Evolutionary Developmental Biology : A Reference Guide

Preface Contents About the Editors About the Section Editors Contributors Part I: Introduction A Reference Guide to Evo-Devo References Part II: Key Concepts in Evo-Devo Heterochrony Introduction Patterns of Heterochrony Heterochronic Shifts Across Life Stages Reconstructing Heterochronic Patterns Appropriate Scale for Heterochronic Inference Heterochronic Processes that Underlie Heterochronic Patterns Integrating Heterochrony Cross-References References Developmental Exaptation Introduction Levels of Adaptation in Developmental Programs Selection on Gene Regulation Selection on Cellular Behavior Selection on Tissue Differentiation Selection on Morphogenetic Movements Selection on Relative Timing of Events Rare Changes as Indicators of Exaptation Developmental Exaptation and Co-Option Developmental Exaptation and Novelties Conclusions Cross-References References Concept of Burden in Evo-Devo Introduction What Is Burden? The Question of Embryological Generality The Question of Dependencies Quantifying Burden Using Anatomical Network Analysis Criticisms Conclusions Cross-References References A Macroevolutionary Perspective on Developmental Constraints in Animals Introduction Genetic Constraints Do Not Constrain Evolution on Macroevolutionary Scales Macroevolutionary Constraints Metazoan Cells Cannot Divide While Differentiated No or More than One Centrosome in a Cell More than One MTOC in a Cell Importance of Primary Cilia Cilia and Centrosomes Regulate Cell Cycle Progression Pleiotropic and Developmental Constraint Evolutionary and Developmental Consequences of the Constraint Low Fidelity of Meiotic Divisions of Oocytes Limited Capacity for Wound Healing and Regeneration Constraints on Development and the Evolution of Body Plans Conservation of Phylotypic Stages Support for the Pleiotropy Hypothesis Why So Much Pleiotropy? Modularity and Evolvability of Later Stages Challenges to the Pleiotropy Hypothesis Consequent Constraints on Body Plan Evolution Breaking of Constraints: Relaxed Stabilizing Selection Developmental Constraints Against the Evolution of Parthenogenesis Replacing the Missing Paternal Centrosome Replacing the Missing Paternal Chromosomes Evolutionary Mechanisms That Facilitate the Alteration of Meiosis: Hybridization and Endosymbionts Conclusions Cross-References References Developmental Innovation and Phenotypic Novelty Introduction Definitions and Classifications Developmental Innovation Genetic Processes Cell and Tissue Level Processes Emergent Behaviors Chemico-Physical Properties Models of Novelty Formation Innovation Theory Cross-References References Developmental Homology Introduction Phylogenetic Versus Developmental Approaches to Homology Characters: The Relata of Homology Serial Homology Homology, Homoplasy, Parallelism, and Deep Homology Challenges and Outlook Cross-References References Developmental System Drift Introduction Types of Evidence for DSD Species Hybrids Embryological Evidence Revealing DSD by Perturbing Cells and Genes: Caenorhabditis as a Model Genus Theoretical Mechanisms of DSD Gene Duplication and Subfunctionalization Compensatory Evolution Implications of DSD The Practice of Evolutionary Developmental Biology Biological Homology and Phylogenetic Inference DSD as Null Hypothesis for Evaluating Conservation Tests of Functional Conservation of Genes Genetic Bases of Convergent Evolution Biomedical Research Cross-References References The Developmental Hourglass in the Evolution of Embryogenesis Introduction The Hourglass Model of Embryonic Development The Hourglass Model and the Evolution of Embryogenesis Gene-Regulatory Networks Early Embryogenesis Middle Embryogenesis/Phylotypic Stage Late Embryogenesis Conclusions Cross-References References Inherency Introduction Plasticity, Genes of Large Effect, and Developmental Bias Inherency Is Not an Extension of the Modern Synthesis A Brief History of Inherent Forms Inherency and the New Evolutionary Theory Cross-References References Evolvability Introduction From Genetic to Phenotypic Concepts of Evolvability and the Role of Development Devo-Evo: Developmental Characteristics That Affect Evolution The Amount of Variation: Robustness Versus Adaptability Correspondence with the Type or Pattern of Selection Facilitated Variation Modularity Evo-Devo: The Evolution of Developmental Characteristics (That Affect Evolvability) Mechanisms for the Evolution of Evolvability Neutral Modifier Alleles and Lineage Selection Short-Term Advantages with Long-Term Consequences Resolving the ``Byproducts Are Just Happenstance´´-Problem: Common Cause Cross-References References Macroevolution Introduction Tempo in Macroevolution Speciation and Extinction Rates The Tempo of Speciation The Tempo of Extinction Morphological Change The Modes of Macroevolution Modes of Speciation Modes of Extinction Modes of Morphological Change Concluding Remarks Cross-References References Evolution of Complexity Introduction Horizontal and Vertical, Objects and Processes Horizontal Complexity and the Zero-Force Law Horizontal Complexity and the Structure of Development A Trend in Horizontal Complexity? Vertical Complexity An Evolutionary Syndrome Cross-References References Convergence Introduction Analyzing Convergent Evolution Causes of Convergent Evolution Quantifying Convergent Evolution Conclusion Cross-References References Coevolution and Macroevolution Introduction Adaptive Coevolutionary Divergence and Geographic Mosaics From Coevolutionary Geographic Mosaics to Ecological Speciation Determining the Role of Coevolution in Patterns of Macroevolutionary Divergence Unresolved Questions on the Evolutionary Developmental Biology of Coevolution Conclusions Cross-References References Part III: History of Evo-Devo Theories of Inheritance: The Evolution and Development of Form Introduction Descent with Modification in Lamarck and Darwin Nuclear Inheritance and Continuity of the Germ Plasm Mendelian Genetics and Its Critics Material Basis of Heredity Epigenetics and Epigenetic Inheritance Evolution and Development Cross-References References Alexander Onufrievich Kowalevsky (1840-1901) Life Work The State of Comparative Animal Embryology Before Alexander Kowalevsky The Works of Alexander Kowalevsky and the Foundation of Evolutionary Comparative Embryology Homology of the Germ Layers Legacy Cross-References Bibliography References Valentin Haecker (1864-1927) Life Work Haecker´s Lamarckism Haecker´s Phenogenetics The Problem of Pluripotency Contributions to General Biology Legacy Cross-References Bibliography References Richard Goldschmidt (1878-1958) Life Work Sex Determination of the Gypsy Moth Physiological Genetics Microevolution and Macroevolution Legacy Cross-References References Sergey S. Chetverikov (1880-1959) Life Chetverikov´s Ideas About Genetics and Evolution Chetverikov´s Importance in the History of Evolutionary Biology Cross-References Selected Bibliography References Ivan I. Schmalhausen (1884-1963) Life Work Stabilizing Selection as a Factor of Evolution The Whole Organism as a Cybernetic System Legacy Cross-References Bibliography References Gavin de Beer (1899-1972) Life Work Heterochrony Embryology, Genetics, and Evolutionary Biology Homology Legacy Cross-References Bibliography References Conrad Hal Waddington (1905-1975) Life Work Early Studies The Rise of Epigenetics Legacy Cross-References References John Tyler Bonner (1920-2019) Life Work Biology of the Dictyostelid Life Cycle Evolution of Development Legacy