Bacteriophages as Drivers of Evolution

                                                                                  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 Migration10     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 Resistance18     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

References22     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