Оглавление
Matthew B. Hamilton. Population Genetics
Table of Contents
List of Tables
List of Illustrations
Guide
Pages
Population Genetics
Preface and acknowledgements
About the companion websites
CHAPTER 1 Thinking like a population geneticist
1.1 Expectations
Parameters and parameter estimates
Inductive and deductive reasoning
1.2 Theory and assumptions
1.3 Simulation
Interact box 1.1 The textbook website
Chapter 1 review
Further reading
CHAPTER 2 Genotype frequencies. 2.1 Mendel's model of particulate genetics
2.2 Hardy–Weinberg expected genotype frequencies
Interact box 2.1 Genotype frequencies for one locus with two alleles
2.3 Why does Hardy–Weinberg work?
2.4 Applications of Hardy–Weinberg
Forensic DNA profiling
Problem box 2.1 The expected genotype frequency for a DNA profile
Testing Hardy–Weinberg expected genotype frequencies
Box 2.1 DNA profiling
Assuming Hardy–Weinberg to test alternative models of inheritance
Problem box 2.2 Proving allele frequencies are obtained from expected genotype frequencies
Problem box 2.3 Inheritance for corn kernel phenotypes
2.5 The fixation index and heterozygosity
Interact box 2.2 Assortative mating and genotype frequencies
Box 2.2 Protein locus or allozyme genotyping
2.6 Mating among relatives
Impacts of non‐random mating on genotype and allele frequencies
Coancestry coefficient and autozygosity
Box 2.3 Locating relatives using genetic genealogy methods
Phenotypic consequences of mating among relatives
The many meanings of inbreeding
2.7 Hardy–Weinberg for two loci
Gametic disequilibrium
Physical linkage
Natural selection
Interact box 2.3 Gametic disequilibrium under both recombination and natural selection
Mutation
Mixing of diverged populations
Mating system
Population size
Interact box 2.4 Estimating genotypic disequilibrium
Chapter 2 review
Further reading
End‐of‐chapter exercises
Problem box answers. Problem box 2.1 answer
Problem box 2.2 answer
Problem box 2.3 answer
CHAPTER 3 Genetic drift and effective population size. 3.1 The effects of sampling lead to genetic drift
Interact box 3.1 Genetic drift
3.2 Models of genetic drift
The binomial probability distribution
Problem box 3.1 Applying the binomial formula
Math box 3.1 Variance of a binomial variable
Markov chains
Interact box 3.2 Genetic drift simulated with a markov chain model
Problem box 3.2 Constructing a transition probability matrix
The diffusion approximation of genetic drift
3.3 Effective population size
Problem box 3.3 Estimating Ne from information about N
3.4 Parallelism between Drift and mating among relatives
Interact box 3.3 Heterozygosity over time in a finite population
3.5 Estimating effective population size
Different types of effective population size
Interact box 3.4 Estimating Ne from allele frequencies and heterozygosity over time
Breeding effective population size
Effective population sizes of different genomes
3.6 Gene genealogies and the coalescent model
Interact box 3.5 Sampling lineages in a Wright‐Fisher population
Math box 3.2 Approximating the probability of a coalescent event with the exponential distribution
Interact box 3.6 Build your own coalescent genealogies
3.7 Effective population size in the coalescent model
Interact box 3.7 Simulating gene genealogies in populations with different effective sizes
Coalescent genealogies and population bottlenecks
Coalescent genealogies in growing and shrinking populations
Interact box 3.8 Coalescent genealogies in populations with changing size
3.8 Genetic drift and the coalescent with other models of life history
Chapter 3 review
Further reading
End of chapter exercises
Problem box answers. Problem box 3.1 answer
Problem box 3.2 answer
Problem box 3.3 answer
CHAPTER 4 Population structure and gene flow. 4.1 Genetic populations
Box 4.1 Are allele frequencies random or clumped in two dimensions?