Cross-References References Stephen Jay Gould (1941-2002) Life Work Punctuated Equilibria Recapitulation, Heterochrony, and Neoteny Spandrels, Developmental Constraints, and Exaptation Macroevolution, Levels of Selection, and Evo-Devo Legacy Cross-References Selected Bibliography References Pere Alberch (1954-1998) Life Work A Theory of Form From Heterochrony to Morphogenetic Processes A Cyclical View of Development A Dynamical Systems Theory of Developmental Evolution An Experimental Approach to Development and Evolution Developmental Constraints and Evolution Developmental Homology Evolvability Legacy Cross-References Bibliography References Part IV: Philosophy of Evo-Devo Explanation in Evo-Devo Introduction: Philosophical Debate About Scientific Explanation What Evo-Devo Seeks to Explain The Concept of a Mechanistic Explanation Evo-Devo and Mechanistic Explanation Several Mechanistic Explanations Difficulties with Individuating Mechanisms The Historical Part of Lineage Explanations Mechanistic Explanation, Integration, and Reduction Cross-References References Generalization in Evo-Devo Introduction The Significance of Exceptions Accidental Products of Evolutionary History From Contingency to Constraints and Generative Entrenchment Disappearance and Return of Laws and Natural Kinds Conclusion Cross-References References Mechanisms in Evo-Devo Introduction The Concept of Mechanism Mechanisms in Development and Evolution Mechanisms in Evo-Devo Scales and Process Ontology Conclusions and Outlook Cross-References References Modeling and Simulation in Evo-Devo Introduction Modeling as a Distinctive Strategy The Aims of the Modeler Two Kinds of Progress in Modeling Trade-Offs and Model-Model Relationships Exploring and Contrasting Possibilities in Evo-Devo Summary Cross-References References Interdisciplinarity in Evo-Devo What Is Evo-Devo? What Is Interdisciplinarity? Complexity and the Phenomena of Evo-Devo Structured Problem Agendas for Interdisciplinary Integration Interdisciplinarity and the Fin-Limb Transition Conclusion Cross-References References Proximate Versus Ultimate Causation and Evo-Devo Introduction The Dichotomy: Proximate and Ultimate Causation Explained Motivating the Black-Boxing of Development Evo-Devo: A Different Perspective Cross-References References Complexity in Evo-Devo Introduction Hierarchical Organization and Complexity Dimensions of Complexity Compositional Complexity Organizational Complexity Intersubstitutability Aggregativity Decomposability Complex Systems The Evolution of Complexity Conclusion Cross-References References Levels of Organization in Evo-Devo Introduction Levels of Organization in Biological Science Defining Levels of Organization Wimsatt on Levels of Organization Levels of Mechanisms Skeptical Approaches to Levels Concluding Remarks Cross-References References Form and Function in Evo-Devo Introduction Form and Function in History Nineteenth-Century Transformations The First Century of Darwinian Evolution Evo-Devo and the Re-emergence of Form Evo-Devo and New Questions of Form Versus Function Cross-References References Dispositional Properties in Evo-Devo Introduction: Evo-Devo as a Science of Dispositions Dispositional Concepts in Evo-Devo From Constraints to Variational Properties Modularity Robustness Plasticity Evolvability Dispositional Properties and Explanatory Models in Evolutionary Biology Cross-References References Typology and Natural Kinds in Evo-Devo Introduction Typology and Body Plans Conceptions of Natural Kinds Capturing Variation and Evolutionary Change Kinds Answering to the Aims of Evo-Devo: Beyond Taxa Cross-References References Teleology in Evo-Devo Introduction Organism and Purpose Purpose in Evolution Novelty Adaptive Bias Constancy of Form Teleological Explanation Conclusion Cross-References References Part V: Evo-Devo of Basic Mechanisms Devo-Evo of Cell Types Introduction The Three Dimensions of the Cell Type Concept Function and Morphology Cell Type Development Cell Type Evolution Molecular Mechanisms of Cell Type Individuation Evolutionary Origin of Cell Types Gene Expression Evolution of Cell Types Cross-References References The Evolution of Cleavage in Metazoans Introduction Cell Processes Involved in Cleavage Cell Division Cell Processes Not Related to Cell Division Evolution of Cleavage in Metazoans Nonbilaterians Xenacoeloelomorpha + Chaetognatha Scalidophora Nematoda + Nematomorpha Arthropoda Spiralia Deuterostomes Conclusions Cross-References References The Evolution and Development of Segmented Body Plans Introduction Segmentation as Morphology The Segmented Phyla Arthropoda Annelida Chordata A Common Origin for Segmentation? Segmentation as a Developmental Process Chordata Arthropoda Annelida Why Did Segmentation Evolve? Cross-References References Mechanisms of Pattern Formation, Morphogenesis, and Evolution Introduction What Gene Products and Cells Can Do What Gene Products Can Do What Cells Can Do Developmental Mechanisms Autonomous Mechanisms Inductive Mechanisms Hierarchic Inductive Mechanisms Emergent Hierarchic Networks Morphogenetic Mechanisms Composite Developmental Mechanisms Evolution by Morphostatic and Morphodynamic Mechanisms Cross-References References Part VI: Plant Evo-Devo Structural Fingerprints of Development at the Intersection of Evo-Devo and the Fossil Record Introduction Beyond Principles: What Has the Inclusion of Data from the Fossil Record Contributed to Evo-Devo Plant Biology Growth Patterns and Dynamics Fundamental Plant Growth Responses Homology and Sporophyte Body Plans Sequence of Character Evolution Developmental Regulation Life Cycles, Reproductive Systems Emblematic Case Studies Gravitropism Polar Auxin Transport Secondary Growth Lepidodendralean Rooting Structures Euphyllophyte Leaf Evolution The Equisetum Strobilus: A Case of Reciprocal Illumination Conclusions and Future Outlook Cross-References References A Process-Based Approach to the Study of Flower Morphological Variation Introduction Patterns and Processes in Flower Evo-Devo ABCs and Patterns Dynamic Processes and Organ Evolution Polarity as a Case Study Beyond Gene Patterns to Morphological Processes Limitations of a Process-Based Approach Duplications, Natural Variation, and Future Promise for Evo-Devo Extensive Literature Review can Provide Powerful Information on Gene Interactions and Their Relation to Phenotypic Variation Genome-Level Information on Nonmodel Taxa Provides a Useful Tool for Studying the Evolution of Developmental Processes at a La... Dynamic Models Provide a Powerful Tool for Flower Evo-Devo Research Concluding Remarks Cross-References References The Impact of Atmospheric Composition on the Evolutionary Development of Stomatal Control and Biochemistry of Photosynthesis o... Introduction Rubisco Specificity and Levels of Atmospheric CO2 and O2 Diffusive Resistances to CO2-Uptake and Stomatal Control of Photosynthesis Conclusion References Alternation of Generations in Plants and Algae Introduction The Diversity of Plant and Algal Life Cycles A Relationship Between Life Cycle Type and Degree of Multicellular Complexity Theoretical Advantages and Disadvantages of Different Types of Life Cycle Genetic Regulation of Life Cycle Transitions The Origins of Sporophyte and Gametophyte Developmental Programs Consequences of Life Cycle Type on Genome Evolution Conclusion References The Evolution of Branching in Land Plants: Between Conservation and Diversity Introduction Why Branching Evolved: The Axial Nature of Plants Similar Branching Modes Are Found Across