”群体遗传学“经典之作

在入门级的“群体遗传学”的教科书中，Andy和 Daniel 的这本书堪称经典之作。 三十多年的考验和补充，使其成为北美的“群遗遗传学”课程的必备参考书。希望看到这本书的英文引进版本.

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.

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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.

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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

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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