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Principles of Population Genetics, Fourth Edition
Daniel L. Hartl and Andrew G. Clark
2007
565 pages, 199 illustrations
casebound
About the Book
Principles of Population Genetics, Fourth Edition is a thoroughly updated introduction to the field that is at last ascending to its rightful position of centrality to evolutionary genomics and human genetics. Rapid and inexpensive genotyping and sequencing have produced a profusion of data on genetic variation, along with a pressing need to inform students from many fields about the models that describe the underlying processes that give rise to observed patterns of genetic variation. This book provides a balanced presentation of theory and observation for students at the undergraduate and graduate levels as well as newcomers from fields like human genetics. The logical development of the models of population genetics encourages a deeper understanding of the principles, and the text has been rewritten with the goal to optimize its use as a teaching aid. It introduces the principles of genetics and statistics that are relevant to population studies, and examines the forces affecting genetic variation from the molecular to the organismic level. Integrated throughout the book are descriptions of molecular methods used to study variation in natural populations, as well as explanations of the relevant estimation theory using actual data.
Chapter 1 presents the fundamental observations and means for quantifying amounts and structure of genetic variation in natural populations. Chapter 2 gives a detailed examination of the implications of random mating for one locus and multiple loci and establishes the basic principles for thinking about mathematical models of variation. Chapter 3 presents the classic Wright-Fisher model as well as the coalescent approaches to random genetic drift. Chapter 4 adds mutation to models of drift and lays down the foundations for the neutral theory of molecular evolution. Natural selection in its many guises gets a thorough coverage in Chapter 5. Chapter 6 examines population subdivision and its consequences for the distribution of genetic variation among subpopulations, including the hierarchical F statistics used in estimating these effects. Molecular population genetics, including applications of coalescent theory, is the subject of Chapter 7. Evolutionary quantitative genetics is covered in Chapter 8, including an up-to-date treatment of the use of molecular markers for mapping and assisting in selection of quantitative characters. Chapter 9 is a new addition and covers the exciting field of population genomics, or the analysis of population genetic principles at a genome-wide scale. Finally, because of the explosion in genome-wide polymorphism data in humans and the realization that many problems in empirical population genetics need to be tuned to special, non-equilibrium circumstances of human populations, the authors devote Chapter 10 to human population genetics.
Applications of principles discussed in the text are illustrated with numerous examples of worked problems, using actual data. Many vital Web links are scattered throughout the text to connect the material to up-to-the-minute progress in this exciting field. Each chapter ends with a complete summary and offers several problems for solution, to reinforce and further develop the concepts.
About the Author(s)
Daniel L. Hartl is Higgins Professor of Biology in the Department of Organismic and Evolutionary Biology at Harvard University. His laboratory studies population genetics, genomics, and molecular evolution. He has been honored with the Samuel Weiner Outstanding Scholar Award and Medal, the Medal of the Stazione Zoologica Anton Dohrn, and is an elected member of the National Academy of Sciences and the American Academy of Arts and Sciences. He is also a Past President of the Genetics Society of America and the Society for Molecular Biology and Evolution. Hartl's Ph.D. was awarded by the University of Wisconsin, he did postdoctoral studies at the University of California in Berkeley, and he has been on the faculty of the University of Minnesota, Purdue University and Washington University Medical School in St. Louis. In addition to more than 300 scientific articles, Hartl has authored or coauthored 24 books.
Andrew G. Clark is Professor of Population Genetics in the Department of Molecular Biology and Genetics at Cornell University. Earning a Ph.D. in Population Genetics at Stanford University, he did postdoctoral work at Arizona State University and the University of Aarhus, Denmark, and a sabbatical at the University of California at Davis. Prior to joining the Cornell faculty in 2002, he was a professor in the Department of Biology at Pennsylvania State University. Dr. Clark's research focuses on the genetic basis of adaptive variation in natural populations, with emphasis on quantitative modeling of phenotypes as networks of interacting genes. He was elected Fellow of the American Association for the Advancement of Science in 1994, and serves on review panels for the NIH, NSF, and the Max Planck Society. He also served as President of the Society for Molecular Biology and Evolution, and is on the Advisory Council for the National Human Genome Research Institute.