Land Plants Diversity in the Cellular Mechanisms of Terminal Branching Hornworts Liverworts Lycophytes Ferns Diversity in the Cellular Mechanisms of Lateral Branching Liverworts Mosses Ferns Gymnosperms and Angiosperms Are Regulatory Mechanisms of Branching Shared Between Land Plants? Perspective Cross-References References The Origin of Angiosperms Introduction: What Are Angiosperms? When, Where and from What Did the Angiosperms Arise? ANA-Grade Angiosperms Provide Clues on the Morphological, Ecological, and Molecular Characteristics of the First Flowering Pla... Evo-Devo Hypotheses for the Origin of Angiosperm-Specific Reproductive Features The Outer Integument and Carpel Bisexuality The Perianth Embryo Sac Anatomy and Fertilization Mechanisms Technical Developments to Help Elucidate the Origin of Angiosperms Integration of Data from Neo- and Paleobotany Cross-References References The Evolution of Sex Determination in Plants Introduction Theories on the Evolution of Dioecy The Routes to Dioecy The Genetics of the Transition to Dioecy Empirical Data on Dioecious Plants Evolution of Dioecy Through Gynodioecy Evolution of Dioecy Through Monoecy The Master Sex-Determining Genes in Dioecious Plants Conclusions and Perspectives Cross-References References Evolution of Floral Organ Identity Introduction A Flower Is a Flower Is a Flower: A Primer on Terminology What Is a Flower? What Is Floral Organ Identity? In a Nutshell: Genetic and Gene Regulatory Models of Floral Organ Identity The ABC Model and Its Derivatives The Floral Quartet Model Phylogeny of Floral Homeotic Genes and Floral Quartets: A MIKC Blessing On the Origin of Floral Organ Identity: From Gymnosperm Cones to the Ancestral Flower Variations on a Theme: The Diversification of Flowers and Floral Organs Fuzzy Floral Organ Identity by Fading Borders Perianth Diversity by Sliding Boundaries or Loss of Whorls New Types of Organs by Changes in Downstream Genes Different Identities Within One Whorl: Zygomorphy and the Orchid Code of Perianth Diversification Outlook Cross-References References Evolution of Symmetry in Plants Introduction Phyllotaxis Leaf Symmetry Genetic Bases of Asymmetry Along the Abaxial-Adaxial Axis Symmetry Changes Along the Mediolateral Axis Floral Symmetry Plant-Pollinator Interactions Have Fueled the Evolution of Floral Symmetry Evolution of Floral Symmetry Across Angiosperms Establishment of Floral Symmetry During Development The Genetic Control of Floral Symmetry Future Prospects Cross-References References Part VII: Invertebrate Evo-Devo Evo-Devo of Butterfly Wing Patterns Introduction Nymphalid Ground Plan and Wing Patterning in Three Dimensions The Development of Eyespots/Border Ocelli Heliconius and the Importance of Extreme Phenotypes Conclusions Cross-References References Twisted Shells, Spiral Cells, and Asymmetries: Evo-Devo Lessons Learned from Gastropods Introduction What Is a Gastropod? Spiral Forms Most Beautiful: Spiral Cleavage, Embryonic Organization, and Pattern Formation Asymmetries Left and Right Larval Biology and Life History Evolution Hard Parts and Body Plan Puzzles Everything Old Is New Again: Future Directions Conclusion Cross-References References Evo-Devo Lessons Learned from Hemichordates Introduction Brief History of Hemichordate Research Molecular Phylogeny Fossil Evidence (Paleontological Studies) Molecular Developmental Biology Animal-Vegetal Patterning in Hemichordates Anteroposterior Patterning in Hemichordates Dorsoventral Patterning in Hemichordates Larval Evolution Insights from Comparative Genomics Conclusions and Perspectives Cross-References References Evo-Devo Lessons from the Reproductive Division of Labor in Eusocial Hymenoptera Introduction: Eusocial Hymenoptera as Superorganisms Nutrition and Behavior: Key Factors Underlying the Origins of Reproductive Division of Labor ``Reproductive Constraints´´ Are Developmental Mechanisms That Facilitated the Elaboration of Reproductive Division of Labor Complete Loss of Ovaries Spermatheca Loss Reduced Ovariole Number Reduced Ovariole Activity Oocyte Axis Specification Defects RCs in the Context of Selection Key Lessons and Future Questions Cross-References References Evo-Devo Lessons Learned from Honeybees Introduction Honeybee Biology Bee Genome and Tools Sex Determination Patterning and Development Polyphenisms Eusociality Summary and Prospects Cross-References References Evo-Devo Lessons Learned from Aphids Introduction Polyphenism The Wing Polyphenism The Reproductive Polyphenism Interspecific Coordination and Control of Development Bacterial Endosymbiosis Gall Formation Cross-References References Part VIII: Vertebrate Evo-Devo Shifting the Black Box: Approaches to the Development and Evolution of the Vertebrate Mesoderm Introduction A Century of Changing Perspectives Development and Evolution of the Vertebrate Mesoderm Vertebrate Musculoskeletal System Descriptive Embryology: Phenomenology of the Lateral Somitic Frontier Modularity in the Vertebrate Mesoderm Evolution on the Frontier: Innovation in the Abaxial Domain Origin of Paired Appendages Toward the Future Cross-References References Development and Evolution of the Neck Muscles Introduction Development of the Amniote Hypobranchial Muscles Development of the Amniote Cucullaris Muscles Comparison of the Neck Among Extant Anamniote Vertebrates Evolutionary Schemes of Acquisition of the Neck Cross-References References Evolution of Skeletal Tissues Introduction Classification of Skeletal Elements in Vertebrates Exoskeleton and Endoskeleton Intramembranous and Endochondral Bone Neurocranium and Viscerocranium Neural Crest Cell-derived Skeleton and Mesoderm-derived Skeleton Fossil Record Evolutionary Genomics Summary of Evolutionary History of Vertebrate Skeletal Tissues Cross-References References History and Current Theories of the Vertebrate Head Segmentation Glossary Introduction: Classical Views Somites in the Head? Somitomeres Nervous System Neural Crest, Placodes, and Generative Constraints Evolutionary Origin of Head Segmentation Cross-References References Evolution and Development of the Vertebrate Cranium Glossary Introduction Morphological Concepts and Development Mesoderm and Neural Crest Exoskeleton Viscerocranium Hox Code and Dlx Code Cyclostome Cranium and the Evolution of the Skull Cross-References References Evo-Devo of the Fin-to-Limb Transition Introduction Fin-to-Limb Transition from the Viewpoint of Morphology Similarities and Differences Between Developmental Mechanisms of Fins and Limbs Developmental Mechanisms of the Loss of Fin Rays Cellular Mechanisms of the AER-to-AF Transition Conclusions Cross-References References Evo-Devo of Scales, Feathers, and Hairs Introduction Feathers Shape Color Keratin Scales Avian Scales Reptilian Scales Hair Evolutionary View of the Hair Follicle Hair Development Formation of Specialized Hair Types Hair Regeneration Conclusions Cross-References References Part IX: Modeling Approaches to Evo-Devo Morphometrics in Evolutionary Developmental Biology Introduction Geometric Morphometrics From Points to Surfaces and Volumes Further Applications in Evo-Devo Current Challenges and Limitations Cross-References References Phenotyping in Evo-Devo Introduction Qualitative Phenotyping Is Prevalent in Macro-Evo-Devo Studies Quantitative Phenotyping Is Prevalent in Micro-Evo-Devo Studies Gene Expression as Intermediate Phenotype Practical Considerations Cross-References References Morphological Disparity Introduction Measuring Disparity Morphological Descriptors Disparity Indices