Encyclopedia of Evolutionary Biology

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Encyclopedia of Evolutionary Biology is the definitive go-to reference in the field of evolutionary biology. It provides a fully comprehensive review of the field in an easy to search structure. Under the collective leadership of fifteen distinguished section editors, it is comprised of articles written by leading experts in the field, providing a full review of the current status of each topic. The articles are up-to-date and fully illustrated with in-text references that allow readers to easily access primary literature. While all entries are authoritative and valuable to those with advanced understanding of evolutionary biology, they are also intended to be accessible to both advanced undergraduate and graduate students. Broad topics include the history of evolutionary biology, population genetics, quantitative genetics; speciation, life history evolution, evolution of sex and mating systems, evolutionary biogeography, evolutionary developmental biology, molecular and genome evolution, coevolution, phylogenetic methods, microbial evolution, diversification of plants and fungi, diversification of animals, and applied evolution. About the pagination of this eBook e9780128000496v1_WEB Front Cover Encyclopedia of Evolutionary Biology Editor in Chief Section Editors List of Contributors Guide to Using the Encyclopedia Structure of the Encyclopedia 1. Alphabetical Contents List 2. Cross-references See also 3. Subject Classification List 4. Index 5. Contributors Subject Classification List Preface Foreword Contents Adaptation, History of Glossary Pre-Darwinian Concepts and Lamarck’s Theory Darwin’s Theory of Evolution by Natural Selection Criticism of Natural Selection as the Mechanism of Adaptation Historical Development of the ‘Adaptationist Program’ Developmental Constraints and Adaptation Non-Darwinian Evolution and Selective Neutrality as a Null Hypothesis for Studying Adaptation Selfish DNA as a Challenge to and Source of Adaptation A Role for Volition in Darwinian Evolution of Adaptation? See also References Adaptive Landscapes Glossary Historical Introduction A Central Position in Evolutionary Theory and Population Genetics Influence on Various Fields of Evolutionary Biology Analytical Approaches and Methods of Study Different Versions of Adaptive Landscapes Landscape Structure Landscape Dynamics Controversies and Criticisms The Problem of Dimensionality Fitness of Individual Genotypes or Allele Frequencies of the Population? The Debate Over the Shifting Balance Theory Mathematical Models of Peak Shifts Adaptive Ridges and the Non-Existing Problem of Peak Shifts Conclusions and Future Outlook See also References Further Reading Relevant Websites Adaptive Molecular Evolution: Detection Methods Glossary Introduction Population Genetic Approaches Comparative Evolutionary Approaches Codon Analyses Amino Acid Analyses Analysis of Noncoding Sequences See also References Adaptive Mutation Controversy Glossary Defining ‘Adaptive Mutation’ The Classical View of Mutation and Selection Challenges to the Idea of Random Mutation The lac System The Adaptive Mutation Paradox How Do Lacplus Mutants Arise under Selection? – Three Models and Their Problems Directed Mutation Selection-Induced Hypermutability Selective Amplification of the Mutant Gene The Philosophical Problem of Adaptive Mutation – Why Has This Question Been So Hard to Resolve? The Generally Accepted Body of Evidence Resolving Conflicts and Deciding between Models Do the Cells That Initiate Stable Revertant Colonies Arise Before or After Selection? Does the Plated Population Grow Before Mutation? What Activates the DinB Polymerase – Induction or Amplification? A Model That Fits with All Available Data Explaining Behavior of the lac System in Terms of Standard Evolutionary Ideas Evolutionary Insights Provided by the lac System See also References Adaptive Radiations: Insights From Evo-Devo Glossary Insights into Adaptive Radiations from Evolutionary Developmental Biology Early Links Between the Study of Adaptive Divergence and Developmental Biology Fish Adaptive Radiations and the Incorporation of Evolutionary Developmental Biology Herpetofauna: Plasticity and Ontogenetic Processes Contribute to Adaptive Divergence Avifauna: Adaptive Bill Diversity through Developmental Change Conclusions See also References Relevant Websites Age-Specific Survivorship and Fertility, Estimating Glossary Introduction Estimating Survivorship Estimating Fertility Conclusions See also References Further Reading Relevant Websites Aging: Why Do We Age? What Is Aging? The Origins of the Theory Adaptive Aging Mutation Accumulation Antagonistic Pleiotropy The Mutation Accumulation and Antagonistic Pleiotropy Dichotomy W.D. Hamilton: Foundations for a Formal Theory Modifying Hamilton’s Model Post-Reproductive Survival Mortality Deceleration and Plateaus Elevated Pre-Reproductive Mortality Tests of the Theory Extrinsic Mortality Segregating Genetic Variation Segregating Genetic Covariances De novo Mutational Correlations Conclusions See also References Amniotes, Diversification of Glossary Introduction Synapsida Reptilia See also References Amniotes, the Origin of Glossary Introduction Fossil Evidence The Earliest Known Amniotes Reptiliomorphs from the Lower Carboniferous Phylogenetic Studies of Reptiliomorphs and Basal Amniota Discussion Acknowledgments See also References Ancestral Reconstruction: Theory and Practice Glossary Introduction Ancestral Character Reconstruction Discrete Characters Continuous Characters Ancestral Sequence Reconstruction Gene Content Gene Order The Complete Reconstruction of Ancestral Genomes See also References Further Reading Angiosperm Phylogeny and Diversification Glossary Introduction The Background – Some Distinctive Angiosperm Features Angiosperm Diversification Diversification in Basal Angiosperms and Monocots Diversification in Core Eudicots Success of a Different Kind Plant–Pollinator Interactions Epilogue See also References Animal: What Is an Animal? Glossary Modern Animals and Their Closest Eukaryotic Relatives What Features Do All Animals Have in Common? Multicellularity Sex and Development Feeding Cells and Tissues A Genomic Perspective Extinct Animals and Future Directions of Animal Evolution Phylogenetic Definition of Animals See also References Antagonistic Interspecific Coevolution Glossary What Is Antagonistic Coevolution? How Does Antagonistic Coevolution Work? Negative Frequency-Dependent Selection: Red Queen Coevolution Positive Directional Selection: Arms Race Coevolution A Critical Role for Population Structure How Is Antagonistic Coevolution Detected? Evidence for Antagonistic Interspecific Coevolution in Nature Red Queen Coevolution: Snail and Trematode Arms Race Coevolution: Newt and Garter Snake Simultaneous and Sequential Red Queen and Arms Race Coevolution: Daphnia, Bacterium-Microsporidian, and Bacterium-Phage Outstanding Questions and Future Directions See also References Further Reading Archaeplastida: Diversification of Red Algae and the Green Plant Lineage Glossary Introduction Evolutionary Origins Morphology Fossil Record Habitats and Diversity Green Plant Origins and Diversification Summary See also References Artificial Selection Glossary Introduction Fundamental Concepts Basic Design Considerations Weaknesses of Artificial Selection Applications in Evolutionary Biology with Examples Evolutionary Constraints Understanding the Genetic Basis of Phenotypic Evolution Understanding Natural Selection Summary and Future Directions Acknowledgments See also References Further Reading Bacterial Diversity, Introduction to Introduction Theoretical Approaches to Describe Bacteria Diversity Experimental Approaches to Describe Bacteria Diversity Implications and Applications of Bacteria Diversity See also References Further Reading Relevant Websites Bacterial Species Concepts Species – A Special Level of Taxonomy? Prokaryotic Systematics: Species as Clusters of Similar Organisms Bacterial Species as Dynamically Defined Groups Genetic Exchange and the Nature of Prokaryotic Species Recombination-Based Approaches to the Origin of Bacterial Species Ecological Speciation in Bacteria Conclusion See also References Basic Science and Evolutionary Biology Glossary Impacts of Evolutionary Biology Food Security Preserving Biodiversity, and Predicting and Mitigating the Effects of Global Climate Change Non-Fossil Fuel Energy Health Justice System Basic and Applied Science Funding for Basic Science Public Perception of Evolutionary Science See also References Further Reading Bayesian Phylogenetic Methods Introduction Priors Markov Chain Monte Carlo Output Analysis from Simulation See also References Biogeography, Conservation Conservation Biogeography – Origins and Aims Evolving Maps Evolving Approaches Evolving Aims Evolving Cross-Disciplinary Links See also References Biogeography, Ecological Theories in Glossary Theories of Species Richness and Composition The Equilibrium Theory of Island Biogeography The Unified Neutral Theory of Biodiversity and Biogeography The Maximum Entropy Theory of Ecology Theories of Geographic Range Size and Geographic Gradients See also References Relevant Websites Biogeography, Evolutionary Theories in Introduction Ancestral Area Reconstructions Inference of Biogeographic Histories with Nonspatial Population Genetic Models Inference of Biogeographic Histories with Spatial Population Genetic Models See also References Biogeography, History of Glossary Introduction Aboriginal Knowledge The Geography of Nature from Regional to Global Scales Fundamental Principles of Modern Biogeography See also References Biogeography, Human African Origins Out of Africa Routes Out of Africa How Do We Know? Where We are Influences What We are Geography and Cultural Diversity See also References Biogeography, Marine Glossary Introduction Marine Biogeographic Barriers Marine Biogeography and Evolution Plate Tectonics and Marine Evolution Marine Biogeographic Provinces of the World Warm Regions (Tropical and Warm-Temperate Waters) Eastern Atlantic Region Lusitania Black Sea Caspian Sea Aral Sea Tropical Eastern Atlantic Benguela St. Helena Ascension Tristan–Gough Western Atlantic Region Carolina Caribbean Brazilian Argentinian Western Pacific Region Sino-Japanese Kermadec Auckland Southeastern Australian Southwestern Australian Agulhas Tropical Indo-West Pacific Region Western Indian Ocean Amsterdam–St. Paul Red Sea Indo-Polynesian Hawaiian Marquesas Easter Island Eastern Pacific Region California Cortez Panamanian Galápagos Peru–Chilean Juan Fernández Cool Regions (Cold-Temperate and Polar Waters): Cold-Temperate and Polar Northern Hemisphere Eastern North Pacific Region Aleutian Oregon Western North Pacific Region Oriental Kuril Okhotsk Western Atlantic Region Eastern Atlantic Region Arctic Region Cool Regions (Cold-Temperate and Polar Waters): Cold-Temperate and Polar Southern Hemisphere South American Region Southern Chile Tierra del Fuego Southern Argentina Falkland Islands (Islas Malvinas) New Zealand–Australian Region Tasmania New Zealand Antipodes Subantarctic Region South Georgia Bouvet Crozet Prince Edward Kerguelen Macquarie Antarctic Region Conclusions Acknowledgments See also References Further Reading Biogeography, Microbial Glossary Introduction What is Microbial Biogeography? The Baas-Becking Hypothesis: The Birth of Microbial Biogeography Molecular Genetics: Enabling Microbial Biogeography Evidence for Microbial Biogeography Endemism Distance-Decay Taxa-Area