(Ebook) Population Genetics 1st Edition by Matthew Hamilton ISBN 1405132779 9781405132770

(Ebook) Population Genetics 1st Edition by Matthew Hamilton ISBN 1405132779 9781405132770

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ISBN 10: 1405132779 
ISBN 13: 9781405132770
Author: Matthew Hamilton

A concise introduction to Population Genetics, which brings students from first principles to modeling problems with common software.

(Ebook) Population Genetics 1st Table of contents:

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
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 for Hardy–Weinberg
Box 2.1 DNA profiling
Interact box 2.2 χ χ 2 test
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 2.3 Assortative mating and genotype frequencies
Box 2.2 Protein locus or allozyme genotyping
2.6 Mating among relatives
Impacts of inbreeding on genotype and allele frequencies
Inbreeding coefficient and autozygosity in a pedigree
Phenotypic consequences of inbreeding
The many meanings of inbreeding
2.7 Gametic disequilibrium
Interact box 2.4 Decay of gametic disequilibrium and a χ χ 2 test
Physical linkage
Natural selection
Interact box 2.5 Gametic disequilibrium under both recombination and natural selection
Mutation
Mixing of diverged populations
Mating system
Chance
Interact box 2.6 Estimating genotypic disequilibrium
Chapter 2 review
Further reading
Problem box answers
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 N from information about N
3.4 Parallelism between drift and inbreeding
3.5 Estimating effective population size
Interact box 3.3 Heterozygosity and inbreeding over time in finite populations
Different types of effective population size
Problem box 3.4 Estimating N e from observed heterozygosity over time
Effective population sizes of different genomes
3.6 Gene genealogies and the coalescent model
Math box 3.2 Approximating the probability of a coalescent event with the exponential distribution
Interact box 3.4 Build your own coalescent genealogies
Interact box 3.5 Simulating gene genealogies in populations with different effective sizes
Coalescent genealogies and population bottlenecks
Coalescent genealogies in growing and shrinking populations
Interact box 3.6 Coalescent genealogies in populations with changing size
Chapter 3 review
Further reading
Problem box answers
CHAPTER 4 Population structure and gene flow
4.1 Genetic populations
Method box 4.1 Are allele frequencies random or clumped in two dimensions?
4.2 Direct measures of gene flow
Problem box 4.1 Calculate the probability of a random haplotype match and the exclusion probability
Interact box 4.1 Average exclusion probability for a locus
4.3 Fixation indices to measure the pattern of population subdivision
Problem box 4.2 Compute FIS, FST , and FIT
4.4 Population subdivision and the Wahlund effect
Interact box 4.2 Simulating the Wahlund effect
Problem box 4.3 Account for population structure in a DNA-profile match probability
4.5 Models of population structure
Continent-island model
Interact box 4.3 Continent-island model of gene flow
Two-island model
Infinite island model
Interact box 4.4 Two-island model of gene flow
Math Box 4.1 The expected value of F ST in the infinite island model
Problem box 4.4 Expected levels of F ST for Y-chromosome and organelle loci
Interact box 4.5 Finite island model of gene flow
Interact box 4.5 Finite island model of gene flow
Stepping-stone and metapopulation models
4.6 The impact of population structure on genealogical branching
Combining coalescent and migration events
The average length of a genealogy with migration
Interact box 4.6 Coalescent events in two demes
Math box 4.2 Solving two equations with two unknowns for average coalescence times
Chapter 4 review
Further reading
Problem box answers
CHAPTER 5 Mutation
5.1 The source of all genetic variation
5.2 The fate of a new mutation
Chance a mutation is lost due to Mendelian
Fate of a new mutation in a finite population
Interact box 5.1 Frequency of neutral mutations in a finite population
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 R ST and F ST as examples of the consequences of different mutation models
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 bi-directional mutation
5.5 The coalescent model with mutation
Interact box 5.5 Build your own coalescent genealogies with mutation
Chapter 5 review
Further reading
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
6.2 General results for natural selection on a diallelic locus