Visualizing Morphospaces Current Issues in Methods Explaining the Evolution of Disparity Developmental Morphospaces and Allometric Disparity Functional Morphospace and Functional Disparity Spatial, Environmental, and Temporal Structure of Morphospace Extinction and Extinction Space Chance and Historical Contingency Concluding Remarks Cross-References References Anatomical Network Analysis in Evo-Devo Introduction Connections in the Context of Organismal Form Anatomical Network Analysis Building an Anatomical Network: Elements and Interactions The Network Model and Its Analysis Network Parameters Types of Network Organization Anatomical Network Analysis in Morphological Evo-Devo Morphological Complexity Hierarchical Organization Morphological Integration Morphological Modularity Null Models in Anatomical Networks The Regular Model The Random Model The Small-World Model The Scale-Free Model The Gabriel Model Using Null Network Models to Study Morphological Systems: An Example Limitations and Cautions in Anatomical Network Modeling Identification of Elements and Relations Typological Simplifications Illusions of Symmetry Conclusion Cross-References References Computational Modeling at the Cell and Tissue Level in Evo-Devo Introduction Mathematical Models of Development as Tools to Integrate Experimental Evidence and Predict the Outcome of New Experiments The Tooth Development Model Predicting Phenotypic Variation from Development and the Developmental Basis of Evolutionary Transitions Predicting the Effectiveness of Natural Selection on Evolving Populations In Silico Using Models of Development Studying the Emergence and Replacement Dynamics of Different Types of Development over the Course of Evolution Future Directions Cross-References References Modeling Evolution of Developmental Gene Regulatory Networks Introduction Simulating Development Within Cells Between Cells Tissue Level Evo-Devo Models Different Approaches In Silico Evolution Discussion and Concluding Remarks Cross-References References Part X: Evo-Devo and Population Genetics Developmental Evolutionary Biology (Devo-Evo) Introduction The Two Approaches in Evolution and Development Early Research Lines in Developmental Evolution Minding Physiological Constraints Minding Mutational Anisotropy The Core Concepts of Developmental Evolution Changing Developmental Rules Conclusions Cross-References References Micro-Evo-Devo Introduction What Is Micro-Evo-Devo? Micro-Evo-Devo in Action Building Blocks of Micro-Evo-Devo Building GP Maps What Can Micro-Evo-Devo Do for Evo-Devo? Do Micro Events Affect Long-Term Evolution? Cross-References References Canalization: A Central but Controversial Concept in Evo-Devo Introduction Canalization: An Elusive Concept in Evolutionary Developmental Biology Phenotypic Robustness Against Genetic and Environmental Factors Mechanisms of Genetic and Environmental Canalization How Do Biologists Measure Canalization? Evolution of Canalization: Adaptive, Congruent, or Intrinsic? Canalization and Evolvability of Phenotypic Traits Future Directions Cross-References References Developmental Plasticity and Evolution Introduction Definitions and Related Concepts Plasticity-First Evolution Evolution of Plasticity Micro-plasticity and the Quantitative Genetics Perspective Exploiting Plasticity in the Laboratory Cross-References References Pleiotropy and Its Evolution: Connecting Evo-Devo and Population Genetics Introduction General Definition Challenges in Determining Pleiotropy What Is a Trait? The Many Mechanisms of Pleiotropy How Many Traits? Pleiotropy and the Evolution of Complexity Phenotypic Traits Versus Fitness Evolution of Pleiotropy Future Challenges Cross-References References Epistasis Introduction Epistasis as a Property of the Genotype-Phenotype Map Statistical Epistasis The Statistical Genotype-Phenotype Map of Quantitative Genetics Epistasis, Inheritance, and Selection Statistical and Biological Epistasis Estimating Epistasis Epistasis Analysis in Molecular Genetics The Importance of Epistasis Summary of Epistasis Terminology Cross-References References Variational Approaches to Evolvability: Short- and Long-Term Perspectives Introduction Defining Evolvability Short-Term Evolvability Long-Term Evolvability Perspectives on the Study of Evolvability Quantitative Approaches: Evolvability at Short Timescales Quantitative Approaches: Multivariate Evolvability Qualitative Approaches: The Genotype-to-Phenotype Map Modularity Robustness Future Challenges Evolution of Evolvability Mutation Morphological Novelty Conclusions Cross-References References Part XI: Extensions of Evo-Devo Evo-Devo´s Contributions to the Extended Evolutionary Synthesis Introduction Extended Evolutionary Synthesis Evo-Devo´s Distinctive Concepts Consequences for Evolutionary Theory Beyond Evolvability Cross-References References Evo-Devo and Phylogenetics Introduction Evo-Devo´s Contribution to Phylogenetics Partitioning the Phenotype into Individual Characters Genes Versus Environment and the GenotypePhenotype Map Saltational Evolution Developmental Genes and Phylogenetic Inference Evolving Gene Functions The Phylotypic Stage Phylogenetic Signal from Heterochronic Patterns Phylogenetics to the Benefit of Evo-Devo Selecting New Model Species Cross-References References Methods and Practices in Paleo-Evo-Devo Introduction Fossils as Biological Entities Reconstructing the Ontogeny of a Fossil Organism Fossils in Evolutionary Reconstructions Practical Work Cross-References References Eco-Evo-Devo Introduction Ecological Development as a Source of Phenotypic Variation Inevitable Effects of Environmental Conditions Adaptive Plasticity Transgenerational Environmental Effects The Internal Environment: Microbial Symbionts Evolution of Eco-Devo Responses Genetic Diversity for Environmental Responses Evolution of Adaptive Plasticity Evolutionary Impact of Eco-Devo Responses A Norm of Reaction View of Fitness Variation Selective Consequences of GxE Variation within Populations Effects of Adaptive Eco-Devo Responses on Evolutionary Diversification Eco-Devo Responses as Niche Construction Eco-Evo-Devo Research Challenges Cross-References References Evo-Devo and Niche Construction Introduction Organism, Environment, and the Promise of Niche Construction Theory To Develop is to Interact with the Environment Organism and Environment as Cause and Effect of Each Other Advancing Evo-Devo Through the Study of Niche Construction Evolutionary Innovation and Diversification Developmental Bias Developmental Plasticity Genetic Accommodation Inclusive Inheritance Conclusions Cross-References References Evo-Devo of Social Behavior Introduction Behavioral Modules of Social Evolution From the Individual to High Society Solitary Ancestors Communal Behavior Primitive Eusociality Advanced Eusociality A Ground Plan for Social Living The Ovarian Ground Plan Hypothesis (OGPH) The Reproductive Ground Plan Hypothesis Food and Society Genetic Toolkits Shape Social Life-Histories Molecular Pathways Associated with Reproduction Molecular Pathways Associated with Nutrition Insulin/Insulin-Like Growth Factor Pathway Genomic Approaches to Social Evo-Devo Epigenetics and Social Behavior Conclusion Cross-References References Evo-Devo and C Preface Contents About the Editors About the Section Editors Contributors Part I: Introduction A Reference Guide to Evo-Devo References Part II: Key Concepts in Evo-Devo Heterochrony Introduction Patterns of Heterochrony Heterochronic Shifts Across Life Stages Reconstructing Heterochronic Patterns