Temporal Changes Latitudinal Gradients Elevation and Depth Gradients Ecological and Evolutionary Mechanisms Framework Relative Importance of Processes Limitations and Outlook Limitations Spatial scales and temporal variations Taxonomic resolution Inferring process from pattern Applications and Significance Anticipating responses to environmental change Improving human well-being and sustainability Underexplored extreme environments See also References Biogeography of Arthropods Age of Arthropods – Insights From Fossils Geological Movements in Arthropod Biogeography Dispersal and Colonization Biogeography of Interactions Island Biogeography Adaptive Radiation Range Expansion and Invasion Target Areas for Biogeographic Study – Oceanic and Continental Islands Hawaiian Islands and French Polynesia Caribbean Macaronesia Galapagos Target Areas for Biogeographic Study – Terrestrial Islands Sky Islands Caves Habitat Fragments The Future of Research in Arthropod Biogeography See also References Relevant Website Biogeography of Interactions Glossary Historical Biogeography of Interactions Reconstruction of Historical Biogeography of Intimate Associations Competitive Exclusion/Extinction in the Evolution of Biotas Biogeography of Interaction Loss, Gain, and Reassembly Ecological Biogeography of Interactions Latitudinal Gradients in Interaction Types, Specialization, and Interaction Diversity Biogeography of Ecological Networks Interactions on Islands Biogeography of Coevolution See also References Further Reading Biogeography of Islands, Lakes, and Mountaintops; Evolutionary Overview Theoretical Setting Places and Players ‘True’ Islands Mountaintops Lakes Outlook Acknowledgments See also References Further Reading Biogeography of Vertebrates Glossary The First Vertebrates Plate Tectonics, Continental Drift, and the Paleotransport of Vertebrates Vicariance and Dispersal: Theory versus Data Patterns: Endemism, Provincialism, Cosmopolitanism, and Disjunct Distributions Empirical Insights into the Biology of Long-Distance Vertebrate Dispersal Biogeographic Barriers, Interchanges, Gradients, and Filter Zones: Stepping Stones, Conduits, and Corridors Insular Extremes: Spectacular Vertebrates of Isolated Islands and Extraordinary Vertebrate Radiations in Island... Future Prospects See also References Further Reading Relevant Websites Biogeography, Patterns in Environmental Dynamics Affecting Evolutionary Processes and Biogeographic Patterns Mechanisms, Structures and Scale Dependence of Biogeographic Patterns Fundamental Evolutionary Patterns in Biogeography Latitudinal Patterns Elevational Patterns Island-Specific Phenomena Conclusion See also References Further Reading Bird Flight Origins Glossary Introduction Trees-Down versus Ground-Up Flight Genesis Mesozoic Experiments in Flight Chinese Discoveries Refocus Debate Conclusions See also References Birds, Diversification of Glossary General Introduction The Origin of Birds Diversity of Extinct (Non-Modern) Birds Timing the Evolutionary History of Modern Birds Phylogeny of Modern Birds Conclusion See also References Further Reading Cambrian Explosion: A Molecular Paleobiological Overview Glossary Introduction The Cambrian Fossil Record The Ediacaran Record and the Origin of Animals Biomarker Evidence for a Pre-Ediacaran Origin of Animals Evidence from the Genomic Record Conclusions Acknowledgment See also References C4 and CAM Photosynthesis in Land Plants, Evolution and Diversification of Glossary C4 and CAM Photosynthesis, Two Adaptations that Reduce Photorespiration Evolutionary Origins of C4 and CAM Photosynthesis Selective Pressures and Species Diversification Effect of CCMs on the Ecological Niche Concluding Remarks See also References Carbon Relations, the Role in Plant Diversification of Glossary Contemporary Carbon Cycle and Roles for Organisms Atmosphere Crust Oceans Land Long-Term Drivers of Change in the Carbon Cycle The Colonization of Land and Rock Weathering Leaf Evolution, Plant Water-Relations and Biomes Stems and the Evolution of Lignin Synthesis and Degradation General Patterns See also References Cellular Behaviors Underlying Pattern Formation and Evolution Glossary Introduction Morphogenetic Gradients and the French Flag Model Embryonic Axis Formation Is Initiated by Maternal Information Evolutionary Modifications of Gradient Formation and Interpretation Scaling of Morphogenetic Gradients during Evolution The AP System Employs Different Scaling Strategies within and across Diptera Species The DV Axis Is Patterned by Two Opposing Gradients: One Regulated by a Fast Evolving Pathway, and Another That Is Highly... The Domains of Neural Identity Genes along the DV Axis Are Highly Constant during Evolution The Germ Layers Formed along the DV Axis Are Unequally Scaled during Evolution A Mathematical Modeling of Dl Gradient Indicates that Scaling Is Achieved by Changes in the Embryo Anatomy and Tl... Contribution of Cell Migration during Morphogenetic Gradient Patterning Acknowledgment See also References Further Reading Climate Change, Quantitative Genetics and Glossary Introduction Biotic Response to Climate Change Is Already Happening Evolution in Response to Climate Change Is Multidimensional Why Use Quantitative Genetics? Questions That Can Be Addressed Using Quantitative Genetic Approaches Basic Quantitative Genetic Concepts Genetic Architecture Genetic variation Heritability Genetic correlations Genetic correlations among traits Genetic correlations across environments Application of Quantitative Genetics to Climate Change Questions Natural Selection Local Adaptation Phenotypic Plasticity Response to Natural Selection Response to Artificial Selection Observations of Evolutionary Change Examining Evolution Using the Resurrection Approach See also References Further Reading Relevant Websites Coalescent and Models of Identity by Descent Glossary Pedigree Identity by Descent Coalescent Identity by Descent Ancestral-Segment Identity by Descent See also References Codon Usage and Translational Selection The Codon Bias Phenomenon Background Substitution Biases and Their Effect on Codon Usage Codon Usage Can Affect Translation Accuracy and Efficiency Translational Selection Increases Codon Bias Selection on Codon Usage Is Ubiquitous but May Vary between Organisms Selection on Codon Usage – Weak and Constant, or Variable and Sometimes Strong? Favored Codon Identity and Shifts in Codon Usage Concluding Remarks Acknowledgments See also References Coevolutionary Fitness Landscapes Glossary Introduction Natural Selection A Multi-Scale View of Fitness Coevolution and Fitness Conclusions See also References Coevolution, Bacterial-Phage Glossary Introduction Phage Life History and Adaptation Lytic Phages Temperate Phages Alternative Phage Life Cycles Phage Adaptation to Host Populations Phage-Mediated Selection Mechanisms of Bacterial Resistance Bacterial Adaptation to Local Phage Populations Phage Counter-Adaptation Evidence for Bacterial-Phage Coevolution Coevolution in Nature See also References Coevolution, Introduction to Glossary Introduction Coevolutionary Dynamics Arms Races Cycles Matching Coevolution and Speciation Coevolution in Mosaics and Networks Conclusions How Often Does Coevolutionary Selection Directly Contribute to the Formation of New Species? How Do Different Kinds of Ecological Interactions Affect Diversification? How Do Coevolutionary Dynamics Extend to Highly Asymmetrical Interactions? See also References Further Reading Commensalism, Amensalism, and Synnecrosis Glossary Commensalism Examples Ambiguity of the term ‘Commensalism’ Coevolution and Selection in Commensal Organisms Amensalism Examples Ambiguity of the Term ‘Amensalism’ Coevolution and Selection in Amensals Synnecrosis See also References Compensatory Evolution Glossary Concept and Definition History and Definitions of Compensatory Mutations Population Genetics Model Potential Evolutionary Role of Compensatory Mutations Molecular Mechanisms of Compensatory Evolution Intramolecular Compensatory Evolution Intermolecular Compensatory Evolution Inter-Genomic Compensation Molecular Evolution Methods for Detecting Compensatory Evolution See also References Complexity, the Role of Oxygen in Evolution of Glossary The Importance of Oxygen for Life The Rise of Oxygen in the Early Earth The First Oxygen-Breathers The Emergence of Eukaryotes by Endosymbiosis From the Rise of Oxygen to the Cambrian Explosion The Impact of Oxygen Fluctuations on Animal and Plant Evolution Adaptations to Low and Changing Oxygen Environments See also References Consensus Methods, Phylogenetic Introduction Consensus Tree Methods Strict Consensus Semi-Strict or Combinable Component Consensus Adams Consensus Majority-Rule consensus Extended Majority-Rule or Greedy consensus Plurality consensus tree R* consensus Q* consensus Consensus Trees for Maximum Likelihood and Bayesian Phylogenetics Consensus of Bootstrapped Trees Consensus of Estimated Posterior Distribution of Trees Median Trees Consensus of Gene Trees to Estimate Species Trees Controversy around Consensus Trees Generalizations: Multilabeled Trees, Supertrees, and Consensus Networks See also References Conservation Biology, Evolution and Glossary Introduction Pattern: What Can Genetic Patterns Tell Us about Biodiversity and Taxa of Conservation Concern? Identification of Units of Biodiversity Conservation Planning Process: The Problem of Small Populations Genetic Drift Inbreeding and Inbreeding Depression Interplay between Genetic versus Nongenetic Processes Affecting Demography Dispersal and Gene Flow Concluding Thoughts See also References Conservation Biology, Quantitative Genetics in Glossary Introduction Fitness Decline in Small Populations Consequences of Bottlenecking and Fragmentation on the Genetic Variance for Quantitative Traits Minimum Viable Population Size Neutral Molecular Variation as a Surrogate or Complementation to Quantitative Genetic Variation Implications of Conservation Management on Quantitative Trait Variation See also References Further Reading Convergent Evolution, Adaptive Radiation, and Species Diversification in Plants Glossary Evolutionary Convergence, Divergence, and Diversification within Plant Communities Summary Acknowledgments See also References Cooperation and Public Goods, Bacterial Definition of Cooperation Benefits of Bacterial Cooperation Explanations for Cooperation Shared Genes Reciprocity Group Selection Examples of Bacterial Cooperation Myxobacteria Pseudomonas fluorescens A Cautionary Note on Microbial Sociobiology Syntrophy Public Goods See also References Cospeciation Glossary Article Outline A Few Examples How Important Is Finding It? Terminology How Does Cospeciation Happen? Failure to Codiverge Other Coevolutionary Events Detecting Cospeciation/Codivergence Summary Why Is It So Hard to Find Cospeciation? See also References Darwin’s Finches, the Galapagos, and Natural Laboratories of Evolution Introduction Darwin and the Finches The Age of Surveys David Lack Peter and Rosemary Grant: Evolution in a Natural Laboratory The Future and the Finches Conclusion See also References Darwin-Wallace Theory of Evolution The Darwin–Wallace Theory of Evolution The Age of the Earth ‘Catastrophism’ ‘Lamarckism’ More Species ‘Uniformitarianism’ Darwin Voyage of the Beagle The Galapagos The Big Three Vestiges of Creation Wallace Malay Archipelago Darwin versus Wallace? See also References Relevant Websites Developmental Biases on Morphological Evolvability Conceptual Definition(s) of Evolvability Development Determines Evolvability Phenotypic Integration and Modularity ‘Constraint’ in Developmental Systems Is Necessary for Evolution Future See also References Developmental-Genetic Toolkit for Evolutionary Developmental Biology Glossary Introduction The Discovery of the Homeobox Genes The Expanded Toolkit: Genes for Body Parts Tinkering with the Toolkit Genes and the Origin of New Forms The Developmental-Genetic Toolkit and the Hourglass Model The Future of Experimental EvoDevo See also References Further Reading Developmental Mechanisms Controlling Cell Fate, Evolution of Glossary Introduction Part I: Competency, Equivalence Groups, and Cryptic Variation Evolution of Equivalence Groups The Rhabditid Nematode Vulva: An Evo-devo Model for Cell Fate Specification Cryptic Evolution and Developmental System Drift Cell Fate Specification Leads to Differentiation and Morphogenesis Part II: Evolution of a Novel Cell Type – Echinoderm Larval Skeleton The Primary Mesenchyme Cells Build the Pluteus Skeleton in Sea Urchins Co-Option of Adult Skeletogenesis for Larval Skeleton Formation What Can Out-Groups Tell Us About the Evolution of the Sea Urchin Pluteus? Convergent Evolution of the Pluteus in Brittle Stars? Part III: Cell Fate Specification in Adult Animals Differentiation in Lineage-Restricted Adult Stem Cells Specification in Pluripotent Adult Stem Cells The Evolution of Stem Cell Fate Specification Conclusions and Future Directions See also References Developmental Paleontology and Paleo-Evo-Devo Glossary Why Is a Developmental Paleontological and Paleo-Evo-Devo Approach Necessary? Taxonomy Minimum Ages Ancestral, but Now Extinct Patterns Evolution of Body Organization Evolutionary Scenarios How Is a Study in Developmental Paleontology and Paleo-Evo-Devo Performed? Largely Post-Embryonic Ontogeny How to Obtain Such Data Single specimens with ontogenetic information Ontogenetic sequences from several specimens Evolutionary Scenarios Interactions of Paleo-Evo-Devo and ‘Neo’-Evo-Devo Acknowledgments See also References Developmental Plasticity and Phenotypic Evolution Glossary What is Developmental Plasticity? The Evolution of Plasticity How Does Plasticity Evolve? When Does Plasticity Evolve? Evolutionary Consequences of Plasticity Mechanisms of Plasticity Future Directions and Implications See also References Further Reading Relevant Website Directed Evolution, History of Directed Evolution Variation and Teleology Orthogenesis and Nomogenesis The Evolutionary Synthesis and Beyond Evo Devo and Devo Evo Evolutionary Directionality See also References Further Reading Directional Selection and Adaptation Glossary Introduction The Dynamics of Selection The Interplay between Selection and Drift Genetic Hitchhiking and Selective Sweeps New Models: Soft Sweeps, Polygenic Selection, and Adaptive Introgression Tests of Selection on Real Data The Site-Frequency Spectrum Haplotype Lengths Population Differentiation Allele Frequency Time Series Conclusion See also References Dispersal Biogeography Glossary Dispersal Biogeography Dispersal as a Predictable Process: Evidence from Life History, Ecology, Biogeography, and Genetics Types of Dispersal Transoceanic Dispersal and Island Colonization Wind/Storm Dispersal Dispersal at Sea Dispersal with Animals Dispersal Routes Past and Future Dispersal See also References Relevant Websites Distance-Based Phylogenetic Inference Glossary Introduction Preliminaries Distance Estimation Tree Reconstruction Least Squares Branch Length Estimation Optimization Criteria: ME NJ and Related Algorithms Beyond Distances Conclusion See also References Divergence and Diversification, Quantitative Genetics of Glossary Introduction Is Divergence Among Populations the Result of Drift or Selection? Does Genetic Architecture Bias the Direction of Evolution (or Vice Versa)? Does Genetic Architecutre Affect Rates of Diversification? Conclusion See also References Further Reading Ecological Evolutionary Developmental Biology Glossary Introduction Phenotypic Plasticity Phenotypic Plasticity and Evolution Phenotypic Plasticity and Ecology Epigenetic Inheritance and Evolution Concluding Remarks See also References Further Reading Ecological Fitting and Novel Species Interactions in Nature Glossary Introduction The Role of Evolution in Ecological and Evolutionary Fitting: Ecophysiological Equivalence and the Expression of... Invasive Species: Highly Visible Examples of Ecological Fitting Bis Interimitur, Qui Suis Armis Perit (What Goes Around, Comes Around) Unwittingly Fitting, and How Manufactured Interactions are Often Used to Explain Biological Processes Summary Acknowledgments See also References Ecological Speciation and Its Consequences Glossary Alternatives to Ecological Speciation Support for Ecological Speciation Genomic Basis of Ecological Speciation Constraints on Ecological Speciation Consequences of Ecological Speciation Conclusions See also References Effective Population Size Glossary Introduction The Early Theory Definitions of the Effective Population Size Calculations of the Effective Population Size The Time Factor Comments about theta See also References Endogenous Retroviruses and Coevolution Glossary Introduction Classification and Identification of Endogenous Retroviruses From Exogenous to Endogenous: How an Endogenous Retrovirus Is Formed? Germ line Integration and Fixation Intragenomic Proliferation The Influence of Endogenous Retroviruses on Hosts The Effect of Endogenous Retroviruses on Genome Architecture The Effect of Endogenous Retroviruses on Gene Expression Endogenous Retroviruses, Recombination and the Emergence of New Viral Types Occasional Beneficial Effects of ERVs on Hosts Endogenous Retroviruses as Tools in the Study of Host–Virus Coevolution Endogenous Retroviruses in the Study of Viruses and Virus–Host Interaction at Evolutionary Timescales See also References Endophytic Microbes, Evolution and Diversification of Glossary Introduction Class I Endophytes The Epichloë Life Cycle and Its Evolutionary Reduction Hybridization and Diversification Examples of Diversification into Different Plant Groups Pseudocercosporella Trichachnicola Morning Glory Symbionts Class II Endophytes Parasitism–Mutualism Continuum Host Role in Regulation of Endophytic Microbes See also References Endosymbiotic Theory Glossary Introduction Mitochondria Plastids Secondary Endosymbiosis The Rationale Behind Mitochondrial Ubiquity Endosymbiotic Gene Transfer Protein Import Conclusion Acknowledgment See also References e9780128000496v2_WEB Encyclopedia of Evolutionary Biology Editor in Chief Section Editors List of Contributors Guide to Using the Encyclopedia Structure of the Encyclopedia 1. Alphabetical Contents List 2. Cross-references See also 3. Subject Classification List 4. Index 5. Contributors Subject Classification List Preface Foreword Contents Epigenetic Inheritance Glossary Epigenetic Modification Inheritance Evolutionary Implications Future Questions See also References Epigenetics and Genome Evolution Glossary Introduction Epigenetics and Evolution: Compatible Concepts? Classical Role of DNA Methylation on Mutation and Sequence Composition Potential Mutational Effects of Histone Tail Modifications and Chromatin Structures Emerging Studies of Epigenetics on Molecular Evolution Recombination Hotspots and Epigenetic Variation Evolutionary Trade-Off between TE Methylation and Gene Expression Concluding Remarks See also References Further Reading Evo-Devo: Regulatory and Protein-Coding Evolution in Plant Diversification Glossary An Historical Perspective on Plant Evo-Devo Gene Expression, Development, and Phenotypic Evolution Transcriptional Control and the Evolution of Gene Expression Posttranscriptional Control and the Evolution of Gene Expression Epigenetic Regulation of Gene Expression Protein-Coding Changes and Developmental Evolution Modularity Can Promote Both Cis-Regulatory and Protein-Coding Evolution Gene Duplications Can Reduce Genetic Pleiotropy and Foster Phenotypic Novelty Conclusions and Future Directions in Plant Evo-Devo See also References Evolution and Agriculture I. The Evolution of Domestication Glossary Spatiotemporal Rise of Domestication The Domestication Syndrome Domestication Evolution Trajectories: Pace, Mode and Mechanism Post Domestication Evolution See also References Evolution and Agriculture II. Evolutionary Applications to Breeding Glossary Introduction Historical Overview Darwin and Wallace in the Nineteenth Century Fisher and Wright in the Twentieth Century Heritability and the Breeders’ Equation Breeding Value Marker-Assisted Selection QTL Mapping Association Mapping and Genome-Wide Association Mapping Genome Selection Long-Term Selection Social Interactions and Indirect Genetic Effects Genomics and Effects of Domestication Concluding Remarks See also References Evolutionary Biology, History of Introduction The Origins of Evolutionary Thought Charles Darwin and Descent with Modification by Means of Natural Selection The Eclipse of Darwin and the Modern Synthesis of Evolution The Convergence of Biological Disciplines and the Emergence of Evolutionary Biology The Watershed: The Darwin Centennial and After Evolutionary Biology in the Post-Sputnik Area and Challenges to the Synthetic Theory See also References Further Reading Evolutionary Computation Glossary Introduction History of Evolutionary Computation Variety in Evolutionary Computation Techniques Contrasts Between Evolutionary Computation and Organic Evolution Contrasts Between Evolutionary Computation and Computational Models of Evolution Parallel Discoveries of Evolutionary Phenomena in Evolutionary Computation The Problem of Evolvability Genetic Modifiers Constructive Neutral Evolution The Evolution of Genetic Robustness Artificial Life Acknowledgments See also References Further Reading Relevant Websites Evolutionary Genetics, History of Glossary Introduction The Origin of Evolutionary Genetics The Argument over Variation The Emergence of Evolutionary Genetics The Maturation of Evolutionary Genetics Common Ground: A Theory of Evolutionary Genetics Contention and Argument: Which Theory Does Nature Follow? Evolutionary Genetics Permeates the Study of the Evolutionary Process The Dominance of Evolutionary Genetics The Randomness of Mutation Genetics and the Formation of New Species The Next Generation of Evolutionary Genetics The Expansion of Theory Empirical Discoveries Challenge Theory: New Problems or Deeper Questions? The Syntheses of Evolutionary Genetics See also References Further Reading Evolutionary Medicine I. An Overview and Applications to Cancer Glossary Overview of Evolutionary Medicine Why We Get Sick Biotic Interactions and Human Health Genomic Conflict Genomics and Evolutionary Medicine Evolutionary Medicine and How Humans Are Evolving Cancer as an Evolutionary Disease Why Cancer? Cancer Susceptibility Tumor Heterogeneity Drivers and Passengers Metastasis Evolutionary Applications for Cancer Therapy Outstanding Questions See also References Evolutionary Medicine II. Use of the Comparative Method and The Animal Model Deep Homology, Distant Relatives, and the Persistence of Ancestral Traits Closer Relationships, Greater Fidelity Common Ancestry, Unique Histories Evolutionary Mutants, Convergent Traits, and Unique Inventions The Challenge of Extrapolating from Models Conclusions See also References Evolutionary Medicine III. Mismatch Glossary Introduction Evolutionary Mismatch Evolutionary Novelty Evolutionarily Novel Range of Exposures Developmental Mismatch Developmental Plasticity Developmental Origins of Obesity and Its Complications Molecular Basis of DOHaD Implications for Human