Bacteriophages as Drivers of Evolution

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Preface Glossary of Terms Acknowledgments Contents Abbreviations Part I: Introductions Chapter 1: Bacteriophages, a Brief Introduction 1.1 Introduction to Phages and Their Biology 1.2 Most Phages Lyse Their Hosts to Release Virion Progeny 1.3 Some Variations on the Concept of Lysogeny 1.4 Phage Infections Start with Adsorption 1.5 Some Phages Can Transport Bacterial DNA Between Bacteria via Transduction References Chapter 2: A Closer Overview of Phage Infections 2.1 Lytic Cycles Kill Bacteria but also Produce New Phage Virions 2.2 Some Vagaries of Lysogenic Cycles 2.3 Looking at Lysogenic Cycles from Ecological Perspectives 2.4 Looking at Lysogenic Cycles from Evolutionary Perspectives 2.5 Chronic Cycles Release New Phage Virions Without Killing Host Bacteria References Chapter 3: Evolutionary Biology Basics 3.1 Introduction to Evolution 3.2 The No-Evolution Default Assumption 3.2.1 Mutational Change as a Violation of Hardy-Weinberg Equilibrium 3.2.2 Sampling Error as a Violation of Hardy-Weinberg Equilibrium: Genetic Drift 3.2.3 Genetic Migration as a Violation of Hardy-Weinberg Equilibrium 3.2.4 Natural Selection as a Violation of Hardy-Weinberg Equilibrium 3.3 Natural Selection and Darwinian Fitness: Relative and Absolute References Chapter 4: Brief Introduction to Phage Ecology 4.1 Phage Organismal Ecology 4.2 Phage Population Ecology 4.3 Phage Community Ecology 4.4 Prophages Are at the Interface of Phage Population and Community Ecologies 4.5 Mobile Genetic Elements Parasitizing Phages References Part II: Mutation, Genetic Drift, and Non-Random Mating Chapter 5: Bacterial Mutation Associated with Phages: Insertions 5.1 Mutations, Mutants, Mutagenesis 5.2 Secondary Insertion Sites 5.2.1 Prophage Integration and Insertional Mutagenesis 5.2.2 Secondary Insertion Sites 5.2.3 Insertions by Non-phage Mobile Genetic Elements 5.3 For Phage Mu, Insertional Mutagenesis Is a Key Aspect of Its Infection Process 5.4 CRISPR Spacer Sequences Are and Are Not Insertion Mutations References Chapter 6: Bacterial Mutation Associated with Phages: Deletions 6.1 Pseudogenes 6.2 Genomic Immunity Against Prophages? 6.3 Evidence for the Existence of Genomic Immunity? 6.4 Just how Dangerous Are Prophages? 6.5 Just how Dangerous Are Pseudogenes? 6.6 Bacterial Chromosomal Rearrangements and Prophages References Chapter 7: Genetic Drift and Phages 7.1 Stochasticism Versus Determinism 7.2 Sampling Error 7.3 Reduction of Bacterial Population Size: Genetic Bottlenecking 7.3.1 Ignoring (for Now) Natural Selection 7.3.2 Bacterial Populations Can Display Numerical Vulnerabilities 7.3.3 Consequences of Reducing Bacterial Population Sizes 7.4 Potential Impact of Spatial Structure: Founder Effects References Chapter 8: Phages and Asexual Bacterial Populations 8.1 Introducing Some Natural Selection: Genetic Hitchhiking 8.1.1 Selection for Phage Resistance 8.1.2 Selection Generally for Prophage Properties 8.1.3 Selection Specifically for Superinfection Immunity 8.2 Muller´s Ratchet References Chapter 9: Phage Impact on Non-random Mating Among Bacteria 9.1 Transduction and Panmixis 9.2 Various Limitations on Random Mating 9.2.1 Sampling Error and Non-random Mating 9.2.2 Spatial Structure and Non-random Mating 9.2.3 Assortment and Non-random Mating 9.3 Bacterial Retention of