Homology, Genes, and Evolutionary Innovation

Homology, Genes, and Evolutionary Innovation

by Günter P. Wagner


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A major synthesis of homology, written by a top researcher in the field

Homology—a similar trait shared by different species and derived from common ancestry, such as a seal's fin and a bird’s wing—is one of the most fundamental yet challenging concepts in evolutionary biology. This groundbreaking book provides the first mechanistically based theory of what homology is and how it arises in evolution.

Günter Wagner, one of the preeminent researchers in the field, argues that homology, or character identity, can be explained through the historical continuity of character identity networks—that is, the gene regulatory networks that enable differential gene expression. He shows how character identity is independent of the form and function of the character itself because the same network can activate different effector genes and thus control the development of different shapes, sizes, and qualities of the character. Demonstrating how this theoretical model can provide a foundation for understanding the evolutionary origin of novel characters, Wagner applies it to the origin and evolution of specific systems, such as cell types; skin, hair, and feathers; limbs and digits; and flowers.

The first major synthesis of homology to be published in decades, Homology, Genes, and Evolutionary Innovation reveals how a mechanistically based theory can serve as a unifying concept for any branch of science concerned with the structure and development of organisms, and how it can help explain major transitions in evolution and broad patterns of biological diversity.

Product Details

ISBN-13: 9780691180670
Publisher: Princeton University Press
Publication date: 07/10/2018
Pages: 496
Product dimensions: 6.00(w) x 9.25(h) x (d)

About the Author

Günter P. Wagner is the Alison Richard Professor of Ecology and Evolutionary Biology at Yale University and a pioneer of the field of evolutionary developmental biology. He is the editor of The Character Concept in Evolutionary Biology.

Table of Contents

Preface xi

Introduction What This Book Aims to Do and What It Is Not 1

PART I: Concepts and Mechanisms

CHAPTER 1 The Intellectual Challenge of Morphological Evolution: A Case for Variational Structuralism 7

Contrasting Ontologies 9

Facts and Ideas about Bodies 20

Re-focusing on the Role of Development 26

The Emergence of Molecular Structuralism 29

The Enigma of Developmental Variation 37

CHAPTER 2 A Conceptual Roadmap to Homology 39

Two Observations: Sameness and Continuity 40

A Detour into Genetics: Homologous Genes 44

Character Identity and Character States 51

Characters and Character States: Who Is Who? 54

Variational Modalities: More Than One Way of Being a Certain Character 58

Character Identity and Repeated Body Parts: Serial Homology 65

Character Swarms: Persistent Cases of Partial Individuality 71

Alternative Conceptualizations of Homology 71

A Case for Conceptual Liberalism 78

Sorting Patterns of Morphological Variation 79

CHAPTER 3 A Genetic Theory of Homology 82

Why Continuity of Genetic Information Is Not Enough 82

Lessons from the Variable Development of Homologs 90

Homeotic Genes and Character Identity 93

A Model: Character Identity Networks 96

Variation and Conservation of Segment Development 98

Eye Development and the ey/so/eya/dac (ESED) Networks 102

The Role of Protein-Protein Interactions 114

Characteristics of Character Identity Networks 117

CHAPTER 4 Evolutionary Novelties: The Origin of Homologs 119

Modes of Evolution 120

Revisiting the Conceptual Roadmap: Which Way to Novelty? 123

Phenomenological Modes for the Origin of Type I Novelties 127

From Phenomenology to Explanation 135

Explaining Robustness and Canalization 151

Natural Selection and the Origin of Novelties: A Roundup 156

CHAPTER 5 Developmental Mechanisms for Evolutionary Novelties 158

The Environment’s Role in Evolutionary Innovations 158

Where Does the Positional Information for Novel Characters Come From? 164

Derived Mechanical Stimuli and the Origin of Novelties in the Avian Hind Limb Skeleton 170

The Origin of Character Identity Networks 173

The Evolution of Novel Signaling Centers 175

The Developmental Biology of Novelties: Reflections 184

CHAPTER 6 The Genetics of Evolutionary Novelties 186

Evolution of cis-Regulatory Elements 187

Are Novel Pigment Spots Novelties, and Why Does It Matter? 195

Sex Combs: The Origin of a ChIN 199

Origin of Novel cis-R egulatory Elements: Transposable Elements 204

The Role of Gene Duplications 209

Evolution of Transcription Factor Proteins 213

The Evolution of miRNAs 224

A Material Difference between Innovation and Adaptation? 227

CHAPTER 7 The Long Shadow of Metaphysics on Research Programs 229

Metaphysics as the Sister of Science 230

Classes and Individuals 232

Individuals and Natural Kinds 238

Definitions and Models 240

PART II : Paradigms and Research Programs

CHAPTER 8 Cell Types and Their Origins 250

Developmental Genetics of Cell Types 253

The Evolutionary Origin of Cell Types 272

Case Studies of Cell Typogenesis 280

Concluding Reflections 292

CHAPTER 9 Skin and a Few of Its Derivatives 294

Developmental Evolution of Amniote Skin and Skin Appendages 296

Mammalian Skin Derivatives: Hairs and Breasts 304

Devo-Evo of Bird Skin: Scales into Feathers 308

Origin of Feathers 313

CHAPTER 10 Fins and Limbs 327

Paired Fins 327

From Fins to Limbs 333

Concluding Reflection on the Nature of Character Identity 354

CHAPTER 11 Digits and Digit Identity 356

The Origin of Digits 356

Digits Come and Go: Is There a Pentadactyl Ground Plan? 357

Developmental and Morphological Heterogeneity of the Tetrapod Hand 359

Digit Loss and Re-evolution in Amniotes 365

The Pentadactyl Autopodium (PDA) Type 366

Developmental Genetics of Digit Identity 369

Digit Identity: Real or Imaginary? 374

A Fingerpost on the Nature of Character Identity 382

CHAPTER 12 Flowers 385

What Is a Flower? 386

Angiosperm Phylogeny and Flower Character Evolution 389

Genetics of Canonical Flower Development 391

The Developmental Genetic Architecture of the Flower Bauplan 396

Flower Variation and Novel Flower Organ Identities 398

The Origin of the Bisexual Flower Developmental Type 401

Perianth Evolution and the Origin of Petals 407

Genetics of Organ Identity: Challenges from Gene Duplication 412

Summary and Conclusions 414

CHAPTER 13 Lessons and Challenges 416

What Are the Core Claims of This Model of Homology? 416

Characters Are Real But Historically Limited 418

Homology Is Not Hierarchical 420

The Quasi-C artesian Model of Character Identity 421

Character Individuality and Gene Regulatory Network Cooperativity 422

Open Questions and Difficulties 423

Population, Tree, and Homology Thinking 424

References 427

Index 467

What People are Saying About This

From the Publisher

"In this remarkably insightful and ambitious book, Wagner argues that homologies are real: they are not just surviving similarities between related organisms that have not yet been erased by selection and drift, and they shape evolutionary trajectories by organizing the flow of variation to selection. He develops a synthesis of adaptationist and structuralist perspectives on evolution that is both conceptually rich and empirically grounded."—Kim Sterelny, author of The Evolved Apprentice: How Evolution Made Humans Unique

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