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Population Biology of Plant Path: Genetics, Ecology, and Evo
Population Biology of Plant Path: Genetics, Ecology, and Evo
"I found this most instructive, well-written, and with examples well-explained. I commend it not only to plant pathologists, but to fungal systematists endeavoring to unravel situations encountered in fungal populations in nature but who rarely consider the plant pathological literature."
—IMA Fungus

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Just like nature itself, the field of population biology in plant pathogens is constantly evolving, yet it has been more than 25 years since a comprehensive book on this important topic has been produced.

Population Biology of Plant Pathogens fills this information gap by explaining how population genetics are applied in plant pathology today. 

This interpretive guide is ideal for teachers and students of graduate-level plant pathology courses, as it provides a conceptual foundation of the genetics, ecology and evolution of plant pathogen populations while also introducing a wide array of examples that include plant pathogens of all major types: fungi, oomycetes, bacteria, viruses, and nematodes.

Researchers and population biologists who wish to specifically study population biology in plant pathogens will also find this book an important tool, as it explains the basic tenets of population biology, population genetics, and the evolution of plant pathogens, and illustrates their applications in epidemiology and applied agriculture.

Population Biology of Plant Pathogens is structured to explain the wonders of evolutionary phenomena in plant pathogens in a logical and orderly fashion

  • Chapters one through six address foundational concepts in population genetics, such as genetic markers, genetic diversity, mutation and random genetic drift, natural selection, and migration and population structure. 
  • Chapters seven and eight cover recombination and clonality
  • Chapters nine and ten address gene-for-gene systems and disease resistance
  • Chapter 11 focuses on emerging plant diseases
  • Chapter 12 illustrates applications of population biology in epidemiology and applied agriculture

Population Biology of Plant Pathogens also contains other important features that further support learning. These include helpful sidebars that highlight topics to initiate discussion; concept summaries at the end of each chapter; a glossary of key terms, a list of commonly used abbreviations; recommended readings; and a comprehensive index.

Author Michael G. Milgroom has been a pioneer and leading researcher in the population genetics and population biology of plant pathogens for nearly 30 years. He has also taught this subject extensively at the graduate level for more than 20 years. His vast knowledge and experience are apparent through the book’s many examples derived from original research, historical accounts, articles, and other sources from himself and his colleagues.


60-Day Evaluation for Instructors

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Population Biology of Plant Pathogens: Genetics, Ecology, and Evolution


1 Introduction to Population Biology and Evolution

Population Genetics
Introduction to Evolutionary Processes

Natural Selection
Mutation
Random Genetic Drift
Migration
Recombination
Interactions among Evolutionary Processes

Challenges in Studying the Population Biology of Plant Pathogens
Hypothesis Testing and Interpretations of Data in Population Biology
The Relevance of Population Biology in Plant Pathology

   Summary of Key Concepts
   Recommended Reading

2 Genetic Markers for Population Genetics

Characteristics of Ideal Genetic Markers

Selective Neutrality
Polymorphisms
Locus Specificity
Minimal Homoplasy
Independent, Unlinked Loci
Codominance
Repeatable, Unambiguous Scoring

Historical Perspectives on Genetic Markers in Plant Pathogens

Phenotypic Markers in Plant Pathogens
Molecular Markers Before the Advent of PCR
Advances in Genetic Markers Because of the Invention of PCR
PCR-Based Markers That Are Not Locus-Specific

Amplified Fragment Length Polymorphisms
Microsatellites

Discovery of Microsatellite Loci
Development and Scoring of Microsatellite Markers

Single Nucleotide Polymorphisms

Multilocus Sequencing and Small-Scale SNP Genotyping
High-Throughput SNP Genotyping with Hybridization Arrays
SNP Discovery and Genotyping Using Next-Generation Sequencing