Reviews and Commentary
“It is a pleasure to read this new edition of a classical textbook on population genetics. It shows very convincingly how population genetics has been revamped in the past 20 years by the introduction of new statistical and computational methods (in particular, coalescent theory), and the advent of genomic data, as well as how these developments changed a formerly rather arcane science and moved it toward the center of modern biology. … In summary, the essence of population genetics is nicely condensed in this book. The presentation is wonderfully balanced between theory and observation, as well as classical and recent data sets and analysis tools.”
—Wolfgang Stephan, The Quarterly Review of Biology
Table of Contents
1. Genetic and Phenotypic Variation
- Relevance of Population Genetics
- Phenotypic Variation in Natural Populations
- Continuous Variation: The Normal Distribution
- Mean and Variance
- The Central Limit Theorem
- Discrete Mendelian Variation
- Multiple-Factor Inheritance
- Maintenance of Genetic Variation
- Molecular Population Genetics
- Electrophoresis
- Allele Frequencies and Genotype Frequencies
- Polymorphism and Heterozygosity
- Allozyme Polymorphisms
- Inferences from Allozyme Polymorphisms
- Polymorphisms in DNA Sequences
- Restriction Enzymes
- The Polymerase Chain Reaction
- Single Nucleotide Polymorphisms
- Synonymous and Nonsynonymous Polymorphisms
- Segregating Sites and Nucleotide Mismatches
- Utility of Genetic Polymorphisms
- Summary
2. Organization of Genetic Variation
- Random Mating
- Nonoverlapping Generations
- The Hardy-Weinberg Principle
- Random Mating of Genotypes versus Random Union of Gametes
- Implications of the Hardy-Weinberg Principle
- Testing for Hardy-Weinberg Equilibrium
- Difficulties in Testing for Hardy-Weinberg Equilibrium
- Complications of Dominance
- Frequency of Heterozygotes
- Extensions of the Hardy-Weinberg Principle
- Three or More Alleles
- X-Linked Genes
- Linkage and Linkage Disequilibrium
- Difficulties in Testing for Linkage Equilibrium
- Relative Measures of Linkage Disequilibrium: D′ and r2
- Causes of Linkage Disequilibrium
- Linkage Disequilibrium Due to Population Admixture
- Linkage Disequilibrium Due to Reduced Recombination
- Summary
3. Random Genetic Drift
- Random Genetic Drift and Binomial Sampling
- The Wright-Fisher Model of Random Genetic Drift
- The Diffusion Approximation
- An Approach Looking Forward
- An Approach Looking Backward
- Absorption Time and Time to Fixation
- Random Drift in a Subdivided Population
- Effective Population Size
- Fluctuation in Population Size
- Unequal Sex Ratio, Sex Chromosomes, Organelle Genes
- Variance in Offspring Number
- Effective Size of a Subdivided Population
- Gene Trees and Coalescence
- Coalescent Effective Size
- Coalescence with Population Growth
- Coalescent Models with Mutation
- Applications of Coalescent Methods
- Theoretical Implications of Coalescence
- Coalescent Models with Recombination
- Linkage Disequilibrium Mapping
- Summary
4. Mutation and the Neutral Theory
- Mutation
- Irreversible Mutation
- Reversible Mutation
- Mutation and Random Genetic Drift
- Probability of Fixation of a New Neutral Mutation
- The Neutral Theory of Molecular Evolution
- The Infinite-Alleles Model
- The Ewens Sampling Formula
- The Ewens-Watterson Test
- Infinite-Sites Model
- Nucleotide Polymorphism and Nucleotide Diversity
- Tajima’s D Statistic
- The Fu and Li Test of Fit to Neutral Coalescence
- Mutation and Recombination
- A Model for the Evolutionary Benefit of Recombination
- Muller’s Ratchet
- Piecewise Recombination in Bacteria
- Animal Mitochondrial DNA
- Summary
5. Darwinian Selection
- Selection in Haploid Organisms
- Discrete Generations
- Continuous Time
- Change in Allele Frequency
- Darwinian Fitness and Malthusian Fitness