Math box 6.1 The change in allele frequency each generation under natural selection
Selection against a recessive phenotype
Selection against a dominant phenotype
General dominance
Heterozygote disadvantage
Heterozygote advantage
The strength of natural selection
Math box 6.2 Equilibrium allele frequency with overdominance
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
The fundamental theorem of natural selection
Interact box 6.1 Natural selection on one locus with two alleles
Chapter 6 review
Further reading
Problem box answers
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 Δ Δ p 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
Natural selection with density-dependent fitness
Math box 7.1 The change in allele frequency with frequency-dependent selection
Interact box 7.2 Frequency-dependent natural selection
Interact box 7.3 Density-dependent natural selection
7.3 Combining natural selection with other processes
Natural selection and genetic drift acting simultaneously
Interact box 7.4 The balance of natural selection and genetic drift at a diallelic locus
aThe balance between natural selection nd mutation
Interact box 7.5Natural selection and mutation
Directional selection and the ancestral selection graph
Problem box 7.2 Resolving possible selection events on an ancestral selection graph
Genealogies and balancing selection
Interact box 7.6 Coalescent genealogies with directional selection
Chapter 7 review
Further reading
Problem box answers
CHAPTER 8 Molecular evolution
8.1 The neutral theory
Polymorphism
Divergence
Nearly neutral theory
Interact box 8.1 The relative strengths of genetic drift and natural selection
8.2 Measures of divergence and polymorphism
Box 8.1 DNA sequencing
DNA divergence between species
DNA sequence divergence and saturation
DNA polymorphism
8.3 DNA sequence divergence and the molecular clock
Interact box 8.2 Estimating π π and S from DNA sequence data
Dating events with the molecular clock
Problem box 8.1 Estimating divergence times with the molecular clock
8.4 Testing the molecular clock hypothesis and explanations for rate variation in molecular evolutio
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
8.5 Testing the neutral theory null model of DNA sequence evolution
HKA test of neutral theory expectations for DNA sequence evolution
MK test
Tajima’s D
Problem box 8.2 Computing Tajima’s D from DNA sequence data
Mismatch distributions
Interact box 8.3 Mismatch distributions for neutral genealogies in stable, growing, or shrinking pop
8.6 Molecular evolution of loci that are not independent
Genetic hitch-hiking due to background or balancing selection
Gametic disequilibrium and rates of divergence
Chapter 8 review
Further reading
Problem box answers
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 (V
Inheritance of additive (V A ), dominance (V D ), and epistasis (V I ) genotypic variation
Genotype-by-environment interaction (V G.潴摥昀..
Additional sources of phenotypic variance
Math box 9.1 Summing two variances
9.2 Evolutionary change in quantitative traits
Heritability
Changes in quantitative trait mean and variance due to natural selection
Estimating heritability by parent–offspring regression
Interact box 9.1 Estimating heritability withparent–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 variatio
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
Biological significance of QTL mapping
Interact box 9.5 Effect sizes and response to selection at QTLs
Chapter 9 review
Further reading
Problem box answers
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 A 1 allele
Problem box 10.2 Compute the allele average effect of the IGF1 A allele 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, V G
Math box 10.2 Deriving the total genotypic variance, V
10.6 Genotypic resemblance between relatives
Chapter 10 review
Further reading
Problem box answers
CHAPTER 11 Historical and synthetic topics
11.1 Historical controversies in population genetics
The classical and balance hypotheses
How to explain levels of allozyme polymorphism
Genetic load
Math box 11.1 Mean fitness in a population at equilibrium for balancing selection
The selectionist/neutralist debates
11.2 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 11 review
Further reading
Appendix
Statistical uncertainty
Problem box A.1 Estimating the variance
Interact box A.1 The central limit theorem
Covariance and correlation
Further reading
Problem box answers
Index
Plates

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Tags: Matthew Hamilton, Population, Genetics