Ascertainment Bias

Quantitative-Trait Loci and Genome-Wide Association Studies

A Simple Guide for Choosing Genetic Markers

   Summary of Key Concepts
   Recommended Reading

3 Sampling and the Estimation of Genetic Diversity

Defining Populations and Individuals
Random Sampling under Ideal Conditions

Defining a Target Population
Random Sampling from Populations of Plant Pathogens
Spatial Scale of Sampling
Temporal Considerations in Sampling
Sample Sizes and Replication
Sampling Plant Pathogen Populations in Practice
Sporadic Occurrence of Some Organisms
Independence of Sampling Units
Accounting for Underlying Genetic Structure

Genotyping
Allele Frequencies and Diversity at Single Loci

Allele Frequencies
Gene Diversity

Genotypic Diversity

Genotypic Richness
Commonly Used Diversity Indices
Genotypic Evenness
Comparing Genotypic Diversity Between Populations

Diversity Estimated from Relatedness of Multilocus Genotypes
Nucleotide Sequence Diversity
Evolutionary Processes That Increase or Decrease Genetic Diversity

Diversity in Populations of the Late Blight Pathogen, Phytophthora infestans

   Summary of Key Concepts
   Recommended Reading

4 Mutation and Random Genetic Drift

Mutation

Types of Mutation
Estimating Mutation Rates in Bacteria
Estimating Mutation Rates in Eukaryotes
Mutation Rates in RNA Viruses

Random Genetic Drift

Bottlenecks in Plant Virus Populations
Effective Population Size

Mutation and Drift: Muller’s Ratchet and Mutational Meltdown
Mutation and Drift: The Neutral Theory of Evolution

The Infinite-Alleles Model
The Infinite-Sites Model

Gene Genealogies and the Coalescent

Applications of the Coalescent Model

   Summary of Key Concepts
   Recommended Reading

5 Natural Selection

Fitness

Predicted Fitness: Single-Generation Components of Fitness
Realized Fitness: Population Growth Rates
Realized Fitness: Estimation of Relative Fitness in Serial-Passage Competition Experiments
Realized Fitness: Continuous Population Growth Models
Practical Considerations for Conducting Selection Experiments

Selection Acting on Single Genes: Experimental Approaches

Comparison of Isogenic Isolates
Randomizing Alleles to Genetic Backgrounds

Types of Selection

Selection Acting on Quantitative Phenotypes
Selection Acting on Single Genes: Negative, Positive, and Balancing Selection
Density-Dependent Selection
Hitchhiking Selection
Epistatic Selection

Detecting Selection Using Molecular Genetic Markers

Detecting Selection from Within-Population Polymorphisms: Tajima’s D Revisited
Detecting Selection from Divergence among Species: dN/dS Ratios
Trans-Species Polymorphisms and Balancing Selection

Selection for Fungicide Resistance

Genetics of Fungicide Resistance and the Strength of Selection
Estimating Baseline Frequencies of Resistance
Fitness Costs Associated with Fungicide Resistance
Epidemiology and Management of Fungicide Resistance

   Summary of Key Concepts
   Recommended Reading

6 Migration and Population Structure

Direct Estimates of Migration on an Ecological Timescale: Tracking Genotypes
Indirect Estimates of Migration on an Evolutionary Timescale: Population Structure

Fixation Index and Gene Diversity Analysis
Additional Methods for Estimating FST
Estimating the Number of Migrants from FST
Private Alleles and Nearest-Neighbor Methods
Caveats for Interpreting FST and Estimates of Migration Rates
Historical Versus Current Migration and Nonequilibrium Populations
Isolation by Distance

Clustering Methods to Assess Population Structure

Distance-Based Trees
Model-Based Bayesian Clustering Methods
Principal Components Analysis

Estimating Migration Using Coalescent Models
Populations Structured by Selection: Adaptation to Local Environments

Differentiation in Neutral Markers and Phenotypes under Selection
Differentiation of Pathogen Populations on Host Species: Evidence of Host Specialization