- Selection in Diploid Organisms
- Change in Allele Frequency in Diploids
- Marginal Fitness and Selection with Multiple Alleles
- Application to the Evolution of Insecticide Resistance
- Equilibria with Selection
- Overdominance
- Local Stability
- Heterozygote Inferiority
- Stable Equilibria with Multiple Alleles
- Adaptive Topography and the Role of Random Genetic Drift
- Mutation-Selection Balance
- Equilibrium Allele Frequencies
- The Haldane-Muller Principle
- More Complex Types of Selection
- Differential Selection in the Sexes
- X-linked Genes
- Frequency-Dependent Selection
- Density-Dependent Selection
- Fecundity Selection
- Age-Structured Populations
- Heterogeneous Environments and Clines
- Diversifying Selection
- Gametic Selection
- Meiotic Drive
- Multiple Loci and Gene Interaction: Epistasis
- Evolution of Recombination Rate
- Sexual Selection
- Kin Selection
- Interdeme Selection in Geographically Subdivided Populations
- Selection in a Finite Population
- Weak Selection and the Nearly Neutral Theory
- Genetic “Draft”
- Summary
6. Inbreeding, Population Subdivision, and Migration
- Inbreeding
- The Inbreeding Coefficient
- Genotype Frequencies with Inbreeding
- Genetic Effects of Inbreeding
- Calculation of the Inbreeding Coefficient from Pedigrees
- Regular Systems of Mating
- Population Subdivision
- Reduction in Heterozygosity Due to Population Subdivision
- Average Heterozygosity
- Wright's F Statistics
- Linanthus Revisited: Evidence for Selection Associated with Flower Color
- Inference of Population Structure from Multilocus Genotype Data
- The Wahlund Principle
- Wahlund's Principle and the Fixation Index
- Genotype Frequencies in Subdivided Populations
- Relation between the Inbreeding Coefficient and the F Statistics
- Assortative Mating
- Migration
- One-Way Migration
- The Island Model of Migration
- How Migration Limits Genetic Divergence
- Estimates of Migration Rates
- Coalescence-Based Estimates of Migration
- Migration-Selection Balance
- Summary
7. Molecular Population Genetics
- The Neutral Theory and Molecular Evolution
- Theoretical Principles of the Neutral Theory
- Estimating Rates of Molecular Sequence Divergence
- Rates of Amino Acid Replacement
- Rates of Nucleotide Substitution
- Statistical Fitting of Nucleotide Substitution Models
- The Molecular Clock
- Variation across Genes in the Rate of the Molecular Clock
- Variation across Lineages in Clock Rate
- The Generation-Time Effect
- The Overdispersed Molecular Clock and the Neutral Theory
- The Nearly Neutral Theory
- Patterns of Nucleotide and Amino Acid Substitution
- Calculating Synonymous and Nonsynonymous Substitution Rates
- Codon Substitution Models
- Observations of Synonymous and Nonsynonymous Substitution Rates
- Polymorphism within Species
- Implications of Codon Usage Bias
- Polymorphism and Divergence in Nucleotide Sequence—The McDonald-Kreitman and HKA Tests
- Polymorphism and Divergence in Noncoding Sequences
- Impact of Local Recombination Rates
- Substitution Models for Structural RNA Genes
- Gene Genealogies
- Hypothesis Testing Using Trees
- Mitochondrial and Chloroplast DNA Evolution
- Chloroplast DNA and Organelle Transmission in Plants
- Maintenance of Variation in Organelle Genomes
- Evidence for Selection in mtDNA
- Molecular Phylogenetics
- Algorithms for Phylogenetic Tree Reconstruction
- Distance Methods versus Parsimony
- Bootstrapping and Statistical Confidence in a Tree
- Bayesian Methods
- Trans-Species Polymorphism
- Multigene Families
- Concerted Evolution
- Subfunctionalization
- Birth-and-Death Process
- Summary
8. Evolutionary Quantitative Genetics
- Types of Quantitative Traits
- Resemblance between Relatives and the Concept of Heritability
- Artificial Selection and Realized Heritability