Health See also References Evolutionary Medicine IV. Evolution and Emergence of Novel Pathogens Glossary Introduction The Phylodynamics of Emerging Infectious Diseases A Short Primer on the Coalescent The Coalescent and Infectious Diseases How Does Selection for Increased Transmissibility Affect Influenza Phylogenies? Using Phylodyanmics to Study Disease Reporting During the 2014 Ebola Outbreak Conclusions See also References Evolvability, Quantitative Genetics of Introduction Definitions and Origins of the Concept Evolvability in Quantitative Genetics Evolvability and Heritability Evolvability for Multivariate Traits Does Evolvability Affect Evolution? Determinants of Evolvability Determinants of Evolvability: Continuity Determinants of Evolvability: Modularity Determinants of Evolvability: Coordination and Integration Determinants of Evolvability: Robustness Determinants of Evolvability: Mutability Determinants of Evolvability: Recombination Determinants of Evolvability: Epistasis The Evolution of Evolvability See also References Founder Speciation Introduction Theoretical Support Theoretical Challenges Experimental Evidence Evidence I: Experimental Evolution Evidence II: Natural Variation Conclusions See also References Fungal Evolution: Aquatic-Terrestrial Transitions Glossary Fungi and Fungal-Like Microoorganisms An Aquatic Origin for the Fungal Lineage Aquatic to Terrestrial Environments – Fossil Evidence of Fungi Evolution of Traits from Primitive to More-Derived Fungi Aquatic Traits (Motile Spores, Non-Hyphal Growth form, Reproduction) Hyphal Habit Sexual Reproduction equal An Ancestral Character in Terrestrial Fungi Acknowledgments See also References Gene Interactions in Evolution Glossary Statistical and Physiological Gene Interactions Gene Interactions within Populations Statistical Gene Interactions and Drift Molecular Genetics and Physiological Epistasis Summary See also References Further Reading Gene Networks Driving Development, Conservation and Evolution of Glossary The Birth of Evolutionary Developmental Biology The Focus on Regulatory Evolution From Gene Regulation to Gene Regulatory Networks Evolution of GRNs Conclusions Acknowledgments See also References Gene Origin, Sex Chromosomes and Glossary Introduction Molecular Processes that Generate New Genes Potential Impact of Sex Chromosomes on New Gene Evolution Gene Evolution with the XY Systems X Chromosomes Y Chromosomes Neo-Sex Chromosomes Gene Evolution with the ZW Systems W Chromosomes Z Chromosomes Final Remarks Acknowledgments See also References Genetic Architecture Glossary Genetic Source of Phenotypic Variation Genetic Effects Individual-referenced formulations Population-referenced formulations Genetic variance decomposition Genetic Architecture Multiple alleles Epistasis Imprinting and epigenetics Gene-by-environment interactions Mapping Genetic Architectures Obtaining the Genotype-to-Phenotype Map Estimating Genetic Effects Genetic Architectures Discovered Evolutionary Quantitative Genetics Acknowledgment See also References Genetic Drift, Models of Random Glossary Overview Core Assumptions of Genetic Drift Models Two Different Genetic Drift Models Wright–Fisher Model Mathematical Framework of the Wright–Fisher Model Direct Results from the Wright–Fisher Model Probability of fixation Variance in allele frequencies over time Reproductive output of individual alleles Approximate Results from the Wright–Fisher Model Time to fixation or loss of a neutral allele Time to fixation (conditional on fixation) Approximation Methods Moran Model Mathematical Framework of the Moran Model Direct Results from the Moran Model Fixation probability of an allele Variance in allele frequencies over time Reproductive output of individual alleles Time-Based Results for the Moran Model See also References Further Reading Genetic Variation in Populations Glossary Introduction Types of Genetic Variation Morphological Variation Chromosomal Variation Protein Variation DNA Variation Highly Polymorphic Molecular Markers Applications of Different Tools Future Directions: Whole Genome Approaches Other Considerations and Controversies for Future Research See also References Genetic Variation, Maintenance of Glossary Introduction The Evidence Hypothesis 1: Natural Selection Hypothesis 2: Genetic Drift and Mutation Problems with the Selectionist Hypothesis Problems with the Neutralist Hypothesis Possible Solutions See also References Genome Evolution’s Role in Developmental Evolution Glossary Transposons Coding Mutations Regulatory Mutations Gene/Genome Duplications Origins of New Genes, Pseudogenes Genome Reduction, Gene Loss (Compact Genomes), Deletions Horizontal Gene Transfer Evolution of Sex Chromosomes Open Questions See also References Genome Organization, Evolution of Glossary Introduction Structural Organization of Genomes Genome Rearrangements Deletions Duplications Inversions Translocations Establishment of Rearrangements in Populations Rearrangements Effect on Nucleotide Variation in Populations Rearrangements as Contributors to the Speciation Process Rearrangements and Sex Chromosome Evolution Computational Methods to Infer Phylogenies from Genome Rearrangements Summary and Future Prospects See also References Genome Plasticity, Bacterial Glossary Mechanisms and Constraints of Bacterial Genome Plasticity The Mosaic Continuum of Mobile and Accessory Genetic Elements as a Toolbox of Genome Plasticity Impact of Nucleoid-Associated Proteins on Genome Plasticity Nucleoid-Associated Proteins and Their Importance for Genome Architecture Nucleoid-Associated Proteins and Gene Regulation NAPs in Transcriptional Silencing of Horizontally Acquired DNA The Role of NAPs in Anti-Silencing of Horizontally Acquired DNA Acknowledgments See also References Genome Size and Structure, Bacterial Glossary Abbreviations The Architecture of Bacterial Genomes Bacteria Have Compact Genomes Determinants of Genome Size in Bacteria Genome Size Variation within Species Genome Organization Maintenance of Chromosome Balance Gene Location and Orientation Genomic Base Composition See also References Genotype-by-Environment Interaction Glossary General Concepts Predicting Genotype-by-Environment Interaction Causes of Phenotypic Plasticity and Genotype-by-Environment Interaction Quantitative-Genetic Consequences of Genotype-by-Environment Interaction The Evolution and Adaptive Value of Phenotypic Plasticity Ecological and Evolutionary Outcomes of Genotype-by-Environment Interaction Acknowledgments See also References Genotype to Phenotype: Insights from Evo-Devo Glossary When the Linear Approximation Does Not Suffice Development and Morphological Diversity The Evolution of Development Conclusions See also References Geographic Mosaic of Coevolution Glossary Introduction Geographic Mosaics of Coevolution Geographic Mosaics of Diversifying Selection in Antagonistic Interactions Morphological evolution of pinecones, squirrels, and crossbills Effects of environment on a geographic mosaic of variation in a plant–galler–natural enemies interaction Geographic mosaics of competitive coevolution Geographic Mosaics of Mutualistic Coevolution The Geographic Mosaic of Coevolution in Human-Modified Environments Humans in Geographic Mosaics of Coevolution Conclusion See also References Hardy-Weinberg Equilibrium and Random Mating Glossary History The Hardy–Weinberg Principle Testing for Hardy–Weinberg Proportions Departures from Hardy–Weinberg Proportions Genotyping Error Non-Random Mating and Population Structure Natural Selection Other Causes See also References Hermaphrodites Glossary Introduction Hermaphroditism in Context The Evolution of Anisogamy and Its Consequences The Adaptive Significance of Having Two Routes to Fitness Local Competition and Sex Allocation Sex in Sequential Hermaphrodites The Role of Ecology and Social Interactions Extensions to the Basic Theory Sex in Simultaneous Hermaphrodites Pre- versus Post-Mating Sexual Selection Sex Role Preference as a Unique Pre-Mating Arena of Conflict Sex Allocation Manipulation as a Unique Post-Mating Arena of Conflict Outcrossing versus Self-Fertilization Outlook Acknowledgments See also References Homo, Diversification of Glossary Homo Habilis and Homo Rudolfensis Homo Erectus Homo naledi Homo Floresiensis Homo Antecessor Homo Heidelbergensis Homo Neanderthalensis The Denisovans Homo Sapiens See also References Human Life Histories, Evolution and Glossary Introduction Gestation Infancy Childhood and Adolescence Adulthood and Reproduction Menopause and Post-Reproductive Life In Conclusion See also References Further Reading Hybrid Speciation Glossary What Is Hybrid Speciation? Theory and Background Allopolyploid Speciation Homoploid Hybrid Speciation Evidence of Hybrid Speciation Is Hybrid Speciation Important? See also References Further Reading Inbreeding and Nonrandom Mating Glossary Inbreeding Inbreeding and Selection Assortative Mating Future for Inbreeding Acknowledgments See also References Industrial Melanism, History of Glossary The Peppered Moth H.B.D. Kettlewell Current Status See also References Inheritance: From Quantitative Genetics to Evolutionary Stable Strategies Glossary Population Level Means and Variation Around Them Individual Variation Finessing Inheritance in Life History Research Structured Models Quantitative Genetics Clonality and Evolutionarily Stable Strategy Simple Genetic Inheritance The Challenge of Inheritance See also References Insects and Ecdysozoa, Diversification of Insecta: Animal’s Major Radiation Arthropod Evolutionary Relationships Panarthropoda Ecdysozoans: The Molting Animals Acknowledgments See also References Further Reading Relevant Websites Intraspecific Coevolutionary Arms Races Glossary Introduction: Intraspecific Arms Races Coevolutionary Arms Races Over Mating Grasping and Anti-Grasping Structures Male Harassment and Female Resistance Traumatic Insemination Coevolutionary Arms Races Over Fertilization Sperm Competition Forced Copulations Toxic Seminal Proteins in Drosophila Conclusions: Who Wins an Intraspecific Arms Race? See also References Invasion Biogeography Introduction Phase Establishment Phase Spread Phase Impact Invasion Biogeography Summary See also References Relevant Websites Invasive Species, Evolution and Glossary Background Defining Invasive Species The Invasion Pathway Scope of the Invasion Problem Evolutionary Characteristics of Invasive Species Evolution of Invasive Species Invasive Species as Drivers of Native Species Evolution Implications for the Future: Applying an Evolutionary Perspective to Invasive Species Management See also References Land Animals, Origins of Glossary Introduction Physiology The Fossil Record Trace Fossils Body Fossils Ludford Lane Rhynie Chert Gilboa Younger Records Routes onto Land Conclusion See also References Land Vertebrates, the Origin and Evolution of Glossary Who Are the Land Vertebrates? A Phylogeny and Timescale for Tetrapod Origins What Were Conditions Like during the Late Devonian? What Stimulated the Evolution of Land-Going by Vertebrates? Among Lobe-Fins, What Advantages Were Crucial to the Move onto Land? What Were the Earliest Tetrapods and Their Immediate Ancestors Like? How Did These Early Tetrapods Move? When Did True Terrestrial Locomotion and Terrestrial Living Develop? See also References Lichen-Forming Fungi, Diversification of Glossary The Evolution of Current Species Diversity in Space and Time Adaptive Radiation and Explosive Diversification Association of Rates of Diversification and Evolutionary Rates The Diversity of the Photobiont in the Lichen