Metapopulation Structure

   Summary of Key Concepts
   Recommended Reading

7 Recombination and Randomly Mating Populations

Evolutionary and Ecological Significance of Sex and Recombination

Ecological Implications of Sexual Reproduction in Eukaryotic Plant Pathogens

Sexual Reproduction and Mating Systems in Eukaryotic Plant Pathogens

Mating Systems in Fungi and Oomycetes
Nematode Mating Systems
Mixed Modes of Reproduction

Nonmeiotic Mechanisms of Recombination in Eukaryotes

Gene Conversion
Mitotic Crossing Over
Parasexuality

Recombination in Bacteria

Mechanisms of Bacterial Recombination

Recombination and Reassortment in Plant Viruses

Viral Recombination
Reassortment of Segmented Viral Genomes

Effects of Sex and Recombination on Genotypic Diversity
Random Mating in Diploid Populations

What Is Random Mating?
Hardy–Weinberg Equilibrium
Inbreeding

Linkage Disequilibrium and Tests for Random Mating in Haploid Populations

Causes of Linkage Disequilibrium

   Selection
   Linkage
   Migration and Population Admixture
   Random Genetic Drift

Statistical Analysis of Linkage Disequilibrium
Multilocus Estimation of Linkage Disequilibrium: The Index of Association
Clone Corrections for Estimating Linkage Disequilibrium

Additional Tests of Random Mating

Parsimony Tree-Length Permutation Test
Mating-Type Ratios
Genotypic Diversity

Frequency of Sex When Populations Appear to Be Randomly Mating
Estimating the Frequency of Sex Experimentally

Changes in Linkage Disequilibrium to Estimate the Contribution of Sexual Inoculum
Mark-Release-Recapture Experiments to Estimate Recombination

The Biological Significance of Recombination in Plant Pathogen Populations

   Summary of Key Concepts
   Recommended Reading

8 Clonal Populations

Evolutionary Significance of Asexual Reproduction

Muller’s Ratchet Revisited
Evolutionary Advantages of Asexual Reproduction: The Disadvantages of Sex

Definitions of Clones and Clonal Lineages

Operational Definition of Clonal Lineages

Deviations from Random Mating Revisited

Overrepresentation of Multilocus Genotypes
Linkage Disequilibrium and Correlation among Different Sets of Markers
Excess Heterozygosity in Clonal Diploid Populations

Detecting Recombination

Phylogenetic Incompatibility Between Loci: The Four-Gamete Test
Phylogenetic Incompatibility Between Loci: Incongruence of Gene Trees
Network Analyses to Detect Recombination
Coalescent Methods to Estimate Recombination Rates

Detecting Signs of Sex

Organismal Signs of Sex
Molecular Signs of Sex

Examples of Clonal Plant Pathogens

A Clonal Rust Fungus: Puccinia triticina
A Mitosporic Fungus: Verticillium dahlia
A Mitosporic Fungus with Evidence of Sex and Recombination: Alternaria brassicicola

The Challenges of Inferring Clonality and Recombination

   Summary of Key Concepts
   Recommended Reading

9 Evolution in Gene-for-Gene Systems

Host Plant Immunity and Defenses

The Classic Gene-for-Gene Model

Races in Gene-for-Gene Systems
Selection for Virulent Races: The Breakdown of Resistance

Evolution of New Races

Coevolution in Gene-for-Gene Systems

The Arms Race and Trench Warfare Models of Coevolution

Fitness Costs in Gene-for-Gene Systems

Fitness Costs of Unnecessary High Virulence

   Bacterial Blight of Rice
   Bacterial Spot in Peppers

Fitness Costs of Disease Resistance

Metapopulation Dynamics in Gene-for-Gene Systems

Metapopulation Models of Gene-for-Gene Systems
Empirical Evidence for Metapopulation Structure in Gene-for-Gene Systems