- Contribution of New Mutations to the Response to Selection
- Prediction Equation for Individual Selection
- Limits to Selection
- Genetic Models for Quantitative Traits
- Change in Allele Frequency
- Change in Mean Phenotype
- Linearity of Response
- Components of Phenotypic Variance
- Genetic and Environmental Sources of Variation
- Components of Genotypic Variation
- Covariance among Relatives
- Twin Studies and Inferences of Heritability in Humans
- Estimation of Genetic Variance Components in Natural Populations
- Norm of Reaction, Threshold Traits, and Genetic Correlation
- Norm of Reaction and Phenotypic Plasticity
- Threshold Traits: Genes as Risk Factors in Disease
- Genetic Correlation and Correlated Response
- Evolutionary Quantitative Genetics
- Inference of Selection from Phenotypic Data
- Evolution of Multiple Intercorrelated Traits
- Random Genetic Drift and Phenotypic Evolution
- Mutational Variance and Mutation–Accumulation Experiments
- Mutation-Selection Balance for Quantitative Traits
- Genes That Affect Quantitative Traits
- The Number of Genes Affecting Quantitative Traits
- Methods for Mapping QTLs
- Summary
9. Population Genomics
- Evolution of Genome Size and Composition
- Organismic Complexity and the C-Value Paradox
- Base Composition of Genomic DNA
- Genome-Wide Patterns of Polymorphism
- Excess Polymorphism in Subtelomeric Regions
- Polymorphism and Rates of Recombination
- Hitchhiking versus Background Selection
- Linkage Disequilibrium and Haplotype Structures
- Decline of Linkage Disequilibrium with Genetic Distance
- Differences between Species
- Comparison of Nonsynonymous and Synonymous Divergence
- Positive Selection
- Exploiting a Phylogenetic Signal
- Polymorphism and Divergence
- Compensated Pathogenic Deviations
- Structure–Function Analysis
- Sexual Selection and the Sex Chromosomes
- Faster-Male Molecular Evolution
- Molecular Evolution of Genes in the X Chromosome
- Haldane's Rule
- Demasculinization of the X Chomosome
- Transposable Elements
- Diverse Types of Transposable Elements
- Factors Controlling the Population Dynamics of Transposable Elements
- Insertion Sequences and Composite Transposons in Bacteria
- Transposable Elements in Eukaryotes
- Population Dynamics of Transposable Elements
- Nonuniformity of Transposition Rates
- Horizontal Transmission of Transposable Elements
- Summary
10. Human Population Genetics
- Human Polymorphism
- Public SNP Resources and the HapMap Project
- Population Genetic Inferences from Human SNPs
- Ascertainment Bias of SNP Genotypes
- Departures from Hardy-Weingerg Frequencies
- Site Frequency Spectrum and Human Population Growth
- Rooting Human Polymorphism
- Inference of Inhomogeneities in the Mutation Process
- Inferences about Male and Female Mutation Rates
- Linkage Disequilibrium across the Human Genome
- The Landscape of Human Linkage Disequilibrium
- Inferences about Local Rates of Recombination
- Population Structure Inferred from Human Polymorphism
- Multilocus Methods of Inference of Stratification
- Heterogeneity in Linkage Disequilibrium across Human Populations
- Linkage Disequilibrium in Admixed Populations: Admixture Mapping
- Inbred Populations and Homozygosity Mapping
- Mendelian Disease and Population Genetics
- Mutation-Selection Balance
- Dating the Origin of Mutant Alleles
- Genetic Basis for Variation in Risk of Complex Disease
- Mapping Methods Based on Linkage
- Linkage Disequilibrium Mapping
- Genome-Wide Association Studies
- Seeking Signatures of Human-Specific Genetic Adaptations
- Interspecific Divergence
- McDonald-Kreitman and Poisson Random Field Tests
- Local Distortions in Linkage Disequilibrium
- FST Tests
- Genome Scans for Selection-Skewed Site Frequency Spectrum
- Human Origins
- Neanderthal Genome Sequence
- Summary
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