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Homology, Genes, and Evolutionary Innovation
Günter P. Wagner

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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

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