Symbiosis See also References Life Histories, Axes of Variation in Glossary A Brief History of the Origin of the Slow–Fast Continuum Empirical Analyses of Life History Variation in Vertebrates Problems of Dimensionality When Assessing a Slow–Fast Continuum What Shapes the Slow–Fast Continuum of Life Histories? Evolutionary Consequences of the Slow–Fast Continuum Are There Other Axes of Life History Variation Than the Slow–Fast Continuum? Perspectives: Beyond Interspecific Analyses and Toward an Integrated Pace of Life Syndrome See also References Life History: Age and Stage Structure Introduction Individual Vital Rates Stable Cohorts Population Structure and Growth Stable Population From Vital Rates to r: Levels and Timing Discussion Acknowledgments See also References Life-History Evolution, Human Glossary Then and Now: The Unusual Life History of Humans Phenotypic Correlations between Human Life-History Traits and Fitness A Crash Course in Quantitative Genetics Case Studies on Using Quantitative Genetics to Understand Life-History Evolution in Humans Life-History Traits are Heritable Genetics of Life-History Traits in the Two Sexes – an Arena for Conflict Genetics of Life-History Traits over the Lifetime Genetics of Life-History Traits Over Time and Across Environments Studying Human Life-History Evolution in the Genomics Era See also References Further Reading Life-History Evolution, Human Impacts on Glossary Introduction Selection and Response to Selection Natural and Anthropogenic Sources of Selection Response to Directional Selection Evolutionary Response to Harvesting Non-Phenotypically Selective Harvesting Phenotypically Selective Harvesting Evolutionary Response to Habitat Loss and Fragmentation Size-Dependent Selection Dispersal-Dependent Selection Evolutionary Response to Climate Warming Reversibility of Trait Changes and Population Recovery Evolvability Change in the Naturally Selected Adaptive Landscape See also References Life History Evolution in Guppies, Experimental Studies of Glossary The Evolution of Life Histories in Guppies Life History Evolution in the 1970s Guppies and Trinidad Comparative Life Histories Experimental Evolution Life History Evolution in the 1990s – Awkward Adolescence Mortality Rate Estimates Comparative Ecology Evolution of Senescence Summary Life History Evolution in the Twenty-First Century Density Regulation Guppy-Rivulus Interactions and the Demise of the Superguppy Experimental Evolution II See also References Life-History Evolution in Island Populations of Birds Body Size and Shape Reproductive Behavior and Life-History See also References Further Reading Life History Evolution, Plants Glossary Background Using Evolutionarily Stable Strategy Methods to Understand Evolution in Perennial Plants Summary See also References Life History Evolution: The Role of Mating Systems Why Mating and Life History Have to be Associated? The Role of Mating on Life History Evolution Timing, Behavior, and Mating Preference Mating System Ways Life History Can Influence Mating Survival Fertility Reproductive Morphs Sex Allocation and Sexual Conflict Sex Allocation Sexual Conflict Modeling Framework Conclusion Acknowledgment See also References Life History Patterns Glossary Background Senescence in Humans Senescence in Non-Human Vertebrates Beyond Mammals and Birds The Plant Kingdom Conclusions See also References Further Reading Life History: Pike Introduction The Goal of This Section Some Aspects of Pike Ecology and Life History Methods Study System and Data Estimation of Vital Rates Model Description Pike life cycle of the model Vital rate functions Offspring number Offspring length distribution Survival probability Somatic growth rate Projection Kernel and Population Dynamics Net Reproductive Rate and Generation Time Discretization of the Model for Numerical Calculations Results Mean Growth Rate (fitness), Stable Structure, and Reproductive Value Net Reproductive Rate and Generation Time Conclusions Acknowledgments See also References Further Reading Relevant Websites Life History Theory: Basics Connection between Population Dynamics and Life History Population Projection Structured by Discrete Age or Stage Classes Markov Chains for Individuals Traversing the Life Cycle Age-Patterns of Survivorship and Fertility in Age-Structured Populations Age-Patterns of Survivorship and Fertility in Stage-Structured Populations Markov Chain Analysis for Stage-Structured Populations Conclusion See also References Life History Trade-offs What Are Trade-offs and Why Do They Exist? Examples of Important Life History Trade-offs Measuring Trade-offs Why Do We Observe a Positive Correlation Where We Expect a Negative One Between Traits? Evolution of Life History Trade-offs See also References Life History, What is? Life History and Life History Traits Life Tables and Euler–Lotka Equation The Fitness Concept Trade-Offs and Constraints Analytical Framework See also References Linkage Disequilibrium: Population Genetics of Multiple Loci Glossary Causes of Linkage Disequilibriuim Measures of Linkage Disequilibrium Strength Multi-Locus Linkage Disequilibrium Measures Linkage Disequilibrium Significance Linkage Disequilibrium and Natural Selection See also References Lophotrochozoa, Diversification of Introduction Members and Relationships Origins See also References Macroevolution, Quantitative Genetics and Glossary Introduction Controversies Nonmetric Traits Continuous Quantitative Phenotypic Traits Selection Regimes and Rates of Evolution Adaptive Peaks Phylogenetic Comparative Methods Hypothesis Testing Units of Analysis Morphometrics and Multivariate Phenotypes Conclusion Supplementary Material See also References Further Reading Mammalian Diversification Introduction Early Phases of Mammalian Diversification Origin and Diversification of Living Mammals Diversification of Placental Mammals Morpho-Ecological Diversification and Convergent Evolution See also References Mammals Everywhere Introduction Hallmarks Body size Life Modes The Age of Mammals See also References Mammals, Origin of Introduction Mammalian Characteristics Early Evolution of Synapsids Evolution of Mammalian Characteristics Mammalian Evolution See also References Mate Choice and Sexually Selected Traits Glossary Introduction Female Preferences for Male Traits The Origin of Female Mating Preferences: Sensory Bias Elaboration of Female Mating Preferences Fisherian Process Direct Benefits of Mate Choice Good Genes Condition-Dependent Indicators Revealing Indicators Pure Epistatic Indicators Heritability of Display Traits The Importance of Mating System Display Traits in Females Trait Evolution during Speciation See also References Maternal Effects Glossary Introduction The Quantitative Genetics of Maternal Effects Models with Fixed Maternal Effect Coefficients Insights from the K–L Model Trait Covariance and Coadaptation Empirical Validation Evolving Maternal Effect Coefficients Phenotypic Plasticity Extensions Heritability Extended: Nongenetic Inheritance See also References Mating and Parental Sex Roles, Diversity in Glossary Introduction What Causes Sexual Differences in Mating and Parental Roles? Mating Roles Parental Roles Variation in Mating and Parental Roles Polyandrous Females Armed and Ornamented Females Choosy Males Caring Males Unresolved Questions about Sex Roles See also References Mating Systems, A Brief History of Glossary Mating Dynamics Are Highly Diverse History of a Name: Defining Mating Systems Mate Monopolization Matters The Link between Operational Sex Ratio, Sexual Selection, and Mating System Parental Investment and Sexual Selection Shape Mating Systems Females Benefit from Multiple Mating and Paternity is often Uncertain Conclusions: Understanding Mating Systems Requires a Focus on Co-Evolutionary Dynamics See also References Mating Systems in A Changing Environment Glossary What Determines Mating Systems? Why are Mating Systems Sensitive to Environmental Change? How Does Environmental Change Influence Mating Systems? Resource Acquisition and Defense Mate Encounter Rate Mate Attraction and Mate Choice Fertilization Parental Care and Offspring Survival Consequences of Altered Mating System? See also References Mating Systems in Flowering Plants Glossary Introduction Evolution of Mating Systems Sexual Systems and Gender Strategies See also References Mating Systems in Plants, Genome Evolution and Glossary Introduction Changes in Breeding Systems and Their Effects on Population Genetics Parameters Effects on Heterozygosity Levels Effects on Effective Recombination Effects on Effective Population Size Effects on the Efficacy of Selection Breeding Systems and Within-Species Neutral Diversity Selfing, Asexuality and Within-Species Neutral Diversity Self-Incompatibility and the S-Locus Neutral Diversity Breeding Systems and the Global Efficacy of Natural Selection The Transition from Outcrossing to Selfing The Transition from Sexuality to Asexuality The Transition from Hermaphroditism to Dioecy Breeding Systems and the Evolution of Genome Base Composition Breeding Systems and the Evolution of Chromosomes and Genome Structure Breeding Systems and the Evolution of Genome Size Breeding Systems and Ploidy Levels Breeding Systems and Insertion/Deletion Breeding Systems and TE Dynamics Breeding Systems and B Chromosomes Global Effect of Breeding Systems on Genome Size Conclusion See also References Further Reading Relevant Website Mating Tactics and Mating Strategies Glossary Introduction What Form Do Alternative Mating Tactics Take in Nature? Why Do Alternative Mating Tactics Interest Evolutionary Biologists? What Mechanisms Allow the Evolution of Alternative Mating Tactics? Conclusions and Future Directions See also References Maximum Likelihood Phylogenetic Inference Glossary Introduction Phylogenetic Likelihood Likelihood Description Likelihood Computation Root Invariance and the Pulley Principle Likelihood Maximization Branch Length Optimization Tree Topology Search Consistency of Maximum Likelihood Estimates Bootstrap for Phylogenies Bootstrap Description Summarizing Bootstrapped Phylogenies Maximum Likelihood and More Complex Models of Evolution Example: Primate Phylogeny Estimation See also References Relevant Websites e9780128000496v3_WEB Encyclopedia of Evolutionary Biology Editor in Chief Section Editors List of Contributors Guide to Using the Encyclopedia Structure of the Encyclopedia 1. Alphabetical Contents List 2. Cross-references See also 3. Subject Classification List 4. Index 5. Contributors Preface Foreword Metazoans, Origins of Origin of Metazoans A Protozoan Ancestor The Oldest Extant Metazoan Origin of the Sponges See also References Microbial Experimental Evolution Glossary Introduction Experimental Evolution Experiments Comparative Method Experimental Method Controls in Short-Term Experiments Long-Term Experimental Evolution Evolution Microevolution Phenotype Change Gene Frequency Change Migration Mutation Natural Selection The Environment Future of Experimental Evolution See also References Microbiome Glossary Introduction How Do We Find Out About Microbiomes? What Differentiates Host-Associated Microbiomes from Environmental Samples? What Factors Shape Microbiomes Across Different Animal Species? What Factors Shape the Microbiome Within a Species? Outlook for Evolutionary Biologists Interested in the Microbiome See also References Mitochondrial and Nuclear Genome Coevolution Glossary Introduction Primer on Mitochondrial Genetics and Genomics Mitochondrial–Nuclear DNA Mutation Rate Differences, Resultant Incompatibilities, and