Transduced DNA 9.4 What Happens If There Is No Horizontal Gene Transfer Within Populations? References Part III: Genetic Migration Chapter 10: Genetic Migration and Phages 10.1 Phage-Mediated Introduction of New Alleles into Bacterial Populations 10.2 Assortative Mating Introduced by Phages 10.3 Reciprocal Versus Non-reciprocal Transduction 10.4 Direct and Indirect Reciprocal Transduction 10.5 Stabilizing Versus Disruptive Transduction References Chapter 11: Bacterial Reproductive Isolation and its Violation by Phages 11.1 Barriers to Transduction as Defining Bacterial Species? 11.2 Zones of Paralogy 11.3 All the World´s a Phage 11.4 Moron Accretion References Chapter 12: Phage-Provided Environmental DNA and Superspreading 12.1 Uptake of Naked DNA 12.2 Phage-Generation of eDNA 12.2.1 A General Feature of all Lytic Phages? 12.2.2 A Role for Biofilms? 12.3 Phages as Mediators of `Superspreading´ 12.3.1 Horizontal Gene Transfer Superspreaders? 12.3.2 Phages as Transformation Superspreaders? 12.3.3 Phages as Transduction Superspreaders? 12.4 Temperate Phages as Generators of eDNA References Chapter 13: Transduction of Large Amounts of DNA 13.1 Generalized Transduction 13.1.1 Criteria for Generalized Transduction 13.1.2 Headful Packaging 13.1.3 Selection Against Rather Than for Generalized Transduction 13.2 Homologous Recombination Versus Illegitimate Recombination 13.3 Genomic Islands 13.4 Generalized Transduction of Plasmids References Part IV: Prophage-Encoding of Bacterium-Expressed Genes Chapter 14: Phage Morons 14.1 What Is a Moron? (Narrow Sense) 14.1.1 Not Useful Especially During Productive Cycles 14.1.2 Newly Acquired Lysogenic Converting Gene 14.2 What Isn´t a Moron? (Narrow Sense) 14.2.1 Morons as Products of Illegitimate Recombination 14.2.2 Morons as Products of Specialized Transduction 14.2.3 Broadening the Definition of Specialized Transduction to Include All Morons 14.2.4 Diversity Even with Specialized Transduction Sensu Stricto? 14.3 Limitations on Phage Acquisition of Additional Genes 14.3.1 Limitations on Encapsidation by Phage Genome Sizes 14.3.2 The Problem of Insertional Mutagenesis 14.3.3 Lack of a Selective Benefit 14.4 Morons as Lysogenic Converting Genes References Chapter 15: Why Lysogenic Conversion? 15.1 More than Lytic Cycle Buttressing of Accessory Gene Encoding? 15.2 A Plethora of Possible Selective Mechanisms 15.3 Indirect Selection for Lysogenic Conversion 15.4 Direct selection for Lysogenic Conversion 15.5 Lysogenic Conversion and Ecotypes 15.6 Phage-Encoded Phage Resistance References Chapter 16: Prophages Preventing Phage Superinfection 16.1 Superinfection Immunity 16.1.1 Selection for Diversification in Phage Immunity Types 16.1.2 Superinfection Immunity as a Benefit to Bacteria 16.2 Superinfection Exclusion 16.2.1 Superinfection Exclusion in a Non-temperate Phage 16.2.2 Why Should Temperate Phages Express Superinfection Exclusion? 