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 Cognitive Science
Introduction
Developmental Cognitive Science
Evolutionary Cognitive Science
Evo-Devo and Cognitive Science
Evolutionary Developmental Cognitive Science
Developmental Systems Theory
Genes X Environment Interactions
Epigenetics
Evolutionary Developmental Comparative Cognitive Science
Evolutionary Developmental Cognitive Neuroscience
Evolutionary Developmental Biology and Cognitive Science
Conclusion
Cross-References
References
Evo-Devo of Language and Cognition
Introduction
The Problem of Ontology
The Problem of Computation(s)
The Problem of Representation(s)
The Problem of Homology/Novelty
The Problem of Selection
Cross-References
References
Evo-Devo and Culture
Introduction
An Evo-Devo of Culture
Naturalizing Culture
How Biological Development Shapes Enculturation
How Enculturation Shapes Biological Development
Cultural Evo-Devo
Cross-References
References
Index