4.2 Gene flow and its impact on allele frequencies in multiple subpopulations
Continent‐island model
Interact box 4.1 Continent‐island model of gene flow
Two‐island model
Interact box 4.2 Two‐island model of gene flow
4.3 Direct measures of gene flow
Problem box 4.1 Calculate the probability of a random haplotype match and the exclusion probability
4.4 Fixation indices to summarize the pattern of population subdivision
Problem box 4.2 Compute FIS, FST, and FIT
Estimating fixation indices
4.5 Population subdivision and the Wahlund effect
Interact box 4.4 Simulating the Wahlund effect
Problem box 4.3 Impact of population structure on a DNA‐profile match probability
4.6 Evolutionary models that predict patterns of population structure
Infinite island model
Math box 4.1 The expected value of FST in the infinite island model
Problem box 4.4 Expected levels of FST for Y‐chromosome and organelle loci
Interact box 4.5 Simulate FIS, FST, and FIT in the finite island model
Stepping‐stone and metapopulation models
Isolation by distance and by landscape connectivity
Math box 4.2 Analysis of a circuit to predict gene flow across a landscape
4.7 Population assignment and clustering
Maximum likelihood assignment
Bayesian assignment
Interact box 4.6 Genotype assignment and clustering
Math Box 4.3 Bayes Theorem
Empirical assignment methods
Interact box 4.7 Visualizing principle components analysis
4.8 The impact of population structure on genealogical branching
Combining coalescent and migration events
Interact box 4.8 Gene genealogies with migration between two demes
The average length of a genealogy with migration
Math box 4.4 Solving two equations with two unknowns for average coalescence times
Chapter 4 review
Further reading
End of chapter exercises
Problem box answers. Problem box 4.1 answer
Problem box 4.2 answer
Problem box 4.3 answer
Problem box 4.4 answer
CHAPTER 5 Mutation. 5.1 The source of all genetic variation
Estimating mutation rates
Evolution of mutation rates
5.2 The fate of a new mutation
Chance a mutation is lost due to mendelian segregation
Fate of a new mutation in a finite population
Interact box 5.1 Frequency of neutral mutations in a finite population
Mutations in expanding populations
Geometric model of mutations fixed by natural selection
Muller's ratchet and the fixation of deleterious mutations
Interact box 5.2 Muller's Ratchet
5.3 Mutation models
Mutation models for discrete alleles
Interact box 5.3 RST and FST as examples of the consequences of different mutation models
Mutation models for DNA sequences
Box 5.1 Single nucleotide polymorphisms
5.4 The influence of mutation on allele frequency and autozygosity
Math box 5.1 Equilibrium allele frequency with two‐way mutation
Interact box 5.4 Simulating irreversible and two‐way mutation
Interact box 5.5 Heterozygosity and homozygosity with two‐way mutation
5.5 The coalescent model with mutation
Interact box 5.6 Build your own coalescent genealogies with mutation
Chapter 5 review
Further reading
End‐of‐chapter exercises
CHAPTER 6 Fundamentals of natural selection
6.1 Natural selection
Natural selection with clonal reproduction
Problem box 6.1 Relative fitness of HIV genotypes
Natural selection with sexual reproduction
Math box 6.1 The change in allele frequency each generation under natural selection
6.2 General results for natural selection on a diallelic locus
Selection against a recessive phenotype
Selection against a dominant phenotype
General dominance
Heterozygote disadvantage
Heterozygote advantage
Math box 6.2 Equilibrium allele frequency with overdominance
The strength of natural selection
6.3 How natural selection works to increase average fitness
Average fitness and rate of change in allele frequency
Problem box 6.2 Mean fitness and change in allele frequency
Interact box 6.1 Natural selection on one locus with two alleles
The fundamental theorem of natural selection
6.4 Ramifications of the one locus, two allele model of natural selection
The Classical and Balance Hypotheses
How to explain levels of allozyme polymorphism
Chapter 6 review
Further reading
End‐of‐chapter exercises
Problem box answers. Problem box 6.1 answers
Problem box 6.2 answer
CHAPTER 7 Further models of natural selection. 7.1 Viability selection with three alleles or two loci
Natural selection on one locus with three alleles
Problem box 7.1 Marginal fitness and Δp for the Hb C allele
Interact box 7.1 Natural selection on one locus with three or more alleles
Natural selection on two diallelic loci
7.2 Alternative models of natural selection
Natural selection via different levels of fecundity
Natural selection with frequency‐dependent fitness
Math box 7.1 The change in allele frequency with frequency‐dependent selection
Interact box 7.2 Frequency‐dependent natural selection
Natural selection with density‐dependent fitness
Interact box 7.3 Density‐dependent natural selection
7.3 Combining natural selection with other processes
Natural selection and genetic drift acting simultaneously
Genetic differentiation among populations by natural selection
Interact box 7.4 The balance of natural selection and genetic drift at a diallelic locus
The balance between natural selection and mutation
Genetic load
Interact box 7.5 Natural selection and mutation