Appropriate Scale for Heterochronic Inference Heterochronic Processes that Underlie Heterochronic Patterns Integrating Heterochrony Cross-References References Developmental Exaptation Introduction Levels of Adaptation in Developmental Programs Selection on Gene Regulation Selection on Cellular Behavior Selection on Tissue Differentiation Selection on Morphogenetic Movements Selection on Relative Timing of Events Rare Changes as Indicators of Exaptation Developmental Exaptation and Co-Option Developmental Exaptation and Novelties Conclusions Cross-References References Concept of Burden in Evo-Devo Introduction What Is Burden? The Question of Embryological Generality The Question of Dependencies Quantifying Burden Using Anatomical Network Analysis Criticisms Conclusions Cross-References References A Macroevolutionary Perspective on Developmental Constraints in Animals Introduction Genetic Constraints Do Not Constrain Evolution on Macroevolutionary Scales Macroevolutionary Constraints Metazoan Cells Cannot Divide While Differentiated No or More than One Centrosome in a Cell More than One MTOC in a Cell Importance of Primary Cilia Cilia and Centrosomes Regulate Cell Cycle Progression Pleiotropic and Developmental Constraint Evolutionary and Developmental Consequences of the Constraint Low Fidelity of Meiotic Divisions of Oocytes Limited Capacity for Wound Healing and Regeneration Constraints on Development and the Evolution of Body Plans Conservation of Phylotypic Stages Support for the Pleiotropy Hypothesis Why So Much Pleiotropy? Modularity and Evolvability of Later Stages Challenges to the Pleiotropy Hypothesis Consequent Constraints on Body Plan Evolution Breaking of Constraints: Relaxed Stabilizing Selection Developmental Constraints Against the Evolution of Parthenogenesis Replacing the Missing Paternal Centrosome Replacing the Missing Paternal Chromosomes Evolutionary Mechanisms That Facilitate the Alteration of Meiosis: Hybridization and Endosymbionts Conclusions Cross-References References Developmental Innovation and Phenotypic Novelty Introduction Definitions and Classifications Developmental Innovation Genetic Processes Cell and Tissue Level Processes Emergent Behaviors Chemico-Physical Properties Models of Novelty Formation Innovation Theory Cross-References References Developmental Homology Introduction Phylogenetic Versus Developmental Approaches to Homology Characters: The Relata of Homology Serial Homology Homology, Homoplasy, Parallelism, and Deep Homology Challenges and Outlook Cross-References References Developmental System Drift Introduction Types of Evidence for DSD Species Hybrids Embryological Evidence Revealing DSD by Perturbing Cells and Genes: Caenorhabditis as a Model Genus Theoretical Mechanisms of DSD Gene Duplication and Subfunctionalization Compensatory Evolution Implications of DSD The Practice of Evolutionary Developmental Biology Biological Homology and Phylogenetic Inference DSD as Null Hypothesis for Evaluating Conservation Tests of Functional Conservation of Genes Genetic Bases of Convergent Evolution Biomedical Research Cross-References References The Developmental Hourglass in the Evolution of Embryogenesis Introduction The Hourglass Model of Embryonic Development The Hourglass Model and the Evolution of Embryogenesis Gene-Regulatory Networks Early Embryogenesis Middle Embryogenesis/Phylotypic Stage Late Embryogenesis Conclusions Cross-References References Inherency Introduction Plasticity, Genes of Large Effect, and Developmental Bias Inherency Is Not an Extension of the Modern Synthesis A Brief History of Inherent Forms Inherency and the New Evolutionary Theory Cross-References References Evolvability Introduction From Genetic to Phenotypic Concepts of Evolvability and the Role of Development Devo-Evo: Developmental Characteristics That Affect Evolution The Amount of Variation: Robustness Versus Adaptability Correspondence with the Type or Pattern of Selection Facilitated Variation Modularity Evo-Devo: The Evolution of Developmental Characteristics (That Affect Evolvability) Mechanisms for the Evolution of Evolvability Neutral Modifier Alleles and Lineage Selection Short-Term Advantages with Long-Term Consequences Resolving the ``Byproducts Are Just Happenstance ́ ́-Problem: Common Cause Cross-References References Macroevolution Introduction Tempo in Macroevolution Speciation and Extinction Rates The Tempo of Speciation The Tempo of Extinction Morphological Change The Modes of Macroevolution Modes of Speciation Modes of Extinction Modes of Morphological Change Concluding Remarks Cross-References References Evolution of Complexity Introduction Horizontal and Vertical, Objects and Processes Horizontal Complexity and the Zero-Force Law Horizontal Complexity and the Structure of Development A Trend in Horizontal Complexity? Vertical Complexity An Evolutionary Syndrome Cross-References References Convergence Introduction Analyzing Convergent Evolution Causes of Convergent Evolution Quantifying Convergent Evolution Conclusion Cross-References References Coevolution and Macroevolution Introduction Adaptive Coevolutionary Divergence and Geographic Mosaics From Coevolutionary Geographic Mosaics to Ecological Speciation Determining the Role of Coevolution in Patterns of Macroevolutionary Divergence Unresolved Questions on the Evolutionary Developmental Biology of Coevolution Conclusions Cross-References References Part III: History of Evo-Devo Theories of Inheritance: The Evolution and Development of Form Introduction Descent with Modification in Lamarck and Darwin Nuclear Inheritance and Continuity of the Germ Plasm Mendelian Genetics and Its Critics Material Basis of Heredity Epigenetics and Epigenetic Inheritance Evolution and Development Cross-References References Alexander Onufrievich Kowalevsky (1840-1901) Life Work The State of Comparative Animal Embryology Before Alexander Kowalevsky The Works of Alexander Kowalevsky and the Foundation of Evolutionary Comparative Embryology Homology of the Germ Layers Legacy Cross-References Bibliography References Valentin Haecker (1864-1927) Life Work Haecker ́s Lamarckism Haecker ́s Phenogenetics The Problem of Pluripotency Contributions to General Biology Legacy Cross-References Bibliography References Richard Goldschmidt (1878-1958) Life Work Sex Determination of the Gypsy Moth Physiological Genetics Microevolution and Macroevolution Legacy Cross-References References Sergey S. Chetverikov (1880-1959) Life Chetverikov ́s Ideas About Genetics and Evolution Chetverikov ́s Importance in the History of Evolutionary Biology Cross-References Selected Bibliography References Ivan I. Schmalhausen (1884-1963) Life Work Stabilizing Selection as a Factor of Evolution The Whole Organism as a Cybernetic System Legacy Cross-References Bibliography References Gavin de Beer (1899-1972) Life Work Heterochrony Embryology, Genetics, and Evolutionary Biology Homology Legacy Cross-References Bibliography References Conrad Hal Waddington (1905-1975) Life Work Early Studies The Rise of Epigenetics Legacy Cross-References References John Tyler Bonner (1920-2019) Life Work Biology of the Dictyostelid Life Cycle Evolution of Development Legacy Cross-References References Stephen Jay Gould (1941-2002) Life Work Punctuated Equilibria Recapitulation, Heterochrony, and Neoteny Spandrels, Developmental Constraints, and Exaptation Macroevolution, Levels of Selection, and Evo-Devo Legacy Cross-References Selected Bibliography References Pere Alberch (1954-1998) Life Work A Theory of Form From