Population genetics / Matthew B. Hamilton.

Format:

Book

Author/Creator:

Hamilton, Matthew B., author.

Language:

English

Subjects (All):

Population genetics.

Physical Description:

xv, 480 pages : illustrations ; 29 cm

Edition:

Second edition.

Place of Publication:

Hoboken, NJ : Wiley-Blackwell, 2021.

Summary:

Population Genetics, Second Edition, provides an up-to-date introduction to the foundation of modern evolutionary biology: the study of the distribution of alleles in a population in relation to evolutionary processes and population structure. Designed for a full one-term course on population genetics, this accessible college-level textbook integrates foundational conceptual approaches, classical hypotheses, and traditional debates to help students understand a wide range of empirical studies based on the first principles of population genetics. In addition to gaining conceptual knowledge, students also develop algorithmic and computational skills that are central to prediction and data analysis in quantitative biology. --

This fully revised edition includes updates on topics such as effective population size, mutation rates and models, recombination in the coalescent model, measures and models of population differentiation, population assignment methods, and models of linked nucleotide site variation. New end-of-chapter problems include numerical and conceptual problems. applications using published data, and exercises that utilize simulation software. --

This popular textbook: --

Presents a comprehensive body of materials that support an innovative approach to teaching population genetics --

Describes the major conceptual advances in population genetics of the last two decades --

Is richly illustrated and includes numerous examples and case studies --

Offers a range of explanatory styles designed to engage different types of learners --

Features a highly accessible and thorough introduction to coalescent theory --

Provides step-by-step explanations of the mathematics required to understand the concepts covered in the text --

Includes boxes with in-depth mathematical derivations and reasoning --

Features Interact Boxes with exercises based on a rich set of spreadsheet models and web-based computer simulations built specifically for the text --Book Jacket.

Contents:

Machine generated contents note: 1.1. Expectations

Parameters and parameter estimates

Inductive and deductive reasoning

1.2. Theory and assumptions

1.3. Simulation

Interactive Box 1.1 The textbook website

Review

Further Reading

2.1. Mendel's model of particulate genetics

2.2. Hardy-Weinberg expected genotype frequencies

Interactive 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

Interactive 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

Interactive Box 2.3 Gametic disequilibrium under both recombination and natural selection

Mutation

Mixing of diverged populations

Mating system

Population size

Interactive Box 2.4 Estimating genotypic disequilibrium

End-of-Chapter Exercises

Problem Box Answers

3.1. The effects of sampling lead to genetic drift

Interactive 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

Interactive 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

Interactive Box 3.3 Heterozygosity over time in a finite population

3.5. Estimating effective population size

Different types of effective population size

Interactive 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

Interactive 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

Interactive Box 3.6 Build your own coalescent genealogies

3.7. Effective population size in the coalescent model

Interactive Box 3.7 Simulating gene genealogies in populations with different effective sizes

Coalescent genealogies and population bottlenecks

Coalescent genealogies in growing and shrinking populations

Interactive Box 3.8 Coalescent genealogies in populations with changing size

3.8. Genetic drift and the coalescent with other models of life history

End of Chapter Exercises

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

Two-island model

Interactive Box 4.1 Continent-island model of gene flow

Interactive 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

Interactive Box 4.3 Average exclusion probability for a locus

4.4. Fixation indices to summarize the pattern of population subdivision

Problem Box 4.2 Compute FISs, FST, and FIT

Estimating fixation indices

4.5. Population subdivision and the Wahlund effect

Interactive 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

Interactive 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

Interactive Box 4.6 Genotype assignment and clustering

Math Box 4.3 Bayes Theorem

Empirical assignment methods

Interactive Box 4.7 Visualizing principle components analysis

4.8. The impact of population structure on genealogical branching

Combining coalescent and migration events

Interactive 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

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

Interactive 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

Interactive Box 5.2 Muller's Ratchet

5.3. Mutation models

Mutation models for discrete alleles

Interactive 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

Interactive Box 5.4 Simulating irreversible and two-way mutation

Interactive Box 5.5 Heterozygosity and homozygosity with two-way mutation

5.5. The coalescent model with mutation

Interactive Box 5.6 Build your own coalescent genealogies with mutation

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

Interactive 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

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

Interactive 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

Interactive Box 7.2 Frequency-dependent natural selection

Natural selection with density-dependent fitness

Interactive 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

Interactive Box 7.4 The balance of natural selection and genetic drift at a diallelic locus

The balance between natural selection and mutation

Genetic load

Interactive 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

Interactive Box 7.6 Build an ancestral selection graph

Contents note continued: 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

8.1. Neutral theory

Polymorphism

Divergence

Nearly neutral theory

Interactive 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

Interactive Box 8.2 Compare nucleotide substitution models

DNA polymorphism measured by segregating sites and nucleotide diversity

Interactive 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

Interactive 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

Interactive Box 8.5 Build an ancestral recombination graph

Consequences of recombination

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 (V GxE)

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

Interactive Box 9.1 Estimating heritability with parent-offspring regression

Response to selection on correlated traits

Interactive Box 9.2 Response to natural selection on two correlated traits

Long-term response to selection

Interactive Box 9.3 Response to selection and the number of loci that cause quantitative trait variation

Neutral evolution of quantitative traits

Interactive 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

Interactive Box 9.5 Effect sizes and response to selection at QTLs

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 Al allele

Problem Box 10.2 Compute average effects for IGF1 in dogs

10.4. Breeding value and dominance deviation

Interactive Box 10.1 Average effects, breeding values, and dominance deviations

Dominance deviation

10.5. Components of total genotypic variance

Interactive 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

Problem A.1 Estimating the variance

Interact box A.1 The central limit theorem

Covariance and Correlation

Further reading

Problem box answers.

Notes:

Includes bibliographical references and index.

Other Format:

Online version: Hamilton, Matthew B., Population genetics

ISBN:

9781118436943

1118436946

OCLC:

1244490560

Publisher Number:

99988112455