Homology, Genes, and Evolutionary Innovation

Gunter 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.

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