16.3 Prophage Encoding of Other Phage-Resistance Mechanisms References Chapter 17: Domestication of Phage Genes 17.1 Merging of Genomes 17.2 Merging of Phage Genomes 17.3 Merging of Phage and Bacterial Genomes 17.4 Phage Gene Domestication without Prophage Integration 17.5 Getting Rid of Plasmid Prophage Genes? References Part V: Phage Resistance Chapter 18: Resistance to Phages, Part I: Overview 18.1 Categorizing Phage Resistance by Outcomes 18.2 Avoidance of Phage Infection 18.3 Negation of Phage Infections 18.4 Bacterial Self-Sacrifice upon Phage Infection 18.5 Delay of Phage Propagation 18.6 Summary References Chapter 19: Resistance to Phages, Part II: Bacteria Live! 19.1 Avoidance of Phage Genome Uptake 19.1.1 Blocking Adsorption 19.1.2 Blocking Phage Genome Uptake 19.1.3 Blocking Virion Encounter with the Bacterial Surface 19.2 Negating Phage Infections Soon after Initiation 19.2.1 Gains and Losses of Gene Function, and Positive Selection 19.2.2 Restriction as a Concept: A Bit of History 19.2.3 Bacteriophage Exclusion (BREX) as a Mechanism of Negation 19.2.4 CRISPR-Cas, Not Always Resulting in Phage-Infection Negation? References Chapter 20: Resistance to Phages, Part III: Bacteria Die 20.1 The Bacterial Self-Sacrifice of Abortive Infections 20.1.1 The Need for Making Distinctions 20.1.2 Self-Sacrifice Acquisition 20.1.3 Negative Selection for Bacterial Self-Sacrifice 20.1.4 Kin Selection for Bacterial Self-Sacrifice 20.2 Delay: Slowing Down Phage Population Growth 20.2.1 Temporary Protection of Microcolonies 20.2.2 A Discovery Challenge 20.2.3 Some Examples of Delay 20.3 Considerations of Costs and Further Considerations of Ecology References Chapter 21: Bacterial Mutation to Phage Resistance 21.1 A Plethora of Possible Targets of Mutation? 21.1.1 Why Everything but Mutation to Avoidance Is Rare 21.1.2 Blocking Lysin Action toward Self-Sacrifice? 21.2 Rates of Mutation to Resistance 21.2.1 Rates Versus Frequencies 21.2.2 Measurements 21.3 A Wee Bit of Advice References Chapter 22: Pleiotropic Costs of Phage Resistance 22.1 Antagonistic Pleiotropies 22.2 Some History 22.2.1 Demerec and Fano 1945 22.2.2 Some Historical Re-calculations 22.3 A Sampling of More Modern Studies References Part VI: Natural Selection Chapter 23: Concepts of Natural Selection in Light of Phage Exposure 23.1 Higher Fitness 23.2 Beneficial Alleles and Adaptation 23.3 Historical Contingencies 23.4 Hard Selection and Soft Selection 23.5 Coevolution References Chapter 24: Frequency-Dependent Selection in Light of Phage Exposure 24.1 Ecological Versus Evolutionary: Three Distinctions 24.2 Stabilizing, Disruptive, Polymorphic, Monomorphic 24.3 Disruptive Frequency-Dependent Selection-Extracellular Toxins 24.4 Disruptive Frequency-Dependent Selection-Induced Prophages 24.5 Frequency Dependence or Instead Density Dependence? 24.5.1 Density Dependence 24.5.2 The Lysogens Are the Exploiters in Disruptive Frequency-Dependent Selection 24.5.3 Or Neither Lysogen Frequency Nor Lysogen Density Dependence? 24.6 Stabilizing Frequency-Dependent Selection Involving Phages 24.6.1 Again, Frequency Dependence or Density Dependence? 24.7 Killing the Winner 24.8 Stabilizing Frequency-Dependent Selection Mimicking Muller´s Ratchet? References Chapter 25: A Primer on Phage-Bacterium Antagonistic Coevolution 25.1 Preamble 25.2 Introduction to Coevolution and Antagonistic Coevolution 25.2.1 Evolution of Interactions 25.2.2 Antagonistic Coevolution 25.3 Short Historical Overview of Phage-Bacterium Antagonistic Coevolution 25.4 Brief Primer on Phage-Bacterium Antagonistic Coevolution 25.5 Different Faces of Phage-Bacterium Antagonistic Coevolution 25.5.1 How Long Must Chains Be? 25.5.2 Greater Constraints on Phage Evolution? 25.5.3 Ecological Scenarios 25.6 An Indefinite Series of Coevolutionary Change? 25.7 Coda References Glossary Index