Variation (eBook)

Variation 3
Variation 5
CONTENTS 7
Variation and Variability: Central Concepts in Biology 25
REFERENCES 31
Variation from Darwin to the Modern Synthesis 33
INTRODUCTION 33
I. VARIATION BEFORE DARWIN 36
II. DARWIN AND VARIATION 37
III. ALTERNATIVE THEORIES OF VARIATION AND EVOLUTION 40
IV. NEO-DARWINISM 43
V. THE EVOLUTIONARY SYNTHESIS 46
VI. CONCLUSIONS 49
REFERENCES 50
The Statistics of Variation 53
ABSTRACT 53
INTRODUCTION 54
I. ABSOLUTE VARIATION: UNIVARIATE CASE 54
II. ABSOLUTE VARIATION: MULTIVARIATE CASE 58
III. RELATIVE VARIATION: UNIVARIATE CASE 64
IV. RELATIVE VARIATION: MULTIVARIATE CASE 65
V. DIMENSIONALITY OF VARIATION 66
VI. TIGHTNESS 67
VII. MEASUREMENT ERROR AND SINGLE SPECIMENS 69
REFERENCES 70
Landmark Morphometrics and the Analysis of Variation 73
INTRODUCTION 73
I. COORDINATE DATA AND THE COORDINATE SYSTEM 75
II. THE GENERAL PERTURBATION MODEL FOR LANDMARK VARIATION 77
III. PROPER ELIMINATION OF NUISANCE PARAMETERS USING A COORDINATE SYSTEM INVARIANT METHOD OF ESTIMATION 80
IV. ADDING ASSUMPTIONS TO THE PERTURBATION MODEL 84
V. CONCLUSIONS 91
ACKNOWLEDGMENTS 92
REFERENCES 92
Variation in Ontogeny 95
INTRODUCTION 95
I. MEASURING VARIATION: A CASE STUDY 98
II. IMPLICATIONS FOR STUDIES OF VARIATION 104
III. CONCLUSIONS 107
ACKNOWLEDGMENTS 107
REFERENCES 108
Constraints on Variation from Genotype through Phenotype to Fitness 111
INTRODUCTION 111
I. RNA EVOLUTIONARY MODEL 113
II. EVOLVING CONSTRAINTS ON VARIATION IN RNA 115
III. MECHANISTIC CONSTRAINTS 120
IV. EPISTATIC CONSTRAINTS 126
V. VIABILITY CONSTRAINTS 128
VI. MODULARITY: A WAY OUT OF THE CONSTRAINTS 129
ACKNOWLEDGMENTS 131
REFERENCES 131
Developmental Origins of Variation 137
INTRODUCTION 137
I. DOES INTRINSIC DEVELOPMENTAL VARIATION EXIST? 139
II. INTRINSIC VARIATION IN DIFFERENT ENVIRONMENTS 142
III. POTENTIAL ORIGINS OF INTRINSIC DEVELOPMENTAL VARIATION 142
IV. AN EXAMPLE OF NOISE IN EUKARYOTIC TRANSCRIPTION 143
V. NOISY BICOID GENE EXPRESSION IN FRUIT FLIES 144
VI. NOISE IN ASYMMETRY PRODUCTION 144
VII. NOISY IMPLICATION FOR EVOLUTION 144
VIII. NETWORKS 145
IX. MORPHOGENETIC FIELDS: A POTENTIAL SOURCE OF VARIATION 149
X. IMPLICATIONS 150
XI. SUMMARY 151
ACKNOWLEDGMENTS 152
REFERENCES 152
Canalization, Cryptic Variation, and Developmental Buffering: A Critical Examination and Analytical Perspective 155
INTRODUCTION 156
I. A REVIEW OF THE REVIEWS 157
II. EMPIRICAL CONCERNS FOR THE STUDY OF CANALIZATION 158
III. DEFINITIONS OF CANALIZATION 160
IV. REACTION NORM OF THE MEAN (RxNM) DEFINITION OF CANALIZATION 161
V. THE VARIATION APPROACH TO CANALIZATION 162
VI. PARTITIONING SOURCES OF VARIATION 163
VII. INFERRING CANALIZATION: WHEN IS A TRAIT CANALIZED? 164