Heterochrony to Morphogenetic Processes A Cyclical View of Development A Dynamical Systems Theory of Developmental Evolution An Experimental Approach to Development and Evolution Developmental Constraints and Evolution Developmental Homology Evolvability Legacy Cross-References Bibliography References Part IV: Philosophy of Evo-Devo Explanation in Evo-Devo Introduction: Philosophical Debate About Scientific Explanation What Evo-Devo Seeks to Explain The Concept of a Mechanistic Explanation Evo-Devo and Mechanistic Explanation Several Mechanistic Explanations Difficulties with Individuating Mechanisms The Historical Part of Lineage Explanations Mechanistic Explanation, Integration, and Reduction Cross-References References Generalization in Evo-Devo Introduction The Significance of Exceptions Accidental Products of Evolutionary History From Contingency to Constraints and Generative Entrenchment Disappearance and Return of Laws and Natural Kinds Conclusion Cross-References References Mechanisms in Evo-Devo Introduction The Concept of Mechanism Mechanisms in Development and Evolution Mechanisms in Evo-Devo Scales and Process Ontology Conclusions and Outlook Cross-References References Modeling and Simulation in Evo-Devo Introduction Modeling as a Distinctive Strategy The Aims of the Modeler Two Kinds of Progress in Modeling Trade-Offs and Model-Model Relationships Exploring and Contrasting Possibilities in Evo-Devo Summary Cross-References References Interdisciplinarity in Evo-Devo What Is Evo-Devo? What Is Interdisciplinarity? Complexity and the Phenomena of Evo-Devo Structured Problem Agendas for Interdisciplinary Integration Interdisciplinarity and the Fin-Limb Transition Conclusion Cross-References References Proximate Versus Ultimate Causation and Evo-Devo Introduction The Dichotomy: Proximate and Ultimate Causation Explained Motivating the Black-Boxing of Development Evo-Devo: A Different Perspective Cross-References References Complexity in Evo-Devo Introduction Hierarchical Organization and Complexity Dimensions of Complexity Compositional Complexity Organizational Complexity Intersubstitutability Aggregativity Decomposability Complex Systems The Evolution of Complexity Conclusion Cross-References References Levels of Organization in Evo-Devo Introduction Levels of Organization in Biological Science Defining Levels of Organization Wimsatt on Levels of Organization Levels of Mechanisms Skeptical Approaches to Levels Concluding Remarks Cross-References References Form and Function in Evo-Devo Introduction Form and Function in History Nineteenth-Century Transformations The First Century of Darwinian Evolution Evo-Devo and the Re-emergence of Form Evo-Devo and New Questions of Form Versus Function Cross-References References Dispositional Properties in Evo-Devo Introduction: Evo-Devo as a Science of Dispositions Dispositional Concepts in Evo-Devo From Constraints to Variational Properties Modularity Robustness Plasticity Evolvability Dispositional Properties and Explanatory Models in Evolutionary Biology Cross-References References Typology and Natural Kinds in Evo-Devo Introduction Typology and Body Plans Conceptions of Natural Kinds Capturing Variation and Evolutionary Change Kinds Answering to the Aims of Evo-Devo: Beyond Taxa Cross-References References Teleology in Evo-Devo Introduction Organism and Purpose Purpose in Evolution Novelty Adaptive Bias Constancy of Form Teleological Explanation Conclusion Cross-References References Part V: Evo-Devo of Basic Mechanisms Devo-Evo of Cell Types Introduction The Three Dimensions of the Cell Type Concept Function and Morphology Cell Type Development Cell Type Evolution Molecular Mechanisms of Cell Type Individuation Evolutionary Origin of Cell Types Gene Expression Evolution of Cell Types Cross-References References The Evolution of Cleavage in Metazoans Introduction Cell Processes Involved in Cleavage Cell Division Cell Processes Not Related to Cell Division Evolution of Cleavage in Metazoans Nonbilaterians Xenacoeloelomorpha + Chaetognatha Scalidophora Nematoda + Nematomorpha Arthropoda Spiralia Deuterostomes Conclusions Cross-References References The Evolution and Development of Segmented Body Plans Introduction Segmentation as Morphology The Segmented Phyla Arthropoda Annelida Chordata A Common Origin for Segmentation? Segmentation as a Developmental Process Chordata Arthropoda Annelida Why Did Segmentation Evolve? Cross-References References Mechanisms of Pattern Formation, Morphogenesis, and Evolution Introduction What Gene Products and Cells Can Do What Gene Products Can Do What Cells Can Do Developmental Mechanisms Autonomous Mechanisms Inductive Mechanisms Hierarchic Inductive Mechanisms Emergent Hierarchic Networks Morphogenetic Mechanisms Composite Developmental Mechanisms Evolution by Morphostatic and Morphodynamic Mechanisms Cross-References References Part VI: Plant Evo-Devo Structural Fingerprints of Development at the Intersection of Evo-Devo and the Fossil Record Introduction Beyond Principles: What Has the Inclusion of Data from the Fossil Record Contributed to Evo-Devo Plant Biology Growth Patterns and Dynamics Fundamental Plant Growth Responses Homology and Sporophyte Body Plans Sequence of Character Evolution Developmental Regulation Life Cycles, Reproductive Systems Emblematic Case Studies Gravitropism Polar Auxin Transport Secondary Growth Lepidodendralean Rooting Structures Euphyllophyte Leaf Evolution The Equisetum Strobilus: A Case of Reciprocal Illumination Conclusions and Future Outlook Cross-References References A Process-Based Approach to the Study of Flower Morphological Variation Introduction Patterns and Processes in Flower Evo-Devo ABCs and Patterns Dynamic Processes and Organ Evolution Polarity as a Case Study Beyond Gene Patterns to Morphological Processes Limitations of a Process-Based Approach Duplications, Natural Variation, and Future Promise for Evo-Devo Extensive Literature Review can Provide Powerful Information on Gene Interactions and Their Relation to Phenotypic Variation Genome-Level Information on Nonmodel Taxa Provides a Useful Tool for Studying the Evolution of Developmental Processes at a La... Dynamic Models Provide a Powerful Tool for Flower Evo-Devo Research Concluding Remarks Cross-References References The Impact of Atmospheric Composition on the Evolutionary Development of Stomatal Control and Biochemistry of Photosynthesis o... Introduction Rubisco Specificity and Levels of Atmospheric CO2 and O2 Diffusive Resistances to CO2-Uptake and Stomatal Control of Photosynthesis Conclusion References Alternation of Generations in Plants and Algae Introduction The Diversity of Plant and Algal Life Cycles A Relationship Between Life Cycle Type and Degree of Multicellular Complexity Theoretical Advantages and Disadvantages of Different Types of Life Cycle Genetic Regulation of Life Cycle Transitions The Origins of Sporophyte and Gametophyte Developmental Programs Consequences of Life Cycle Type on Genome Evolution Conclusion References The Evolution of Branching in Land Plants: Between Conservation and Diversity Introduction Why Branching Evolved: The Axial Nature of Plants Similar Branching Modes Are Found Across Land Plants Diversity in the Cellular Mechanisms of Terminal Branching Hornworts Liverworts Lycophytes Ferns Diversity in the Cellular Mechanisms of Lateral Branching Liverworts Mosses Ferns Gymnosperms and Angiosperms Are Regulatory Mechanisms of Branching Shared Between Land Plants? Perspective Cross-References References The Origin of