean fitness and change in allele frequency 203 The fundamental theorem of natural selection 203 Interact box 6.1 Natural selection on one locus with two alleles 203 Chapter 6 review 206 Further reading 206 Problem box answers 206 7 Further models of natural selection 208 7.1 Viability selection with three alleles or two loci 208 Natural selection on one locus with three alleles 209 Problem box 7.1 Marginal fitness and Δp for the Hb C allele 211 Interact box 7.1 Natural selection on one locus with three or more alleles 211 Natural selection on two diallelic loci 212 7.2 Alternative models of natural selection 216 Natural selection via different levels of fecundity 216 Natural selection with frequency-dependent fitness 218 Natural selection with density-dependent fitness 219 Math box 7.1 The change in allele frequency with frequency-dependent selection 219 Interact box 7.2 Frequency-dependent natural selection 220 Interact box 7.3 Density-dependent natural selection 222 7.3 Combining natural selection with other processes 222 Natural selection and genetic drift acting simultaneously 222 Interact box 7.4 The balance of natural selection and genetic drift at a diallelic locus 224 The balance between natural selection and mutation 225 Interact box 7.5 Natural selection and mutation 226 7.4 Natural selection in genealogical branching models 226 Directional selection and the ancestral selection graph 227 Problem box 7.2 Resolving possible selection events on an ancestral selection graph 230 Genealogies and balancing selection 230 Interact box 7.6 Coalescent genealogies with directional selection 231 Chapter 7 review 232 Further reading 233 Problem box answers 234 8 Molecular evolution 235 8.1 The neutral theory 235 Polymorphism 236 Divergence 237 Nearly neutral theory 240 Interact box 8.1 The relative strengths of genetic drift and natural selection 241 8.2 Measures of divergence and polymorphism 241 Box 8.1 DNA sequencing 242 DNA divergence between species 242 DNA sequence divergence and saturation 243 DNA polymorphism 248 8.3 DNA sequence divergence and the molecular clock 250 Interact box 8.2 Estimating π and S from DNA sequence data 251 Dating events with the molecular clock 252 Problem box 8.1 Estimating divergence times with the molecular clock 254 8.4 Testing the molecular clock hypothesis and explanations for rate variation in molecular evolution 255 The molecular clock and rate variation 255 Ancestral polymorphism and Poisson process molecular clock 257 Math box 8.1 The dispersion index with ancestral polymorphism and divergence 259 Relative rate tests of the molecular clock 260 Patterns and causes of rate heterogeneity 261 8.5 Testing the neutral theory null model of DNA sequence evolution 265 HKA test of neutral theory expectations for DNA sequence evolution 265 MK test 267 Tajima’s D 269 Problem box 8.2 Computing Tajima’s D from DNA sequence data 271 Mismatch distributions 272 Interact box 8.3 Mismatch distributions for neutral genealogies in stable growing or shrinking populations 274 8.6 Molecular evolution of loci that are not independent 274 Genetic hitch-hiking due to background or balancing selection 278 Gametic disequilibrium and rates of divergence 278 Chapter 8 review 279 Further reading 280 Problem box answers 281 9 Quantitative trait variation and evolution 283 9.1 Quantitative traits 283 Problem box 9.1 Phenotypic distribution produced by Mendelian inheritance of three diallelic loci 285 Components of phenotypic variation 286 Components of genotypic variation (VG) 288 Inheritance of additive (VA) dominance (VD) and epistasis (VI) genotypic variation 291 Genotype-by-environment interaction (VG×E) 292 Additional sources of phenotypic variance 295 Math box 9.1 Summing two variances 296 9.2 Evolutionary change in quantitative traits 297 Heritability 297 Changes in quantitative trait mean and variance due to natural selection 299 Estimating heritability by parent–offspring regression 302 Interact box 9.1 Estimating heritability with parent–offspring regression 303 Response to selection on correlated traits 304 Interact box 9.2 Response to natural selection on two correlated traits 306 Long-term response to selection 307 Interact box 9.3 Response to selection and the number of loci that cause quantitative trait variation 309 Neutral evolution of quantitative traits 313 Interact box 9.4 Effective population size and genotypic variation in a neutral quantitative trait 314 9.3 Quantitative trait loci (QTL) 315 QTL mapping with single marker loci 316 Problem box 9.2 Compute the effect and dominance coefficient of a QTL 321 QTL mapping with multiple marker loci 322 Problem box 9.3 Derive the expected marker-class means for a backcross mating design 324 Limitations of QTL mapping studies 325 Biological significance of QTL mapping 326 Interact box 9.5 Effect sizes and response to selection at QTLs 328 Chapter 9 review 330 Further reading 330 Problem box answers 331 10 The Mendelian basis of quantitative trait variation 334 10.1 The connection between particulate inheritance and quantitative trait variation 334 Scale of genotypic values 334 Problem box 10.1 Compute values on the genotypic scale of measurement for IGF1 in dogs 335 10.2 Mean genotypic value in a population 336 10.3 Average effect of an allele 337 Math box 10.1 The average effect of the A1 allele 339 Problem box 10.2 Compute the allele average effect of the IGF1 A2 allele in dogs 341 10.4 Breeding value and dominance deviation 341 Interact box 10.1 Average effects breeding values and dominance deviations 345 Dominance deviation 345 10.5 Components of total genotypic variance 348 Interact box 10.2 Components of total genotypic variance VG 350 Math box 10.2 Deriving the total genotypic variance VG 350 10.6 Genotypic resemblance between relatives 351 Chapter 10 review 354 Further reading 354 Problem box answers 355 11 Historical and synthetic topics 356 11.1 Historical controversies in population genetics 356 The classical and balance hypotheses 356 How to explain levels of allozyme polymorphism 358 Genetic load 359 Math box 11.1 Mean fitness in a population at equilibrium for balancing selection 362 The selectionist/neutralist debates 363 11.2 Shifting balance theory 366 Allele combinations and the fitness surface 366 Wright’s view of allele-frequency distributions 368 Evolutionary scenarios imagined by Wright 369 Critique and controversy over shifting balance 372 Chapter 11 review 374 Further reading 374 Appendix 376 Statistical uncertainty 376 Problem box A.1 Estimating the variance 378 Interact box A.1 The central limit theorem 379 Covariance and correlation 380 Further reading 382 Problem box answers 382 References 383 Index 396 Color plates appear in between pages 114 –115

Reviews

Both population biologists and upper-level biology students will appreciate the relatively clear explanations of exceptionally difficult material. (CHOICE, November 2009)

“The most catching aspect of Hamilton's book is its extremely well thought-out structure and pedagogical concept. All sections are well motivated in the respective introduction and all chapters have reviews at the end. A large number of problems have been interspersed throughout the text for students to work on, and the solutions are provided at the end of each chapter. A very interesting and novel feature is the use of so-called ‘interact boxes', which are essentially links to interactive learning and simulation software available on the internet. (Human Genetics, December 2009) Hamilton's volume would be the best choice for someone seeking a thorough grounding in the subject. (The Quarterly Review of Biology, April 2010) Both population biologists and upper-level biology students will appreciate the relatively clear explanations of exceptionally difficult material. (CHOICE, November 2009)

Author Information

Matthew B. Hamilton teaches population genetics, evolutionary processes, and similar undergraduate and graduate courses at Georgetown University. He conducts research on the processes that shape genetic variation within species using molecular genetic markers as well as predictive mathematical models.

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