VIII. WHAT ARE THE APPROPRIATE TESTS FOR MAKING STATISTICAL INFERENCES ABOUT CANALIZATION? 166
IX. IN THE INTERIM ÷ 168
X. ANALYSIS FOR THE RxNM APPROACH 168
XI. THE ANALYSIS OF CRYPTIC GENETIC VARIATION 170
XII. MAPPING CRYPTIC GENETIC VARIANTS 171
XIII. IS THE GENETIC ARCHITECTURE OF CRYPTIC GENETIC VARIATION DIFFERENT FROM THAT OF OTHER GENETIC VARIATION INVOLVED WITH TRAIT EXPRESSION? 173
XIV. NOW THAT I HAVE ALL OF THIS CRYPTIC GENETIC VARIATION, WHAT DO I DO WITH IT? 177
XV. THE FUTURE FOR STUDIES OF CANALIZATION 178
ACKNOWLEDGMENTS 179
REFERENCES 179
Mutation and Phenotypic Variation: Where is the Connection? Capacitators, Stressors, Phenotypic Variability, and Evolutionary Change 183
ABSTRACT 183
INTRODUCTION: VARIABILITY AND LIMITS 184
I. MUTATORS, RECOMBINATORS, STRESSORS, AND GENETIC VARIABILITY 185
II. RECOMBINATION 188
III. THE IMPACT OF NEW MUTANTS AND RECOMBINANTS: CANALIZATION AND CAPACITATORS 190
IV. IN SEARCH OF CAPACITATORS: GENES THAT INFLUENCE DEVELOPMENTAL STABILITY AND CANALIZATION 192
V. CAPACITATORS, STRESSORS, AND QUANTITATIVE VARIATION 199
VI. DO WE NEED VARIABILITY GENERATORS? 203
VII. CONCLUDING REMARKS: EXPERIMENTAL PROGRAMS FOR DEFINING THE ROLE OF VARIABILITY GENERATORS 207
REFERENCES 208
Within Individual Variation: Developmental Noise versus Developmental Stability 215
INTRODUCTION 215
I. CAUSES OF DEVELOPMENTAL NOISE 217
II. MECHANISMS OF DEVELOPMENTAL STABILITY 227
III. IMPLICATIONS 238
REFERENCES 239
Developmental Constraints, Modules, and Evolvability 243
ABSTRACT 243
INTRODUCTION 244
I. EVOLVABILITY AND CONSTRAINTS 245
II. INTEGRATION AND MODULARITY 248
III. DEVELOPMENTAL ORIGINS OF COVARIATION AMONG TRAITS 250
IV. DEVELOPMENTAL INTERACTIONS AND PLEIOTROPY 253
V. EVOLUTION OF PLEIOTROPY AND DEVELOPMENTAL INTERACTIONS 255
VI. MODULARITY OF PLEIOTROPIC EFFECTS: INHERENT IN DEVELOPMENTAL SYSTEMS OR EVOLVED PROPERTY? 260
VII. FROM PLEIOTROPIC GENE EFFECTS TO G MATRICES 262
VIII. G MATRICES, CONSTRAINTS, AND EVOLUTIONARY DYNAMICS 263
IX. PERSPECTIVE: DEVELOPMENTAL PROCESSES AND EVOLUTIONARY CONSTRAINTS 265
ACKNOWLEDGMENTS 266
REFERENCES 266
Developmental Regulation of Variability 273
INTRODUCTION 273
I. EMPIRICAL PATTERNS 275
II. THE ONTOGENY OF VARIATION IN MALE NORWAY RAT CRANIAL SHAPE 279
III. BIOLOGICAL PATTERNS VERSUS ARTIFACTS 281
IV. MECHANISMS GENERATING AND REGULATING CRANIOFACIAL SHAPE VARIANCE 283
V. TARGETED GROWTH 285
VI. ORGANISMAL DEVELOPMENTAL TIMING 288
VII. VARIATION IN RELATIVE DEVELOPMENTAL TIMING OF MODULES 290
VIII. NEURAL REGULATION OF MUSCULOSKELETAL INTERACTIONS 292
IX. CANALIZED SHAPE AS AN EPIPHENOMENON 294
ACKNOWLEDGMENTS 296
REFERENCES 296
Role of Stress in Evolution: From Individual Adaptability to Evolutionary Adaptation 301
INTRODUCTION 301
I. EVOLUTION OF RESPONSE TO STRESS 303