Angiosperms Introduction: What Are Angiosperms? When, Where and from What Did the Angiosperms Arise? ANA-Grade Angiosperms Provide Clues on the Morphological, Ecological, and Molecular Characteristics of the First Flowering Pla... Evo-Devo Hypotheses for the Origin of Angiosperm-Specific Reproductive Features The Outer Integument and Carpel Bisexuality The Perianth Embryo Sac Anatomy and Fertilization Mechanisms Technical Developments to Help Elucidate the Origin of Angiosperms Integration of Data from Neo- and Paleobotany Cross-References References The Evolution of Sex Determination in Plants Introduction Theories on the Evolution of Dioecy The Routes to Dioecy The Genetics of the Transition to Dioecy Empirical Data on Dioecious Plants Evolution of Dioecy Through Gynodioecy Evolution of Dioecy Through Monoecy The Master Sex-Determining Genes in Dioecious Plants Conclusions and Perspectives Cross-References References Evolution of Floral Organ Identity Introduction A Flower Is a Flower Is a Flower: A Primer on Terminology What Is a Flower? What Is Floral Organ Identity? In a Nutshell: Genetic and Gene Regulatory Models of Floral Organ Identity The ABC Model and Its Derivatives The Floral Quartet Model Phylogeny of Floral Homeotic Genes and Floral Quartets: A MIKC Blessing On the Origin of Floral Organ Identity: From Gymnosperm Cones to the Ancestral Flower Variations on a Theme: The Diversification of Flowers and Floral Organs Fuzzy Floral Organ Identity by Fading Borders Perianth Diversity by Sliding Boundaries or Loss of Whorls New Types of Organs by Changes in Downstream Genes Different Identities Within One Whorl: Zygomorphy and the Orchid Code of Perianth Diversification Outlook Cross-References References Evolution of Symmetry in Plants Introduction Phyllotaxis Leaf Symmetry Genetic Bases of Asymmetry Along the Abaxial-Adaxial Axis Symmetry Changes Along the Mediolateral Axis Floral Symmetry Plant-Pollinator Interactions Have Fueled the Evolution of Floral Symmetry Evolution of Floral Symmetry Across Angiosperms Establishment of Floral Symmetry During Development The Genetic Control of Floral Symmetry Future Prospects Cross-References References Part VII: Invertebrate Evo-Devo Evo-Devo of Butterfly Wing Patterns Introduction Nymphalid Ground Plan and Wing Patterning in Three Dimensions The Development of Eyespots/Border Ocelli Heliconius and the Importance of Extreme Phenotypes Conclusions Cross-References References Twisted Shells, Spiral Cells, and Asymmetries: Evo-Devo Lessons Learned from Gastropods Introduction What Is a Gastropod? Spiral Forms Most Beautiful: Spiral Cleavage, Embryonic Organization, and Pattern Formation Asymmetries Left and Right Larval Biology and Life History Evolution Hard Parts and Body Plan Puzzles Everything Old Is New Again: Future Directions Conclusion Cross-References References Evo-Devo Lessons Learned from Hemichordates Introduction Brief History of Hemichordate Research Molecular Phylogeny Fossil Evidence (Paleontological Studies) Molecular Developmental Biology Animal-Vegetal Patterning in Hemichordates Anteroposterior Patterning in Hemichordates Dorsoventral Patterning in Hemichordates Larval Evolution Insights from Comparative Genomics Conclusions and Perspectives Cross-References References Evo-Devo Lessons from the Reproductive Division of Labor in Eusocial Hymenoptera Introduction: Eusocial Hymenoptera as Superorganisms Nutrition and Behavior: Key Factors Underlying the Origins of Reproductive Division of Labor ``Reproductive Constraints ́ ́ Are Developmental Mechanisms That Facilitated the Elaboration of Reproductive Division of Labor Complete Loss of Ovaries Spermatheca Loss Reduced Ovariole Number Reduced Ovariole Activity Oocyte Axis Specification Defects RCs in the Context of Selection Key Lessons and Future Questions Cross-References References Evo-Devo Lessons Learned from Honeybees Introduction Honeybee Biology Bee Genome and Tools Sex Determination Patterning and Development Polyphenisms Eusociality Summary and Prospects Cross-References References Evo-Devo Lessons Learned from Aphids Introduction Polyphenism The Wing Polyphenism The Reproductive Polyphenism Interspecific Coordination and Control of Development Bacterial Endosymbiosis Gall Formation Cross-References References Part VIII: Vertebrate Evo-Devo Shifting the Black Box: Approaches to the Development and Evolution of the Vertebrate Mesoderm Introduction A Century of Changing Perspectives Development and Evolution of the Vertebrate Mesoderm Vertebrate Musculoskeletal System Descriptive Embryology: Phenomenology of the Lateral Somitic Frontier Modularity in the Vertebrate Mesoderm Evolution on the Frontier: Innovation in the Abaxial Domain Origin of Paired Appendages Toward the Future Cross-References References Development and Evolution of the Neck Muscles Introduction Development of the Amniote Hypobranchial Muscles Development of the Amniote Cucullaris Muscles Comparison of the Neck Among Extant Anamniote Vertebrates Evolutionary Schemes of Acquisition of the Neck Cross-References References Evolution of Skeletal Tissues Introduction Classification of Skeletal Elements in Vertebrates Exoskeleton and Endoskeleton Intramembranous and Endochondral Bone Neurocranium and Viscerocranium Neural Crest Cell-derived Skeleton and Mesoderm-derived Skeleton Fossil Record Evolutionary Genomics Summary of Evolutionary History of Vertebrate Skeletal Tissues Cross-References References History and Current Theories of the Vertebrate Head Segmentation Glossary Introduction: Classical Views Somites in the Head? Somitomeres Nervous System Neural Crest, Placodes, and Generative Constraints Evolutionary Origin of Head Segmentation Cross-References References Evolution and Development of the Vertebrate Cranium Glossary Introduction Morphological Concepts and Development Mesoderm and Neural Crest Exoskeleton Viscerocranium Hox Code and Dlx Code Cyclostome Cranium and the Evolution of the Skull Cross-References References Evo-Devo of the Fin-to-Limb Transition Introduction Fin-to-Limb Transition from the Viewpoint of Morphology Similarities and Differences Between Developmental Mechanisms of Fins and Limbs Developmental Mechanisms of the Loss of Fin Rays Cellular Mechanisms of the AER-to-AF Transition Conclusions Cross-References References Evo-Devo of Scales, Feathers, and Hairs Introduction Feathers Shape Color Keratin Scales Avian Scales Reptilian Scales Hair Evolutionary View of the Hair Follicle Hair Development Formation of Specialized Hair Types Hair Regeneration Conclusions Cross-References References Part IX: Modeling Approaches to Evo-Devo Morphometrics in Evolutionary Developmental Biology Introduction Geometric Morphometrics From Points to Surfaces and Volumes Further Applications in Evo-Devo Current Challenges and Limitations Cross-References References Phenotyping in Evo-Devo Introduction Qualitative Phenotyping Is Prevalent in Macro-Evo-Devo Studies Quantitative Phenotyping Is Prevalent in Micro-Evo-Devo Studies Gene Expression as Intermediate Phenotype Practical Considerations Cross-References References Morphological Disparity Introduction Measuring Disparity Morphological Descriptors Disparity Indices Visualizing Morphospaces Current Issues in Methods Explaining the Evolution of Disparity Developmental Morphospaces and Allometric Disparity Functional Morphospace and Functional Disparity Spatial, Environmental, and Temporal Structure of Morphospace Extinction and Extinction Space Chance and Historical Contingency Concluding Remarks