Coevolution Coevolution and Physical Interaction Mitochondrial–Nuclear Coevolution in the Mitochondrial Protein Translation System Mitochondrial–Nuclear Coevolution of Regulatory Elements Heteroplasmy and Its Effect on Mitochondrial–Nuclear Coevolution Interference with Mitochondrial–Nuclear Interactions Cause Diseases See also References Further Reading Model Systems: The Key Roles of Traditional and New Models in Evolutionary Developmental Biology Glossary Introduction The Role of Traditional Model Organisms in Evolutionary Developmental Biology The Role of New Model Organisms in Evolutionary Developmental Biology See also References Modularity and Integration Glossary What Is Modularity and Integration? The Causes of Modularity: Development and Function The Origin of Modularity and Integration from a Genetic Perspective Empirical Studies Investigating Modular Patterns Evolutionary Implications and Some Caveats See also References Modularity and Integration in Evo-Devo Glossary Measuring Integration and Modularity Experimental Analysis and Direct Measurement of Integration Evolution May Favor Modularity; Modularity May Bias Evolution See also References Molecular Evolution, Functional Synthesis of Glossary Background Setting the Stage Rise of the Functional Synthesis Epistasis and Ancestral Sequence Reconstruction Some Consequences of Epistasis Causes of Selection Adaptive Constraints Mechanisms of Gene Duplication and Functional Divergence On the Use and Abuse of Statistics Epilogue See also References Molecular Evolution, History of Introduction Experimenting with Molecular Evolution A Troubled Beginning Making Molecular Evolution The Coming of the DNA Era See also References Molecular Evolution, Models of Glossary Introduction Mathematical Modeling of Substitution Dynamics Continuous Time Substitution Rates Calculating Substitution Probabilities Steady-State Distribution Time-Reversibility Modeling the Evolution of Molecular Sequences Models for DNA Sequences Models for Double-Strand RNA Models for Protein Coding Sequences Heterogeneous Evolutionary Dynamics and More Complex Models Model Selection Bias and Variance Testing Model Fit Robustness See also References Multivariate Quantitative Genetics Glossary Evolution Is a Multivariate Process What Does G Tell Us about Evolution? An Empirical Example Evolvability and Genetic Constraint Based on Estimates of G Evolvability and Genetic Constraint Based on Estimates of G and Selection The Limitations Associated with Using G to Understand Multivariate Evolution See also References Mutation and Genome Evolution Glossary Introduction Theoretical Considerations: Rate of Substitution and Stable Polymorphisms For Neutral and Harmful Mutations Genome Size Under Mutational Pressure Variation at Microsatellite Sites CG Content Across and Within Genomes Replication and Mutation Do Mutation Rates Evolve? See also References Further Reading Mutation, Population Genetic Models of See also References Mutualism, the Evolutionary Ecology of Glossary Introduction The Origin of Mutualism The Maintenance of Mutualism Mutualism, Specialization, and Coevolution The Community Context of Mutualism Synthesis See also References Mycorrhizal Fungi, Evolution and Diversification of Glossary Overview Common Patterns and Key Drivers of Diversification Diversification of Arbuscular Mycorrhizal Fungi Diversification of Orchid Mycorrhizal Fungi Diversification of Ericoid Mycorrhizal Fungi Diversification of Ectomycorrhizal Fungi Specialized Mycorrhizal Forms Within the Ericaceae Diversification of Arbutoid Mycorrhizal Fungi Diversification of Monotropoid Mycorrhizal Fungi Summary See also References Natural Selection, Introduction to Glossary Genotype versus Phenotype Fitness and Strength of Selection Effects of Selection Stochasticity Factors Affecting the Action of Selection Acknowledgments See also References Natural Selection, Measuring Glossary What Is Selection? The Data: Phenotypes and Fitness Modes of Selection How to Measure Selection The Details of a Selection Analysis Selection gradients (β and γ): Direct selection on a trait Selection differentials (S and C): Total selection on a trait Limitations and Underlying Assumptions Exploring the Complexity of Fitness Functions Rugged Fitness Functions Selection on Many Traits at Once Identifying the trait combinations containing the most variance Identifying the trait combinations under the strongest selection Complex Causal Relationships between Phenotypes and Fitness Targets and Agents of Selection Targets of Selection Agents of Selection Conclusion See also References Further Reading Neutral Evolution, Population Genetic Tests of Glossary Introduction Site Frequency Spectrum-Based Methods HKA MK Comparison of the HKA and MK Tests Other Tests of the Neutral Model Haplotype-Based Tests Population Differentiation See also References Further Reading Neutral Models of Genetic Drift and Mutation Glossary Random Genetic Drift The Wright–Fisher Model Loss of Diversity in the WF Model The Diffusion Approximation Mutation Models K-Alleles Model Infinite Alleles Model Infinite Sites Model Patterns of Neutral Genetic Variation Under Mutation and Drift The Coalescent Process Adding Mutations to the Coalescent Site-Frequency Spectrum in an Infinite Sites Model Ewen’s Sampling Formula for the Infinite Alleles Model The Neutral Theory of Molecular Evolution See also References Noncoding DNA Evolution: Junk DNA Revisited Glossary Introduction CRE Structure/Function CREs and Length Variation of ncDNA Preservation by Functional Constraint Preservation of Function and Evolutionary Changes in CREs Models of Enhancer Evolution Origin of Cis-Elements with Novel Function Conclusion Acknowledgment See also References Further Reading Noncoding RNAs, Origin and Evolution of Glossary General Introduction microRNAs Origin of microRNAs Evolution of microRNAs Short-Interfering RNAs Origin of Short-Interfering RNAs Evolution of Short-Interfering RNAs Piwi-Interacting RNAs Origin of Piwi-Interacting RNAs Evolution of Piwi-Interacting RNAs Small RNAs in Prokaryotes Interconnected Evolution of Small RNA Machinery Conclusion Acknowledgments See also References Novel Structures in Animals, Developmental Evolution of Glossary Overview Historical Perspective What Is an Evolutionary Novelty? How Do Novel Structures Arise? Case Studies Turtle Shells Bat Wings Beetle Horns Insights Prospects for Advancing Inquiry See also References Novel Structures in Plants, Developmental Evolution of Glossary Introduction Habit or Life Form Leaves Leaf Morphology Variation Genetic Basis of Leaf Development Inflorescences Cauliflory and Ramiflory Pseudanthia and Peloria Genetic Basis of Inflorescence Development Flowers Case Study – Floral Synorganization in Aristolochiaceae and Aristolochia (Aristolochiaceae) Floral organ identity genes Floral symmetry genes Orchidaceae Floral organ identity genes Floral symmetry genes Fruits Acknowledgements See also References Further Reading Relevant Website Operational Sex Ratio Glossary Introduction The Origins of OSR Changes in Definition Changes in Emphasis Changes in Personnel Evolutionary Interpretations What OSR Does Measure? What OSR Doesn’t Measure? OSR in Experimental Situations Summary See also References Origin of Life, RNA World and Glossary Getting Life Started Factors Pointing to RNA Alternatives to RNA Synthesis of RNAs and Ribozymes Evolutionary Theory See also References Origins of Life, History of Introduction Origin of Life in the Ancient Period Seventeenth-Century Thoughts and Discoveries on Spontaneous Generation Spontaneous Generation and Uniformitarianism in the Eighteenth Century Nineteenth-Century Materialism and Cell Division Alternation of Generations End of Spontaneous Generation Panspermia The Biogeochemical Hypothesis What Is Life? Origin of Life: Urey–Miller’s Experiments RNA/DNA Biochemistry ‘Life’ in Recent Philosophical Debates Astrobiology: The Past, the Present, and the Future Conclusion See also References Paleobiogeography and Fossils Glossary Introduction Historical Background Some Basic Concepts Reconstructing Ancient Geography Analyzing Ancient Biogeography Biogeographical Patterns through Deep Time See also References Relevant Websites Paleobiological Revolution, History of Glossary The Prehistory of Paleobiology Synthetic Paleobiology The Paleobiological Impulse Paleobiology’s New Start A Chancy Young Man’s Game Establishing Paleobiology Paleobiology Comes of Age See also References Further Reading Parallel and Convergent Molecular Evolution Glossary Introduction Integrating Molecular Convergence from Molecules to Phenotypes A Conceptual Understanding of Convergence and Parallelism Discriminating Adaptive and Nonadaptive Molecular Convergence Molecular Convergence, Ancestral Reconstruction, and Phylogenetic Inference Conclusion See also References Parallel Speciation Glossary What is Parallel Evolution? Evidence for Parallel Evolution Parallel Speciation Evidence for Parallel Speciation Molecular Basis of Parallelism Conclusion Acknowledgments See also References Further Reading Parsimony Methods in Phylogenetics Glossary Parsimony History and Philosophy The Basic Procedure Evidence Trees Character Polarity Tree Properties and Metrics Character Weighting Uses of Parsimony Trees See also References Pathogen Epidemiology Glossary The Reproductive Number Transmission Routes and the Target of Selection Molecular Epidemiology: The Short and Long Term Genomic Epidemiology Phylodynamics and Using DNA Sequence to Study Transmission Conclusion See also References Pest Management, Evolution and Glossary Overview Retarding Resistance Biological Control Wolbachia Selfish Genetic Elements MEDEA Homing Elements The Mutagenic Chain Reaction The Evolution of Generalist Pests and the Niche Explosion See also References Philosophy, Evolutionary Biology and Introduction: Philosophy and Evolutionary Biology Philosophy and Conceptual Analysis Levels of Selection/Multilevel Selection Theory The Organism and Individuality Niche Construction The Nature of Selection, Fitness, and Drift Adaptations and Functions The Nature of Populations The Gene Concept Philosophy and Evidentiary Questions The Implications of Evolutionary Biology on Philosophical Problems Final Thoughts See also References Phylogenetic Approach to Studying Developmental Evolution: A Model Clade Approach Glossary Toward the Use of Phylogenetics in Evo-Devo Model Clade Approach Dipsacales, an Example of a Model Clade for Floral Symmetry Phylogenetic Evo-Devo Studies Gene Expression across Model Clades Gene Function or Regulation across Model Clades Phylogenomics Conclusion Acknowledgments See also References Phylogenetic Comparative Method Glossary See also References Phylogenetic Invariants Introduction Phylogenetic Models on Gene and Species Trees Phylogenetic Models on Gene Trees Site Pattern Probabilities for Species Trees under the Coalescent Phylogenetic Invariants Splits and Flattenings Edge invariants Using Phylogenetic Invariants Identifiability Species and Gene Tree Inference Conclusion Acknowledgments See also References Phylogenetic Networks Glossary Phylogenetic Trees First Beyond a Single Tree The Data Data-Display Networks Evolutionary Networks Summary See also References Relevant Websites Phylogenetic Tree Glossary Introduction Tree Terminology What a Tree Represents Do Trees Show Advancement and Progress? Relatedness Branch Length Unrooted Trees Trees as Substrate See also References Phylogenetic Tree Comparison Glossary Likelihood Ratio Is (Almost Always) the Best Test Statistic Null