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Intro; Foreword; Preface; Contents; About the Editor; Chapter 1: The Relevance and Challenges of Studying Microbial Evolution; 1 Introduction; 2 Why Understanding Microbial Evolution Is Important; 2.1 Major Events in Lifeś History Was, and Continuous to Be, Influenced by Microbes; 2.1.1 How the Earthś Atmosphere Got Oxygen; 2.1.2 Microbes May Have Caused Earthś Biggest Mass Extinction; 2.1.3 Microbes Control Critical Biogeochemical Processes; 2.1.4 Climate Change and Microbial Evolution; 2.2 Models to Understand General Principles of Evolution; 2.3 Animal Origins and Evolution
2.4 Microbes and Humans2.5 Pathogen Evolution; 2.6 Microbial Evolution Can Be Used to Solve Global Problems; 3 Challenges in the Study of Microbial Evolution; References; Chapter 2: Mayr Versus Woese: Akaryotes and Eukaryotes; 1 Introduction; 2 Unrooted Gene Trees; 3 Rooted rRNA and Protein Trees; 4 The Unholy Sanctity of Genotype; 5 More Than One Way to Skin a Genome; 5.1 The Dimensionality of Molecular Phenotypes; 6 Phylogenies of Protein Domains; 7 Preserving the Purity of the Lineage; 8 Novel Protein Discovery; 9 Akaryotes: Less Is More; 10 No Genome Is an Island; 11 Darwin Rules
4.2 The Pandora Box of New Archaeal and Bacterial Lineages4.3 The Conundrum of Fast-Evolving Species; 4.4 The Problem of Contamination in TOL Analyses; 4.5 Contradictory Signals in Protein Datasets; 4.6 TOLs Based on RNA Polymerase; 4.7 The Archaeal Root; 4.8 Where Are the Viruses in the TOL?; 5 Perspectives; 6 Conclusion; References; Chapter 4: Multiple Clocks in the Evolution of Living Organisms; 1 Introduction; 2 Prologue: Against Any Singular Origin in General Physical Processes; 2.1 No Eve, No Adam; 2.2 Multiple Origins of the First Cells; 3 The Master Functions of Life
4 Horizontal Gene Transfer5 Microbial Genomes Organisation; 6 The Making of a Progeny; 7 Evolution of Resting Cells Progeny; 8 Provisional Conclusion: No Universal Molecular Clock; References; Chapter 5: Natural Strategies of Spontaneous Genetic Variation: The Driving Force of Biological Evolution; References; Chapter 6: The Evolution of Gene Regulatory Mechanisms in Bacteria; 1 Introduction; 2 The Emergence and Evolution of RNA Polymerase; 2.1 Alternative Sigma Factors of RNA Polymerase; 3 Transcription and Its Regulation; 3.1 Promoter Architecture and Transcription Regulation
2.4 Microbes and Humans2.5 Pathogen Evolution; 2.6 Microbial Evolution Can Be Used to Solve Global Problems; 3 Challenges in the Study of Microbial Evolution; References; Chapter 2: Mayr Versus Woese: Akaryotes and Eukaryotes; 1 Introduction; 2 Unrooted Gene Trees; 3 Rooted rRNA and Protein Trees; 4 The Unholy Sanctity of Genotype; 5 More Than One Way to Skin a Genome; 5.1 The Dimensionality of Molecular Phenotypes; 6 Phylogenies of Protein Domains; 7 Preserving the Purity of the Lineage; 8 Novel Protein Discovery; 9 Akaryotes: Less Is More; 10 No Genome Is an Island; 11 Darwin Rules
4.2 The Pandora Box of New Archaeal and Bacterial Lineages4.3 The Conundrum of Fast-Evolving Species; 4.4 The Problem of Contamination in TOL Analyses; 4.5 Contradictory Signals in Protein Datasets; 4.6 TOLs Based on RNA Polymerase; 4.7 The Archaeal Root; 4.8 Where Are the Viruses in the TOL?; 5 Perspectives; 6 Conclusion; References; Chapter 4: Multiple Clocks in the Evolution of Living Organisms; 1 Introduction; 2 Prologue: Against Any Singular Origin in General Physical Processes; 2.1 No Eve, No Adam; 2.2 Multiple Origins of the First Cells; 3 The Master Functions of Life
4 Horizontal Gene Transfer5 Microbial Genomes Organisation; 6 The Making of a Progeny; 7 Evolution of Resting Cells Progeny; 8 Provisional Conclusion: No Universal Molecular Clock; References; Chapter 5: Natural Strategies of Spontaneous Genetic Variation: The Driving Force of Biological Evolution; References; Chapter 6: The Evolution of Gene Regulatory Mechanisms in Bacteria; 1 Introduction; 2 The Emergence and Evolution of RNA Polymerase; 2.1 Alternative Sigma Factors of RNA Polymerase; 3 Transcription and Its Regulation; 3.1 Promoter Architecture and Transcription Regulation