Cross-References References Anatomical Network Analysis in Evo-Devo Introduction Connections in the Context of Organismal Form Anatomical Network Analysis Building an Anatomical Network: Elements and Interactions The Network Model and Its Analysis Network Parameters Types of Network Organization Anatomical Network Analysis in Morphological Evo-Devo Morphological Complexity Hierarchical Organization Morphological Integration Morphological Modularity Null Models in Anatomical Networks The Regular Model The Random Model The Small-World Model The Scale-Free Model The Gabriel Model Using Null Network Models to Study Morphological Systems: An Example Limitations and Cautions in Anatomical Network Modeling Identification of Elements and Relations Typological Simplifications Illusions of Symmetry Conclusion Cross-References References Computational Modeling at the Cell and Tissue Level in Evo-Devo Introduction Mathematical Models of Development as Tools to Integrate Experimental Evidence and Predict the Outcome of New Experiments The Tooth Development Model Predicting Phenotypic Variation from Development and the Developmental Basis of Evolutionary Transitions Predicting the Effectiveness of Natural Selection on Evolving Populations In Silico Using Models of Development Studying the Emergence and Replacement Dynamics of Different Types of Development over the Course of Evolution Future Directions Cross-References References Modeling Evolution of Developmental Gene Regulatory Networks Introduction Simulating Development Within Cells Between Cells Tissue Level Evo-Devo Models Different Approaches In Silico Evolution Discussion and Concluding Remarks Cross-References References Part X: Evo-Devo and Population Genetics Developmental Evolutionary Biology (Devo-Evo) Introduction The Two Approaches in Evolution and Development Early Research Lines in Developmental Evolution Minding Physiological Constraints Minding Mutational Anisotropy The Core Concepts of Developmental Evolution Changing Developmental Rules Conclusions Cross-References References Micro-Evo-Devo Introduction What Is Micro-Evo-Devo? Micro-Evo-Devo in Action Building Blocks of Micro-Evo-Devo Building GP Maps What Can Micro-Evo-Devo Do for Evo-Devo? Do Micro Events Affect Long-Term Evolution? Cross-References References Canalization: A Central but Controversial Concept in Evo-Devo Introduction Canalization: An Elusive Concept in Evolutionary Developmental Biology Phenotypic Robustness Against Genetic and Environmental Factors Mechanisms of Genetic and Environmental Canalization How Do Biologists Measure Canalization? Evolution of Canalization: Adaptive, Congruent, or Intrinsic? Canalization and Evolvability of Phenotypic Traits Future Directions Cross-References References Developmental Plasticity and Evolution Introduction Definitions and Related Concepts Plasticity-First Evolution Evolution of Plasticity Micro-plasticity and the Quantitative Genetics Perspective Exploiting Plasticity in the Laboratory Cross-References References Pleiotropy and Its Evolution: Connecting Evo-Devo and Population Genetics Introduction General Definition Challenges in Determining Pleiotropy What Is a Trait? The Many Mechanisms of Pleiotropy How Many Traits? Pleiotropy and the Evolution of Complexity Phenotypic Traits Versus Fitness Evolution of Pleiotropy Future Challenges Cross-References References Epistasis Introduction Epistasis as a Property of the Genotype-Phenotype Map Statistical Epistasis The Statistical Genotype-Phenotype Map of Quantitative Genetics Epistasis, Inheritance, and Selection Statistical and Biological Epistasis Estimating Epistasis Epistasis Analysis in Molecular Genetics The Importance of Epistasis Summary of Epistasis Terminology Cross-References References Variational Approaches to Evolvability: Short- and Long-Term Perspectives Introduction Defining Evolvability Short-Term Evolvability Long-Term Evolvability Perspectives on the Study of Evolvability Quantitative Approaches: Evolvability at Short Timescales Quantitative Approaches: Multivariate Evolvability Qualitative Approaches: The Genotype-to-Phenotype Map Modularity Robustness Future Challenges Evolution of Evolvability Mutation Morphological Novelty Conclusions Cross-References References Part XI: Extensions of Evo-Devo Evo-Devo ́s Contributions to the Extended Evolutionary Synthesis Introduction Extended Evolutionary Synthesis Evo-Devo ́s Distinctive Concepts Consequences for Evolutionary Theory Beyond Evolvability Cross-References References Evo-Devo and Phylogenetics Introduction Evo-Devo ́s Contribution to Phylogenetics Partitioning the Phenotype into Individual Characters Genes Versus Environment and the GenotypePhenotype Map Saltational Evolution Developmental Genes and Phylogenetic Inference Evolving Gene Functions The Phylotypic Stage Phylogenetic Signal from Heterochronic Patterns Phylogenetics to the Benefit of Evo-Devo Selecting New Model Species Cross-References References Methods and Practices in Paleo-Evo-Devo Introduction Fossils as Biological Entities Reconstructing the Ontogeny of a Fossil Organism Fossils in Evolutionary Reconstructions Practical Work Cross-References References Eco-Evo-Devo Introduction Ecological Development as a Source of Phenotypic Variation Inevitable Effects of Environmental Conditions Adaptive Plasticity Transgenerational Environmental Effects The Internal Environment: Microbial Symbionts Evolution of Eco-Devo Responses Genetic Diversity for Environmental Responses Evolution of Adaptive Plasticity Evolutionary Impact of Eco-Devo Responses A Norm of Reaction View of Fitness Variation Selective Consequences of GxE Variation within Populations Effects of Adaptive Eco-Devo Responses on Evolutionary Diversification Eco-Devo Responses as Niche Construction Eco-Evo-Devo Research Challenges Cross-References References Evo-Devo and Niche Construction Introduction Organism, Environment, and the Promise of Niche Construction Theory To Develop is to Interact with the Environment Organism and Environment as Cause and Effect of Each Other Advancing Evo-Devo Through the Study of Niche Construction Evolutionary Innovation and Diversification Developmental Bias Developmental Plasticity Genetic Accommodation Inclusive Inheritance Conclusions Cross-References References Evo-Devo of Social Behavior Introduction Behavioral Modules of Social Evolution From the Individual to High Society Solitary Ancestors Communal Behavior Primitive Eusociality Advanced Eusociality A Ground Plan for Social Living The Ovarian Ground Plan Hypothesis (OGPH) The Reproductive Ground Plan Hypothesis Food and Society Genetic Toolkits Shape Social Life-Histories Molecular Pathways Associated with Reproduction Molecular Pathways Associated with Nutrition Insulin/Insulin-Like Growth Factor Pathway Genomic Approaches to Social Evo-Devo Epigenetics and Social Behavior Conclusion Cross-References References Evo This reference work provides an comprehensive and easily accessible source of information on numerous aspects of Evolutionary Developmental Biology. The work provides an extended overview on the current state of the art of this interdisciplinary and dynamic scientific field. The work is organized in thematic sections, referring to the specific requirements and interests in each section in far detail. ?Evolutionary Developmental Biology {u2013} A Reference Guide? is intended to provide a resource of knowledge for researchers engaged in evolutionary biology, developmental biology, theoretical biology, philosophy of sciences and history of biology