Evolution of Gene-for-Gene Systems in Agriculture

   Summary of Key Concepts
   Recommended Reading

10 Durability and the Deployment of Disease Resistance

Quantitative and Qualitative Resistance
Durability of Quantitative Resistance

Differential Interactions to Detect Pathogen Specificity to Quantitative Resistance
Selection Experiments to Detect Pathogen Specificity to Quantitative Resistance
The Lack of Erosion of Quantitative Resistance

Factors Affecting Durability of Qualitative Resistance in Gene-for-Gene Systems

Epidemiological Factors Affecting Durability in Gene-for-Gene Systems
Fitness of Virulent Races
Predicting Durability Based on Pathogen Population Biology

Race Surveys

Sampling Pathogen Populations
Differential Cultivars for Determining Races
Estimating Effector Allele Frequencies

Breeding for Resistance and Gene Deployment

Screening for Resistance Against Diverse Pathogen Populations
Gene Pyramids
Exploiting Linkage Disequilibrium in Pathogen Populations for Breeding Gene Pyramids

Gene Deployment

Cultivar Mixtures

Integrated Disease Management and Durability

   Summary of Key Concepts
   Recommended Reading

11 Emerging and Reemerging Plant Diseases

Invasive Plant Pathogens: Introductions to New Geographic Areas

Biology of Invasive Plant Pathogens

Phylogeographic Methods to Infer the Sources of Introductions
Speciation and the Evolution of Host Specificity

What Is a Species?
Reproductive Isolation and Speciation
Host-Shift Speciation
Host Shifts and Cospeciation

Mechanisms for the Rapid Evolution of Novel Pathogen Genotypes

Plant Viruses Emerging by Recombination
Interspecific Hybrids in Eukaryotic Plant Pathogens
Horizontal Gene Transfer That Affects Pathogenicity and Virulence

   Horizontal Gene Transfer in Bacteria
   Horizontal Gene Transfer in Eukaryotes

Selection for Novel Pathogen Genotypes

Role of Agriculture and Other Extrinsic Factors in Disease Emergence

Host Populations in Modern Agriculture Promote Disease Emergence
Additional Effects of Agriculture on Pathogen Evolution
Environmental Factors That Promote Disease Emergence

   Climate Change
   Vector Populations
   Cultural Practices

Countermeasures to Reduce the Risk of Disease Emergence

   Summary of Key Concepts
   Recommended Reading

12 Contributions of Population Genetics in Plant Disease Epidemiology

Historical Links Between Population Genetics and Epidemiology
Descriptive Studies of Genetic Variation in Populations of Plant Pathogens

Identification of Cryptic Species
Epidemiological Inferences from Clonal Population Structure
Epidemiological Inferences from Population Subdivision
Epidemiological Inferences about Sexual Reproduction

Direct Tracking of Pathogen Genotypes for Epidemiological Inference

Identifying Sources of Primary Inoculum Using Genetic Markers
Inferences from Spatial Patterns of Pathogen Genotypes

Applications of Genetic Variation to Disease Management: Diagnosis and Quantification of Plant Pathogens
A Critical Assessment of the Relevance of Pathogen Genetic Variation to Plant Disease Management
Future Directions for Population Biology in Plant Pathology

Metagenomics and Plant Microbiomes
Landscape Genetics
Population Genomics and Association Mapping

   Summary of Key Points
   Recommended Reading

Appendix: Genetic Markers Historically Used for Genotyping Plant Pathogens

Glossary

Abbreviations

References

Index

Population Biology of Plant Pathogens is available at a special student discount rate for professors who are ordering for their classes through campus bookstores or for APS student members ordering directly. Student pricing is $150. Please contact customer care for more information about ordering for students or purchasing a book at the student rate.
Publish Date: 2015
Format: 8.5” × 11” hardcover
ISBN: 978-0-89054-450-1
Pages: 399
Images: 151 images
Publication Weight: 4 lbs

By Michael G. Milgroom

Population Biology of Plant Pathogens: Genetics, Ecology, and Evolution

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