Table of Contents

Preface
Acronyms and Abbreviations


Chapter 1. Genetic Variation

Genetic and Molecular Essentials
Genotype and Phenotype
Gene Expression
DNA Cleavage, Manipulation, and Amplification

Types of Polymorphisms
DNA Polymorphisms
Uses of DNA Polymorphisms
Protein Polymorphisms
Gene and Genotype Frequencies

Organization of Genetic Variation
Populations
Models
Random Mating
The Hardy-Weinberg Principle
Implications of Random Mating
Chi-square Test for HWE
Recessive Alleles Hidden in Heterozygotes
Multiple Alleles and X-Linked Genes
Multiple Loci: Linkage and Linkage Disequilibrium

Inbreeding
Genotype Frequencies with Inbreeding
The Inbreeding Coefficient
Inbeeding Depression
Calculation of the Inbreeding Coefficient from Pedigrees
Regular Systems of Mating

Further Readings
Problems


Chapter 2. The Causes of Evolution

Mutation
Forward Mutation
Reversible Mutation
Remote Inbreeding in a Finite Population
Equilibrium Heterozygosity with Mutation

Migration
The Island Model of Migration
How Migration Limits Genetic Divergence
Wahlund's Principle
Hierarchical Population Structure

Natural Selection
Haploid Selection
Diploid Selection
Time Required for Changes in Gene Frequency
Overdominance and Underdominance
Mutation-Selection Balance
More Complex Modes of Selection

Random Genetic Drift
Diffusion Approximations
Probability of Fixation and Time to Fixation
Effective Population Number

Further Readings
Problems


Chapter 3. Molecular Population Genetics

Molecular Polymorphisms
The Information Content of Molecular Sequences
The Coalescent
Nucleotide Polymorphism
Nucleotide Diversity
Tajima's D Statistic

Patterns of Change in Nucleotide and Amino Acid Sequences
Synonymous and Nonsynonymous Substitutions
Codon Usage Bias
Selection for Optimal Codons and Amino Acids
Selective Sweeps versus Background Selection

Polymorphism and Divergence
The Hudson-Kreitman-Aguadé (HKA) Test
The McDonald-Kreitman Test
Polymorphism and Divergence in a Poisson Random Field
Convergence to Adaptation

Molecular Phylogenetics
The Multiple-Hit Problem
Phylogenetic Inference
Molecular Clocks

Transposable Elements
Insertion Sequences and Transposons in Bacteria
Transposable Elements in Eukaryotes

Further Readings
Problems


Chapter 4. The Genetic Architecture of Complex Traits

Types of Complex Traits

Phenotypic Variation

Genetics and Environment
Genotypic Variance and Environmental Variance
Broad-Sense Heritability
Genotype-Environment and Other Interactions
Genetic Effects on Complex Traits
Components of Genotypic Variation

Artificial Selection
Prediction Equation for Individual Selection
Genetic Basis of Complex Traits
Change in Allele Frequency
Change in Mean Phenotype

Correlation between Relatives
Parent-Offspring Correlation
Heritability Estimates from Resemblance between Relatives
Offspring-on-Parent Regression

Quantitative Genetics of Natural Populations
Directional Selection with Mutation-Selection-Drift
Stabilizing Selection with Mutation-Selection-Drift
Antagonistic Pleiotropy

Complex Traits with Discrete Expression
Threshold Traits: Genes as Risk Factors
Heritability of Liability
Applications to Human Disease
Linkage Analysis and Lod Scores

Quantitative Trait Loci (QTLs)
Number of Genes
QTL Mapping
Candidate Genes

Further Readings
Problems


Literature Cited
Index

About the Author

Daniel L. Hartl is a Professor of Biology in the Department of Organismic and Evolutionary Biology at Harvard University. He received his Ph.D. in Genetics from the University of Wisconsin-Madison, with James F. Crow, then did postdoctoral work with Spencer W. Brown at the University of California-Berkeley. Prior to taking on his current role at Harvard in 1993, Dr. Hartl held teaching positions at the University of Minnesota-St. Paul, Purdue
University, the University of Zurich, and the Washington University School of Medicine. In addition to Principles of Population Genetics, Third Edition (written with Andrew G. Clark), he has authored or co-authored several
other genetics books. Dr. Hartl served as President of the Genetics Society of America in 1989. His research interests include population genetics, molecular evolutionary genetics, and molecular genetics.