| Preface |
| Figure Index |
| Aim and Scope of the Book |
| | Evolutionary Biology Describes the History of Life and Explains Why Organisms Are the Way They Are |
| | Evolutionary Biology Is a Valuable Tool |
| | Molecular Biology and Evolutionary Biology Are Overlapping Fields of Study |
| |
| I | AN OVERVIEW OF EVOLUTIONARY BIOLOGY |
| |
| | 1 | The History of Evolutionary Biology: Evolution and Genetics |
| | | A Brief Summary of Modern Genetics and Evolution |
| | | Evolution before Darwin |
| | | Charles Darwin |
| | | The Eclipse of Natural Selection |
| | | The Evolutionary Synthesis |
| | 2 | The Origin of Molecular Biology |
| | | The Beginnings of Molecular Biology |
| | | Evolutionary and Molecular Biology: A New Synthesis? |
| | 3 | Evidence for Evolution |
| | | Evidence for Evolution |
| | | Objections to Evolution |
| | | Science and Society |
| |
| II | THE ORIGIN AND DIVERSIFICATION OF LIFE |
| |
| | 4 | The Origin of Life |
| | | When Did Life Begin on Earth? |
| | | How Did Life Begin on Earth? |
| | 5 | The Last Universal Common Ancestor and the Tree of Life |
| | | Tracing Early Evolutionary History |
| | | Universal Homologies, LUCA, and the Tree of Life |
| | 6 | Diversification of Bacteria and Archaea. I: Phylogeny and Biology |
| | | Introduction to the Bacteria and Archaea |
| | | Phylogenetic Diversification of Bacteria and Archaea |
| | | Biological Diversification of Bacteria and Archaea |
| | 7 | Diversification of Bacteria and Archaea. II: Genetics and Genomics |
| | | The Nature of Archaeal and Bacterial Genomes |
| | | Lateral Transfer of DNA |
| | 8 | The Origin and Diversification of Eukaryotes |
| | | Introduction to the Eukaryotes |
| | | Endosymbioses Have Played a Key Role in the Evolution of Eukaryotes |
| | | Structure and Evolution of the Nuclear Genome |
| | | Eukaryotic Diversification |
| | 9 | Multicellularity and Development |
| | | How Multicellularity Happens |
| | | Division of Labor through Differentiation |
| | | Diversity of Body Plans |
| | | Genetics of Building a Body Plan |
| | 10 | Diversification of Plants and Animals |
| | | Fossilization and Geological Time |
| | | The Flow of the Evolution of Life-forms |
| | | The Next 500 Million Years—Life Since the Cambrian Period |
| | | Patterns of Evolution |
| | 11 | Evolution of Developmental Programs |
| | | Anterior–Posterior Patterning: Hox Gene Regulation of Development and Evolutionary Change |
| | | Hox Genes Are Shown to Be Involved in Evolutionary Change |
| | | Skeletal Evolution in Sticklebacks |
| | | Evolution of Maize from Teosinte |
| | | Universality of Developmental Systems |
| |
| III | EVOLUTIONARY PROCESSES |
| |
| | 12 | Generation of Variation by Mutation and Recombination |
| | | Mutations and Mechanisms for Their Generation |
| | | Protection, Prevention, and Correction Mechanisms Limit the Number of Mutations Caused by DNA Damage and Replication Errors |
| | | Rates and Patterns of Mutations |
| | | Generation of Variation by Mixing: Sex and Lateral Gene Transfer |
| | 13 | Variation in DNA and Proteins |
| | | Genetic Variation |
| | | Types of Genetic Variation |
| | 14 | Variation in Genetically Complex Traits |
| | | Introduction to Quantitative Traits |
| | | Analyzing Quantitative Variation |
| | | The Genetic Basis of Quantitative Variation |
| | | Generation of Quantitative Variation |
| | 15 | Random Genetic Drift |
| | | Evolution Is a Largely Random Process |
| | | Random Drift of Allele Frequencies |
| | | The Neutral Theory |
| | | Recombination and Random Drift |
| | 16 | Population Structure |
| | | Gene Flow |
| | | Gene Flow Interactions with Other Evolutionary Forces |
| | | Genealogies in Structured Populations |
| | 17 | Selection on Variation |
| | | The Nature of Selection |
| | | Selection on Quantitative Traits |
| | | Selection on Multiple Genes |
| | 18 | The Interaction between Selection and Other Forces |
| | | Selection and Random Drift |
| | | Selection and Gene Flow |
| | | Balancing Selection |
| | | Mutation and Selection |
| | 19 | Measuring Selection |
| | | Direct Measurement of Selection |
| | | Indirect Measurement |
| | | Selection on Linked Loci |
| | | Selection on Noncoding DNA |
| | | The Extent of Selection |
| | 20 | Phenotypic Evolution |
| | | Evolutionary Optimization |
| | | Aging |
| | | Evolutionary Games |
| | | Sexual Selection |
| | 21 | Conflict and Cooperation |
| | | Social Evolution |
| | | Conflict between Genes |
| | | Interactions between Relatives |
| | | Evolution of Cooperation |
| | 22 | Species and Speciation |
| | | Defining Species |
| | | The Genetics of Speciation |
| | | Mechanisms of Speciation |
| | | The Geography of Speciation |
| | 23 | Evolution of Genetic Systems |
| | | Studying the Evolution of Genetic Systems |
| | | Evolution of Mutation Rates |
| | | Evolution of Sex and Recombination |
| | | Consequences of Sex |
| | | Evolution of Evolvability |
| | 24 | Evolution of Novelty |
| | | The Basic Features of Novelty |
| | | Changes in the Activity of Gene Products |
| | | Changes in Gene Regulation and Interactions within a Network: Targeting, Differentiation, and Development |
| | | Redundancy |
| | | Robustness, Modularity, and Compartmentalization |
| | | Acquiring New Functions from Other Species: Gene Transfer and Symbiosis |
| | | Natural Selection over Long Periods of Time Leads to the Origin of Novelty |
| |
| IV | HUMAN EVOLUTION |
| |
| | 25 | Human Evolutionary History |
| | | Placing Humans on the Tree of Life |
| | | The Evolution of Hominins |
| | | Genetics and Human Evolution |
| | | Genomics and Humanness |
| | 26 | Current Issues in Human Evolution |
| | | The Genetic Basis of Disease |
| | | Understanding Human Nature |
| |
| IV | ONLINE CHAPTERS |
| |
| | 27 | Phylogenetic Reconstruction PDF HTML |
| | | Generating a Molecular Sequence Matrix for Phylogenetic Analysis |
| | | Methods to Infer Phylogenetic Trees |
| | | Evaluation of Methods and Trees |
| | | Problems and Questions in Phylogenetic Reconstruction |
| | | Using Gene Trees |
| | 28 | Models of Evolution PDF HTML |
| | | Deterministic Processes |
| | | Random Processes |
| |
| Glossary |
| Figure Credits |
| Index |