Hypotheses Calculating the δ Statistic in Phylogenetics The Null Distribution of the Likelihood Ration Is Not Trivial to Obtain The Null Hypothesis That Expected Likelihood Is the Same for Multiple Trees Using Per-Character δ’s to Generate a Null Distribution Kishino-Hasegawa Test Selection Bias Problems Shimodaira–Hasegawa Test Tests Based on Parametric Bootstrapping Quick and Dirty Methods Pure Resampling Approaches Adjusted Bootstrap Proportion Further Considerations See also References Relevant Website Phylogenetic Tree Distances Introduction Squared Euclidean Distances Robinson–Foulds Distance Quartet Distance Dissimilarity Map Distance Path Difference Tree Rearrangement Distances Nearest-Neighbor Interchange Distance Subtree-Prune-and-Regraft Distance Tree-Bisection-and-Regrafting Distance Disagree Distance Billera–Holmes–Vogtmann Geodesic Distance Other Tree Distances Matching Splits Distance Maximum Parsimony Distance See also References Phylogeography Glossary Integrating Across Disciplines History and Development Current Status Challenges and Future Directions See also References Plant-Pollinator Interactions and Flower Diversification Glossary Effects of Floral Traits on Speciation Rates Ethological Isolation Mechanical Isolation Effects of Floral Traits on Extinction Rates Effects of Diversity on the Evolution of Specialized Flowers Conclusions See also References Plasmid Driven Evolution of Bacteria Glossary Plasmids and Horizontal Gene Transfer Coevolution of Plasmids and Bacteria Conclusions Acknowledgments See also References Polyandry and Female Postcopulatory Choice Glossary Defining Cryptic Female Choice The Problem of Paternity Patterns in Investigating CFC Differential Sperm Storage as Mechanism Sexual Conflict and CFC Conclusion See also References Polyploid Speciation Glossary Introduction Polyploid Speciation I: The Formation of New Species by Polyploidization Mechanisms of Polyploidization The Nature of New Polyploids The Rate at Which New Polyploids Establish The Role of Polyploidization in the Formation of Species Polyploid Speciation II: The Speciation of Polyploids The Influence of Ploidy on Diversification Rates Conclusions See also References Population Structure and Gene Flow Glossary Inference of Structure The Context of Population Structure See also References Predation and Parasitism Introduction Coevolutionary Arms Races Codiversification Parasite Transmission and the Attenuation of Virulence Coevolution and Ecological Dynamics Macroevolutionary Patterns See also References Further Reading Protein Biophysics and Evolution Glossary Introduction Biophysical Mechanisms Protein Folding and Protein Stability Protein Function: Catalytic Sites, Protein–Protein Interactions, Ligand Binding Toxic Functions and Protein Misfolding Biophysical Effects of Mutations Mutations and Stability Changes Epistasis Protein Stability and Mutations that Generate Novel Function How Protein Biophysics Shapes Sequence Evolution Purifying Selection in the Core of Proteins and in Protein–Protein Interfaces Positive Selection in Viral Immune Escape See also References Protist Diversification Glossary What are Protists? Evolutionary and Ecological Importance The Origin of Eukaryotes – A Brief Overview Ancient History of Eukaryotes Endosymbiosis; The Mitochondrion Primary Plastids Secondary Endosymbiosis Complex Plastids, Complex History Uncovering Protist Diversity and Phylogeny The Diversity of Living Eukaryotes Archaeplastida Sar Stramenopiles Alveolata Rhizaria Excavata Amorphea Amoebozoa Obazoa (including opisthokonta) Other Groups Concluding Remarks Acknowledgments See also References Quantitative Genetics in Natural Populations Glossary Introduction Why Study Wild Populations? Genetic Variation and Covariation: A Brief Primer Development of Quantitative Genetics in the Wild Inferring Relatedness Linear Mixed Effect Modeling and the ‘Animal Model’ Lessons and Limitations Genetic Variance Is Widespread and Abundant Evolutionary Change Is Hard to Predict and to Detect Trade-Offs May Not Be as Important as We Thought Increasing the Range of Study Organisms and Focal Traits Analytical and Statistical Challenges Emerging Directions Toward a Multivariate View of Adaptation and Constraint Social Interactions and Shared Phenotypes Genetic Architecture of Quantitative Traits Conclusions Acknowledgments See also References Quantitative Genetic Variation Properties of Quantitative Traits Partitioning Variance Components Heritability Quantitative Trait Loci Mapping Lessons Learned Future Prospects See also References Quantitative Genetic Variation, Comparing Patterns of Glossary How do We Describe G? How do We Compare G? Flury and Krzanowski Methods A. General Formulae B. Krzanowski Common Subspace C. Vector-Based Approaches D. Tensors Vector Approaches References Tensors Evolutionary Processes and G See also References Quantitative Trait Variation, Molecular Basis of Glossary Introduction Characterizing the Molecular Basis of a Quantitative Trait Identifying QTGs Characterizing QTNs Studying the Mechanisms by which Multiple QTNs Influence a Trait The Molecular Underpinnings of Quantitative Genetic Effects Additivity Dominance Pleiotropy Genetic Interactions Gene–Environment and Genotype–Environment Interactions Conclusion Acknowledgments See also References Quaternary Biogeography and Climate Change Glossary Introduction Quaternary Climate Change Orbital Variation and Quaternary Glacial–Interglacial Cycles Rapid Climate Change and the Last Glacial–Interglacial Transition Holocene Variability Quaternary Biogeography Population and Species Responses to Climate Change Abundance change Genetic change Range shifts Speciation Extinction Community Responses to Climate Change Conclusion See also References r- and K-Selection in Fluctuating Environments, Theory of Glossary An Introduction to r- and K-Selection Deterministic Models r- and K-Selection in Fluctuating Environments Discussion Acknowledgments See also References Recombination and Molecular Evolution Glossary Introduction Recombination and Adaptation Theoretical Background Empirical Evidence for an Advantage of Recombination Recombination and Neutral Variation Conclusion See also References Recombination and Selection Glossary The Interaction between Recombination and Selection Optimality Arguments Modifier Theory Important Optimality Models of Recombination and Selection The Fisher-Muller Model and the Role of Negative Linkage Disequilibrium Hill-Robertson Effect Muller’s Ratchet Selection Fluctuating Over Time and Space – the Red Queen and Other Models Modifier Theories of Recombination Modifier Theory in Large Populations Modifier Theory in Small Populations – The Role of Genetic Drift Modifiers of Recombination and Genetic Drift in Large Populations Epistasis, Genomic Architecture, and Fitness Landscapes Acknowledgments See also References Further Reading Recombination in Bacterial Populations Glossary Introduction What Is Bacterial Recombination? Core and Noncore Genomes Is Bacterial Recombination Akin to Eukaryotic Sex? The Multiple Ways in Which Recombination Rates Vary Bacterial Sex Is Localized Recombination and Evolutionary Analyses Sex with the Dead Promiscuity and Specious Species Why Do Bacteria Recombine? Concluding Comments See also References Regulatory and Coding Changes in Developmental Evolution, Roles of Glossary Coding versus cis-Regulatory Sequences Changes in Coding Sequences Nature of changes in coding sequence The Edar mutation in Asian populations The Oca2 gene in Astyanax populations and albinism Changes in cis-Regulatory Sequences The yellow gene and the Drosophila pigmentation Pitx1 enhancers in sticklebacks and the evolution of the pelvic region The Primacy of Coding versus CRE in the Generation of Novelties The First Debate The Coding and CRE Changes in the Actual View of Genotype/Phenotype Relationship See also References Reinforcement Glossary Introduction The History of Reinforcement From Pattern to Process – Criteria for Reinforcement Macro-Evolutionary Patterns Reproductive Isolation with Gene Flow The Genetics of Reinforcement Future Directions See also References Further Reading Reproductive Isolation, Postzygotic Glossary Structural Genomic Variation and Postzygotic Isolation Allelic Divergence, Genomic Conflict, and Postzygotic Isolation Meiotic Drive and Postzygotic Isolation Haldane’s Rule Genetic Incompatibilities and the Dominance Theory Postzygotic Isolation Contributing to Increased Behavioral Isolation See also References Further Reading Relevant Websites Reproductive Isolation, Prezygotic Glossary Prezygotic Isolation Causes of Prezygotic Isolation Allochronic Isolation Pollinator Isolation Sexual Isolation in Animals Mechanical Isolation Gametic Isolation Relative Rates of Evolution Conclusions See also References Responses to Climate Change, Evolution and Glossary Introduction Retrospective Studies: Responses to Recent Climate Change Emergence Date in Pitcher Plant Mosquitoes Breeding Date in Birds Shifting Allele Frequencies in Australian Drosophila Prospective Studies: What Is the Potential for Future Adaptation? Quantitative Genetics Experimental Evolution Artificial Selection Will Evolution Matter? Incorporating Evolutionary Thinking into Management Decisions See also References Ring Species Uses of the Ring Species Concept Illustrating the Fact that Species Evolve Showing the Importance of Geography in Speciation Reconstructing the History of Changes During Speciation Illustrating that Speciation Can Occur Despite Gene Flow Types of Ring Species How Do Ring Species Form? Example Ring Species Greenish Warblers Ensatina Salamanders Other Proposed Cases Conclusion See also References Relevant Websites RNA Viruses, Evolution of Glossary The Origins and Evolutionary History of RNA Viruses The Origins of RNA Viruses The Timescale of Virus Evolution Evolutionary Relationships among RNA Viruses RNA Virus Emergence Genome-Scale Evolution The Evolution of Genome Structure and Size Mechanisms of Genome Evolution Processes of RNA Virus Evolution Rates of Viral Evolution Processes of Molecular Evolution in RNA Viruses Interactions between Virus Mutations and Genomes RNA Virus Recombination See also References Further Reading Relevant Websites Robustness and Evolvability in Molecular Evolution Glossary Proteins RNA Gene Regulation and Gene Regulation Circuits Caveats See also References Further Reading Rooting Trees, Methods for Rooted versus Unrooted Why Do We Need a Rooted Tree? When Do We Need an Unrooted Tree? How Do You Root a Phylogenetic Tree? Outgroup Rooting Midpoint Rooting Molecular Clock Rooting Bayesian Molecular Clock Rooting Acknowledgment See also References Schools of Classification Glossary Classifications before Linnaeus Linnaeus Developments Immediately after Linnaeus Darwin and Ideas of Relationships Species Collecting and Collections Biology, Natural History, and Botany See also References Searching Tree Space, Methods for Glossary Introduction Top-Level View of Search Algorithms Building Starting Trees Changing Topologies Search Strategies Advanced Topics Computational Costs of Tree Moves Terraces in Tree Space Discussion See also References Regulatory and Coding Changes in Developmental Evolution, Roles of Glossary Coding versus cis-Regulatory Sequences Changes in Coding Sequences Nature of changes in coding sequence The Edar mutation in Asian populations The Oca2 gene in Astyanax populations and albinism Changes in cis-Regulatory Sequences The yellow gene and the Drosophila pigmentation Pitx1 enhancers in sticklebacks and