A Primer of Population Genetics / Edition 3

by Daniel L. Hartl

Overview

In response to many requests, A Primer of Population Genetics, Third Edition, has been dramatically shortened and streamlined for greater accessibility. Designed primarily for undergraduates, it will also serve for graduate students and professionals in biology and other sciences who desire a concise but comprehensive overview of the field with a primary focus on the integration of experimental results with theory. The abundance of experimental data generated by the use of molecular methods to study genetic polymorphisms sparked a transformation in the field of population genetics. Present in virtually all organisms, molecular polymorphisms allow populations to be studied without regard to species or habitat, and without the need for controlled crosses, mutant genes, or for any prior genetic studies. Thus a familiarity with population genetics has become essential for any biologist whose work is at the population level. These fields include evolution, ecology, systematics, plant breeding, animal breeding, conservation and wildlife management, human genetics, and anthropology. Population genetics seeks to understand the causes of genetic differences within and among species, and molecular biology provides a rich repertoire of techniques for identifying these differences.

The book is organized as a user's guide to population genetics. Chapter 1 starts with the basic concepts of molecular genetics and examines the principal methods by which DNA (or proteins) can be manipulated to reveal genetic polymorphisms in any population. Chapter 1 also includes the principles of population genetics underlying the organization of genetic variation in populations, with special emphasis on random mating, linkage equilibrium and disequilibrium, and inbreeding.

Chapter 2 examines the evolutionary processes that can change allele frequencies, including mutation, migration and population admixture, natural selection of various types, and random genetic drift. This chapter also includes an elementary explanation of the diffusion equations as used in population genetics.

Chapter 3 is the core of molecular population genetics. It includes the analysis of nucleotide polymorphism and diversity based on coalescents, patterns of change in nucleotide and amino acid sequences with special emphasis on codon usage bias and amino acid polymorphisms, inferences based on comparisons of levels of polymorphism and divergence, molecular phylogenetics, and the population dynamics of transposable elements.

Chapter 4 focuses on complex traits whose expression is influenced by multiple genes and environmental factors. It examines genetic effects on the components of phenotypic variation and the correlations between relatives, the evolution of quantitative traits in natural populations, and comes full circle with the use of molecular polymorphisms and candidate genes in the identification of quantitative trait loci underlying complex inheritance.

As for mathematical rigor, while there are some equations, the emphasis is on explanation rather than derivation. Only elementary algebra is necessary to follow most of the material, but a familiarity with basic calculus is helpful for understanding diffusion equations, Poisson random fields, and complex threshold traits. Mathematical symbols are used consistently throughout the book, and when results from the theoretical literature are quoted, the original symbols have been changed as necessary to maintain consistency.

Modern population genetics makes liberal use of acronyms—these are all defined in the text, and their interrelations and implications are discussed. For ease of reference there is a glossary of acronyms and other common abbreviations used in population genetics. The text also includes numerous practical examples showing how the theoretical concepts are applied to actual data, as well as chapter-end problems.

Product Details

ISBN-13:	9780878933044
Publisher:	Sinauer Associates is an imprint of Oxford University Press
Publication date:	10/06/1999
Edition description:	REVISED
Pages:	221
Product dimensions:	8.90(w) x 6.10(h) x 0.50(d)

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.

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

Editorial Reviews

Hartl (population biology, Harvard U.) provides graduate and advanced undergraduate students, as well as scientists in allied fields, with a concise but thorough introduction to population genetics. Four sections address genetic variation, the causes of evolution, molecular population genetics, and the genetic architecture of complex traits. Annotation c. Book News, Inc., Portland, OR (booknews.com)

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