Math box 7.2 Mean fitness in a population at equilibrium for balancing selection
7.4 Natural selection in genealogical branching models
Directional selection and the ancestral selection graph
Problem box 7.2 Resolving possible selection events on an ancestral selection graph
Interact box 7.6 Build an ancestral selection graph
Genealogies and balancing selection
7.5 Shifting balance theory
Allele combinations and the fitness surface
Wright's view of allele frequency distributions
Evolutionary scenarios imagined by wright
Critique and controversy over shifting balance
Chapter 7 review
Further reading
End‐of‐chapter exercises
Problem box answers. Problem box 7.1 answer
Problem box 7.2 answer
CHAPTER 8 Molecular evolution. 8.1 The neutral theory
Polymorphism
Divergence
Nearly neutral theory
Interact box 8.1 Compare the neutral theory and nearly neutral theory
The selectionist–neutralist debates
8.2 Natural selection
Hitch‐hiking and rates of divergence
Empirical studies
8.3 Measures of divergence and polymorphism
Box 8.1 DNA sequencing
DNA divergence between species
DNA sequence divergence and saturation
Interact box 8.2 Compare nucleotide substitution models
DNA polymorphism measured by segregating sites and nucleotide diversity
Interact box 8.3 Estimating π and S from DNA sequence data
8.4 DNA sequence divergence and the molecular clock
Dating events with the molecular clock
Problem box 8.1 Estimating divergence times with the molecular clock
Interact box 8.4 Molecular clock estimates of evolutionary events
8.5 Testing the molecular clock hypothesis and explanations for rate variation in molecular evolution
The molecular clock and rate variation
Ancestral polymorphism and poisson process molecular clock
Math box 8.1 The dispersion index with ancestral polymorphism and divergence
Relative rate tests of the molecular clock
Patterns and causes of rate heterogeneity
8.6 Testing the neutral theory null model of DNA sequence polymorphism
HKA test of neutral theory expectations for DNA sequence evolution
The McDonald–Kreitman (MK) test
Mismatch distributions
Tajima's D
Problem box 8.2 Computing Tajima’s D from DNA sequence data
8.7 Recombination in the genealogical branching model
Box Interact Box 8.5 Build an Ancestral Recombination Graph
Consequences of recombination
Chapter 8 review
Further reading
End‐of‐chapter exercises
Problem box answers. Problem box 8.1 answer
Problem box 8.2 answer
CHAPTER 9 Quantitative trait variation and evolution. 9.1 Quantitative traits
Problem box 9.1 Phenotypic distribution produced by Mendelian inheritance of three diallelic loci
Components of phenotypic variation
Components of genotypic variation (VG)
Inheritance of additive ( VA), dominance ( VD), and epistasis ( VI) genotypic variation
Genotype‐by‐environment interaction ( VG×E)
Additional sources of phenotypic variance
Math box 9.1 Summing two variances
9.2 Evolutionary change in quantitative traits
Heritability and the Breeder's equation
Changes in quantitative trait mean and variance due to natural selection
Math box 9.2 Selection differential with truncation selection
Estimating heritability by parent–offspring regression
Interact box 9.1 Estimating heritability with parent–offspring regression
Response to selection on correlated traits
Interact box 9.2 Response to natural selection on two correlated traits
Long‐term response to selection
Interact box 9.3 Response to selection and the number of loci that cause quantitative trait variation
Neutral evolution of quantitative traits
Interact box 9.4 Effective population size and genotypic variation in a neutral quantitative trait
9.3 Quantitative trait loci (QTL)
QTL mapping with single marker loci
Problem box 9.2 Compute the effect and dominance coefficient of a QTL
QTL mapping with multiple marker loci
Problem box 9.3 Derive the expected marker‐class means for a backcross mating design
Limitations of QTL mapping studies
Genome‐wide association studies
Biological significance of identifying QTL
Interact box 9.5 Effect sizes and response to selection at QTLs
Chapter 9 review
Further reading
End‐of‐chapter exercises
Problem box answers. Problem box 9.1 answer
Problem box 9.2 answer
Problem box 9.3 answer
CHAPTER 10 The Mendelian basis of quantitative trait variation. 10.1 The connection between particulate inheritance and quantitative trait variation
Scale of genotypic values
Problem box 10.1 Compute values on the genotypic scale of measurement for IGF1 in dogs
10.2 Mean genotypic value in a population
10.3 Average effect of an allele
Math box 10.1 The average effect of the A1 allele
Problem box 10.2 Compute average effects for IGF1 in dogs
10.4 Breeding value and dominance deviation
Interact box 10.1 Average effects, breeding values, and dominance deviations
Dominance deviation
10.5 Components of total genotypic variance
Interact box 10.2 Components of total genotypic variance, VG
Math box 10.2 Deriving the total genotypic variance, VG
10.6 Genotypic resemblance between relatives
Chapter 10 review
Further reading
End‐of‐chapter exercises
Problem box answers. Problem box 10.1 answer
Problem box 10.2 answer
Appendix
Problem A.1 Estimating the variance
Interact box A.1 The central limit theorem
A.1 Covariance and Correlation
Further reading
Problem box answers
Bibliography
Index
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