the evolution of the pelvic region The Primacy of Coding versus CRE in the Generation of Novelties The First Debate The Coding and CRE Changes in the Actual View of Genotype/Phenotype Relationship See also References e9780128000496v4_WEB Encyclopedia of Evolutionary Biology V4 Editor in Chief Section Editors List of Contributors Guide to Using the Encyclopedia Structure of the Encyclopedia 1. Alphabetical Contents List 2. Cross-references See also 3. Subject Classification List 4. Index 5. Contributors Preface Foreword Contents Secondary Metabolites, the Role in Plant Diversification of Glossary What are Secondary Metabolites? Diversity of Secondary Metabolites Biosynthesis and Storage of Secondary Metabolites Function of Secondary Metabolites as Defense and Signal Comp Secondary metabolites as defense compounds Secondary metabolites as signaling compounds Exceptions to the rule When Did the Secondary Metabolism Evolve? How Did Plants Acquire the Genes for Secondary Metabolism? How to explain the patchy distribution of SM? Evolutionary Pharmacology and Phytotherapy See also References Security, Evolution and Key Definitions Introduction Approaches Direct Analogies from Nature Emergent Properties Evolutionary and Ecological Models Targets and Prospects See also References Further Reading Relevant Websites Seedless Land Plants, Evolution and Diversification of Glossary Bryophytes Bryophytes as the Earliest Land Plants? Alternating Generations and the Haploid Lifestyle Ambiguity in Relationships Among Bryophytes Ancient Origins Followed by Later Diversifications Lycophytes Diversity in Morphology and Habitat Preferences The First Branch in Vascular Plants Converging on the Leaf and Tree Habit Ferns Fern Distributions and Diversifications Rearranging the Family Tree: Horsetails Among the Ferns Understanding Why Rates of DNA Evolution Vary Polyploidization and the Origin of Species See also References Selective Sweeps Glossary Introduction Examples of Selective Sweeps Basic Population Genetic Models of Natural Selection Expected Patterns Methods for Inference Site Frequency Spectrum Methods Tajima’s D and others Composite likelihood of site frequency spectrum Haplotype Methods Extended haplotype homozygosity Integrated haplotype score Cross-population extended haplotype homozygosity Alternatives to using a genetic map Simulation Methods Structured Coalescent Forward Simulations Some Caveats Nonequilibrium Demography Background Selection Alternative Models See also References Sensory Systems: Molecular Evolution in Vertebrates Introduction Photoreception Chemoreception Odorant Perception Olfactory receptors Vomeronasal receptors Gustatory Perception Auditory Perception Electroreception and Electrogenesis Thermoreception Concluding Remarks and Future Research See also References Sequential Speciation Glossary The Biodiversity Question and Sequential Speciation General Implications of Sequential Speciation Distinguishing Sequential Speciation from Strict Co-speciation Conditions Conducive for Sequential Speciation Evidence Supporting Sequential Speciation Case 1: One Host, One Natural Enemy: The Goldenrod Stem Galler, Eurosta solidaginis, and the Tumbling Flower Beetle,... Speciation of host Sequential speciation of natural enemy Case 2: One Host, Many Natural Enemies: The Apple Maggot Fly, Rhagoletis pomonella, and Three Parasitoids: Diachasma... Speciation of host Sequential speciation of natural enemies Systems Lacking Evidence Concluding Remarks: Future Directions Acknowledgment See also References Sex and Recombination in Snails Glossary Introduction Gastropod Reproductive Systems Patellogastropoda Vetigastropoda Cocculiniformia Neritimorpha Caenogastropoda Heterobranchia Opisthobranchia Pulmonata Conclusions Acknowledgments See also References Sex and Selfish Genetic Elements Glossary Introduction Short-Term Impacts of Mating Behavior on SGEs: Sperm-Killing Meiotic Drive and Polyandry Summary Long-Term Impacts of Mating Systems on SGEs: Transposable Elements, Sex, and Mating Systems Summary Long-Term Impacts of SGEs on Mating Systems: The Case of Cytoplasmic Male Sterility Summary Short-Term Impacts of SGEs on Mating Systems: Endosymbiont Manipulation Summary Final Thoughts Acknowledgments See also References Sex Chromosome Evolution: Birth, Maturation, Decay, and Rebirth Glossary Introduction Acquisition of a Sex-Determining Function Sexual Conflict and Sex Chromosomes Suppression of Recombination Why Does Suppression of Recombination Occur? How Is Recombination Suppressed? Sex Chromosome Degeneration Recombination and Selection Intralocus Competition and Selective Gene Silencing Gene Content of Late-Stage Sex Chromosomes Degeneration-Driven Loss and Turnover of Sex Chromosomes Does Degeneration Lead to Loss of the Minor Sex Chromosome? Escape from Degeneration and Neo-Sex Chromosomes Sex Chromosome Turnover and SD System Transitions Conclusions and Open Questions See also References Further Reading Sex Determination Glossary A Brief History of the Sexes How Sex Is Determined? Genetic Sex Determination Environmental Sex Determination Other Sex Determining Mechanisms Evolution of Different Sex Determining Systems Sex Ratio Selection Sexual Conflict Endosymbiotic Bacteria Evolution of Sex Chromosomes Sex Ratio Distorters Molecular Mechanism of Sex Determination Insects Vertebrates Flowering Plants Why Are Some Groups so Variable? Outstanding Questions See also References Sex, Evolution and Maintenance of Introduction Short-Term Benefits of Sex Epistasis Temporal Changes in Selection Migration and Spatial Changes in Selection Drift and the Hill–Robertson Effect Short-term benefits of sex not related to linkage disequilibria Lineage-Level Selection for Sex The Diversity and Taxonomic Distribution of Reproductive Modes Evolution of Parthenogenesis from Sexual Ancestors Empirical Evidence for Benefits of Sex Conclusion See also References Sexual Conflict Glossary Introduction: What Is Sexual Conflict? Interlocus Sexual Conflict Why Harm Your Mate? Interlocus Sexual Conflict: An Evolutionary Battle of the Sexes Interlocus Sexual Conflict and Sexually Antagonistic Coevolution Can Interlocus Sexual Conflict Lead to Speciation? Intralocus Sexual Conflict Intralocus Sexual Conflict: A Genetic Tug-of-War Between the Sexes Empirical Evidence for Intralocus Sexual Conflict Specific Traits Involved in Intralocus Sexual Conflict Can Intralocus Sexual Conflict Be Resolved? How Does Sexual Conflict Affect Populations? See also References Sexual Dimorphism Glossary What Is Sexual Dimorphism? Primary and Secondary Sexual Dimorphisms Why Do Sexual Dimorphisms Evolve? How Do Sexual Dimorphisms Evolve? The Prevalence and Distribution of Sexual Dimorphism in Animals Variation among Animal Classes Variation among Traits Sexual Dimorphisms in Plants See also References Sexual Networks Glossary Introduction Sexual Networks Sexual Selection and Competitive Structure Phenotypic Assortment Sperm Competition Intensity Determinants of Competitive Structure Ecology Individual Strategies Potential Applications Conclusion See also References Sexual Selection, Theory of Glossary Introduction The Intensity of Sexual Selection Selection and Mating Patterns The Maximum Strength of Precopulatory Sexual Selection Factors Affecting the Mating Differential and the Bateman Gradient Anisogamy The environmental potential for polygamy The operational sex ratio and the potential reproductive rates of the sexes Parental care and parental investment Social and genetic mating systems The Evolution of Intra- and Intersexual Selection Intrasexual Selection Intersexual Selection Sensory bias Direct benefits Good genes The Fisherian process Summary See also References Shifting Balance Theory, Sewall Wright and Glossary Wright’s Shifting Balance Theory Gene Interactions Create a Multiplicity of Fitness Peaks Gene Interactions Limit Mass Selection Interdemic Selection Experimental Tests of Wright’s Shifting Balance Theory Nonrandom Phase III Migration and FST Several Open Questions Remaining See also References Social Effects Glossary Theoretical Background Indirect Genetic Effects Social Selection Empirical Examples Indirect Genetic Effects Social Selection Conclusion See also References Further Reading Sociobiology, History of Glossary The Emergence of Sociobiology The Rise of Neo-Darwinism The Theoretical Pioneers Spreading the New Ideas and Establishing the Field The Name ‘Sociobiology’ Sociobiological Key Concepts Inclusive Fitness Hamilton’s Rule The Hymenoptera Case and the Haplodiploidy Hypothesis Kin Selection Kin Selection Explanation as Opposed to Group Selection Explanation Kin Selection and Group Selection Explanations as Equivalent Reciprocal Altruism (or Reciprocity) Selfish Gene Theory Behavioral Strategies and Game Theory The Sociobiology Debate Bringing in Culture and the Mind Sociobiology and Anthropology The Move Toward Coevolution The Emergence of Evolutionary Psychology A Change of Climate Later Developments Group Selection, an Update Cooperation – A Broader Umbrella for Prosocial Behavior The Role of Culture in Gene-Culture Coevolution The Test of Sociobiology The Flourishing of Sociobiology Kin Selection – Attack and Defense The Mathematical Model – From Contention to Agreement? See also References Further Reading Speciation, Chromosomal Rearrangements and Glossary CRs Within and Between Natural Populations The Establishment of CRs in Natural Populations Early Models for the Role of CRs in Speciation A New Role for CRs in Speciation Evidence for the Role of CRs in Speciation Concluding Remarks Acknowledgments See also References Further Reading Speciation Continuum Glossary Introduction Reproductive Isolating Barriers along the Continuum Mechanisms that Initiate the Speciation Process The Genetic Basis of Isolating Barriers Different Narratives of Speciation The Selection-Based Narrative of Speciation Alternatives to the Selection-Based Narrative of Speciation Geography and the Continuum Mechanisms that Complete the Speciation Process The Reversibility of the Speciation Continuum Reinforcement Mechanisms Involved in the Completion of Speciation Species Concepts and the Continuum of Speciation See also References Speciation Genes Glossary What are Speciation Genes and How are They Identified? An Inclusive Definition Genetic Characterization of Speciation Genes Candidate gene identification Functional characterization of speciation genes Evolutionary Characterization of Speciation Genes What Have We Learned from Known Speciation Genes? The Identities of Speciation Genes are Predictable for Some Isolating Barriers Hybrid Incompatibilities Evolve by Diverse Paths and are Often Polymorphic Diverse Evolutionary Models Supported Ecological speciation Evolutionary arms races, mutation pressure, and hybrid incompatibilities Hybridization as a driver of speciation See also References Speciation Genomics Glossary Overview: Speciation Genomics – Toward the Periodic Table of Speciation How are Whole Genomes Analyzed? Genome-Wide Evidence for Speciation with Gene Flow in Heliconius Butterflies The Genomic Landscape of Phenotypic Integrity in the Face of Gene Flow in European Crows Conclusion See also References Further Reading Relevant Websites Speciation, Geography of Introduction History From Darwin to Jordan The Great Debate: Allopatric versus Sympatric Speciation Redefining the Geography of Speciation Speciation with Minimal Gene Flow (m≈0): Allopatric or Nearly So Theoretical support for allopatric speciation Empirical support for allopatric speciation Speciation with Gene Flow (~0