Main description:

This monograph emphasizes the many facets of bacterial evolution as impacted by bacterial interactions with phages, as well as, to a lesser degree, the evolutionary impact of phages on other organisms, including other phages.

The book starts with a general overview of bacteriophages. Topics discussed in detail include but are not limited to mutagenesis, migration, natural selection and genetic drift as the drivers of evolution as well as an extensive discussion from the author's unique perspective on phage ecology.

Contents:

Part I. Introductions

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

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

3 Evolution Biology Basics

3.1 Introduction to Evolution

3.2 The No-Evolution Default Assumption

3.3 Natural Selection and Darwinian Fitness: Relative and Absolute

References

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

5 Bacterial Mutation Associated with Phages: Insertion

5.1 Mutations, Mutants, Mutagenesis

5.2 Secondary Insertion Sites

5.3 For Phage Mu, Insertional Mutagenesis Is a Key Aspect of Its Infection Cycle

5.4 CRISPR Spacer Sequences Are and Are Not Insertion Mutations

References

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

7 Genetic Drift and Phages

7.1 Stochasticism versus Determinism

7.2 Sampling Error

7.3 Reduction of Bacterial Population Size: Genetic Bottlenecking

7.4 Potential Impact of Spatial Structure: Founder Effects

References

8 Phages and sexual Bacterial Populations

8.1 Introducing Some Natural Selection: Genetic Hitchhiking

8.2 Muller's Ratchet

References

9 Phage Impact on Non-Random Mating Among Bacteria

9.1 Transduction and Panmixis

9.2 Various Limitations on 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

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

11 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

12 Phage-Provided Environmental DNA and Superspreading

12.1 Uptake of Naked DNA

12.2 Phage-Generation of eDNA

12.3 Phages as Mediators of 'Superspreading'

12.4 Temperate Phages as Generators of eDNA

References

13 Transduction of Large Amounts of DNA

13.1 Generalized Transduction

13.2 Homologous Recombination versus Illegitimate Recombination

13.3 Genomic Islands

References

Part IV. Prophage-Encoding of Bacterium-Expressed Genes

14 Phage Morons

14.1 What Is a Moron? (Narrow Sense)

14.2 What Isn't a Moron? (Narrow Sense)

14.3 Limitations on Phage Acquisition of Additional Genes

14.4 Morons as Lysogenic Converting Genes

References

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

16 Prophages Preventing Phage Superinfection

16.1 Superinfection Immunity

16.2 Superinfection Exclusion

16.3 Prophage Encoding of Other Phage-Resistance Mechanisms

References

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

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

19 Resistance to Phages, Part II: Bacteria Live!

19.1 Avoidance of Phage Genome Uptake

19.2 Negating Phage Infections Soon after Initiation

References

20 Resistance to Phages, Part III: Bacteria Die...

20.1 The Bacterial Self-Sacrifice of Abortive Infections

20.2 Delay: Slowing Down Phage Population Growth

References

21 Bacterial Mutation to Phage Resistance

21.1 A Plethora of Possible Targets of Mutation?

21.2 Rates of Mutation to Resistance

21.3 A Wee Bit of Advice

References

22 Pleiotropic Costs of Phage Resistance

22.1 Antagonistic Pleiotropies

22.2 Some History

22.3 A Sampling of More Modern Studies

References

Part VI. Natural Selection

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

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?

24.6 Stabilizing Frequency-Dependent Selection Involving Phages

24.7 Killing the Winner

24.8 Stabilizing Frequency-Dependent Selection Mimicking Muller's ratchet?

References

25 A Primer on Phage-Bacterium Antagonistic Coevolution

25.1 Preamble

25.2 Introduction to Coevolution and 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

25.6 An Indefinite Series of Coevolutionary Change?

25.7 Coda

References