Matthew B. Hamilton - Population Genetics

1 Cover

2 Title Page

3 Copyright Page

4 Dedication Page

5 Preface and acknowledgements

6 About the companion websites

7 CHAPTER 1: Thinking like a population geneticist 1.1 Expectations 1.2 Theory and assumptions 1.3 Simulation Chapter 1 review Further reading

8 CHAPTER 2: Genotype frequencies2.1 Mendel's model of particulate genetics 2.2 Hardy–Weinberg expected genotype frequencies 2.3 Why does Hardy–Weinberg work? 2.4 Applications of Hardy–Weinberg 2.5 The fixation index and heterozygosity 2.6 Mating among relatives 2.7 Hardy–Weinberg for two loci Chapter 2 review Further reading End‐of‐chapter exercises

9 CHAPTER 3: Genetic drift and effective population size3.1 The effects of sampling lead to genetic drift 3.2 Models of genetic drift 3.3 Effective population size 3.4 Parallelism between Drift and mating among relatives 3.5 Estimating effective population size 3.6 Gene genealogies and the coalescent model 3.7 Effective population size in the coalescent model 3.8 Genetic drift and the coalescent with other models of life history Chapter 3 review Further reading End of chapter exercises

10 CHAPTER 4: Population structure and gene flow4.1 Genetic populations 4.2 Gene flow and its impact on allele frequencies in multiple subpopulations 4.3 Direct measures of gene flow 4.4 Fixation indices to summarize the pattern of population subdivision 4.5 Population subdivision and the Wahlund effect 4.6 Evolutionary models that predict patterns of population structure 4.7 Population assignment and clustering 4.8 The impact of population structure on genealogical branching Further reading End of chapter exercises

11 CHAPTER 5: Mutation5.1 The source of all genetic variation 5.2 The fate of a new mutation 5.3 Mutation models 5.4 The influence of mutation on allele frequency and autozygosity 5.5 The coalescent model with mutation Further reading End‐of‐chapter exercises

12 CHAPTER 6: Fundamentals of natural selection 6.1 Natural selection 6.2 General results for natural selection on a diallelic locus 6.3 How natural selection works to increase average fitness 6.4 Ramifications of the one locus, two allele model of natural selection Further reading End‐of‐chapter exercises

13 CHAPTER 7: Further models of natural selection7.1 Viability selection with three alleles or two loci 7.2 Alternative models of natural selection 7.3 Combining natural selection with other processes 7.4 Natural selection in genealogical branching models 7.5 Shifting balance theory Further reading End‐of‐chapter exercises

14 CHAPTER 8: Molecular evolution8.1 The neutral theory 8.2 Natural selection 8.3 Measures of divergence and polymorphism 8.4 DNA sequence divergence and the molecular clock 8.5 Testing the molecular clock hypothesis and explanations for rate variation in molecular evolution 8.6 Testing the neutral theory null model of DNA sequence polymorphism 8.7 Recombination in the genealogical branching model Further reading End‐of‐chapter exercises

15 CHAPTER 9: Quantitative trait variation and evolution9.1 Quantitative traits 9.2 Evolutionary change in quantitative traits 9.3 Quantitative trait loci (QTL) Further reading End‐of‐chapter exercises

16 CHAPTER 10: The Mendelian basis of quantitative trait variation10.1 The connection between particulate inheritance and quantitative trait variation 10.2 Mean genotypic value in a population 10.3 Average effect of an allele 10.4 Breeding value and dominance deviation 10.5 Components of total genotypic variance 10.6 Genotypic resemblance between relatives Further reading End‐of‐chapter exercises

17 Appendix A.1 Covariance and Correlation Further reading

18 Bibliography

19 Index

20 End User License Agreement

1 Chapter 2 Table 2.1 Punnett square to predict genotype frequencies for loci on sex chro... Table 2.2 An example DNA profile for three STR (“simple tandem repeat”) loci ... Table 2.3 Allele frequencies for nine STR loci commonly used in forensic case... Table 2.4 Expected numbers of each of the three MN blood group genotypes unde... Table 2.5 χ 2values and associated cumulative probabilities in the right‐hand... Table 2.6 Hardy–Weinberg expected genotype frequencies for the ABO blood grou... Table 2.7 Expected numbers of each of the four blood group genotypes under th... Table 2.8 Observed genotype counts and frequencies in a sample of N = 200 indi... Table 2.9 Estimates of the fixation index ( ) for various species based on pe... Table 2.10 The mean phenotype in a population that is experiencing consanguin... Table 2.11 A summary of the Mendelian basis of inbreeding depression under th... Table 2.12 Expected frequencies of gametes for two diallelic loci in a random... Table 2.13 Example of the effect of population admixture on gametic disequili... Table 2.14 Joint counts of genotype frequencies observed at two microsatellit...

2 Chapter 3 Table 3.1 Typical results of sampling from beaker populations of micro‐centri... Table 3.2 The equations used to calculate the expected frequency of populatio... Table 3.3 The level of heterozygosity found in island and mainland population... Table 3.4 Data from simulated allele frequencies in Figure 3.20 used to estim...Table 3.5 Simulated allele frequencies in Figure 3.20 used to estimate the ef...Table 3.6 Empirical estimates of effective population size ( ) or effective n...

3 Chapter 4Table 4.1 Microsatellite genotypes with allelic states given in base pairs fo...Table 4.2 Seed progeny genotypes given with the known maternal parent genotyp...Table 4.3 Allele frequencies for five Corythophora alta microsatellite loci us...Table 4.4 The chance of a random match for the included fathers in Table 4.2....Table 4.5 The mathematical and biological definitions of heterozygosity for t...Table 4.6 The mathematical and biological definitions of fixation indices for...Table 4.7 Allele and genotype frequencies for the hypothetical example of alb...Table 4.8 Expected frequencies for individual DNA profile loci and the three ...Table 4.9 Estimates of the fixation index among subpopulations ( F ST) for dive...Table 4.10 An example of population assignment of a genotype using Bayes rule...Table 4.11 Distribution of natural log posterior probability values for clust...

4 Chapter 5Table 5.1 Per‐locus mutation rates measured for five loci that influence coat...Table 5.2 Rates of spontaneous mutation expressed per base pair per generatio...Table 5.3 The expected frequency of each family size per pair of parents ( k ) ...Table 5.4 Hypothetical allele frequencies in two subpopulations used to compu...Table 5.5 A comparison of hypothetical estimates of population subdivision as...

5 Chapter 6Table 6.1 The expected frequencies of two genotypes after natural selection f...Table 6.2 Assumptions of the basic natural selection model with a diallelic l...Table 6.3 The expected frequencies of three genotypes after natural selection...Table 6.4 The general categories of relative fitness values for viability sel...

6 Chapter 7Table 7.1 Relative fitness estimates for the six genotypes of the hemoglobin ...Table 7.2 Matrix of fitness values for all combinations of the four gametes f...Table 7.3 Expected frequencies of gametes under viability selection for two d...Table 7.4 Fitness values based on the fecundities of mating pairs of male and...

7 Chapter 8Table 8.1 Nucleotide diversity (π) estimates reported from comparative studie...Table 8.2 DNA divergence estimates for three loci in maize and wheat, both mo...Table 8.3 Mean and variance in the number of substitutions at a neutral locus...Table 8.4 Number of substitutions per nucleotide site observed over 49 nuclea...Table 8.5 Estimates of polymorphism and divergence for two loci sampled from ...Table 8.6 Estimates of polymorphism and divergence (fixed sites) for nonsynon...