II. EVOLUTIONARY CONSEQUENCES OF STRESS 306
III. EVOLUTIONARY ADAPTATION 316
IV. CONCLUSIONS 317
ACKNOWLEDGMENTS 318
REFERENCES 318
Environmentally Contingent Variation: Phenotypic Plasticity and Norms of Reaction 327
INTRODUCTION 328
I. PLASTICITY CONCEPTS 329
II. THE GENETIC AND DEVELOPMENTAL BASIS OF PHENOTYPIC PLASTICITY 333
III. HOW PLASTICITY INTERACTS WITH CONSERVED DEVELOPMENTAL PATTERNS 341
IV. WHAT EFFECTS DOES PLASTICITY HAVE ON POPULATIONS AND COMMUNITIES? 346
V. RESEARCH AGENDA 350
ACKNOWLEDGMENTS 351
REFERENCES 351
Variation and Life-History Evolution 357
INTRODUCTION 357
II. PHENOTYPIC VARIATION IN A STOCHASTIC ENVIRONMENT 365
III. PREDICTABLE ENVIRONMENTS 371
IV. CONCLUDING COMMENTS 378
REFERENCES 379
Antisymmetry 383
INTRODUCTION 384
I. ASYMMETRY TERMINOLOGY 385
II. THE HISTORY OF ANTISYMMETRY 391
III. TAXONOMIC DISTRIBUTION AND FUNCTIONAL SIGNIFICANCE OF ANTISYMMETRY 392
IV. DEVELOPMENT AND REGENERATION OF ASYMMETRY IN ANTISYMMETRIC SPECIES 400
V. INHERITANCE OF DIRECTION IN ANTISYMMETRIC SPECIES 402
VI. INHERITANCE OF DIRECTION IN DIRECTIONALLY ASYMMETRIC SPECIES 405
VII. EVOLUTIONARY SIGNIFICANCE OF ANTISYMMETRY 406
VIII. WHAT NEXT? 408
ACKNOWLEDGMENTS 408
REFERENCES 414
Variation in Structure and Its Relationship to Function: Correlation, Explanation, and Extrapolation 423
ABSTRACT 424
INTRODUCTION 424
I. BACKGROUND 426
II. APPROACHES TO THE STUDY OF STRUCTURAL VARIATION 427
III. VARIATION AS AN OBSERVABLE PHENOMENON 428
IV. IN SITU CORRELATIONAL STUDIES OF THE RELATIONSHIP BETWEEN STRUCTURAL VARIATION AND FUNCTIONAL ATTRIBUTES 432
V. EX SITU STUDIES OF THE RELATIONSHIP BETWEEN STRUCTURAL VARIATION AND PERFORMANCE 439
VI. CONCLUDING REMARKS 450
REFERENCES 452
A Universal Generative Tendency toward Increased Organismal Complexity 459
INTRODUCTION 459
I. INTERNAL VARIANCE AS COMPLEXITY 462
II. THREE SIMPLE MODELS 465
III. THE EFFECT OF INCREASED DIMENSIONALITY 472
IV. APPARENT DIFFICULTIES 472
V. IS THERE AN UPWARD BIAS IN REAL LINEAGES? 473
VI. IF SO, THE PRINCIPLE IS SUPPORTED 474
VII. IF NOT, WHY NOT? 474
VIII. TESTING THE PRINCIPLE 476
IX. A REVERSAL OF INTUITION 476
REFERENCES 477
Variation and Versatility in Macroevolution 479
I. PRINCIPLES 479
II. EXAMPLES 484
III. OVERVIEW AND CONCLUSION 492
ACKNOWLEDGMENTS 494
REFERENCES 494
Variation and Developmental Biology: Prospects for the Future 499
INTRODUCTION 499
I. MODEL ORGANISMS: EXPANDING THE FOLD 501
II. ECOLOGICALLY SIGNIFICANT DIFFERENCES IN FORM BETWEEN SPECIES 504
III. HOW MANY WAYS TO MAKE A PHENOTYPE: DEVELOPMENTAL VARIATION AND MORPHOLOGICAL SIMILARITY 509
IV. INTRASPECIFIC DEVELOPMENTAL VARIATION: CANALIZATION AND DEVELOPMENTAL PLASTICITY 511
V. CONCLUSIONS 514
REFERENCES 515
Phenogenetics: Genotypes, Phenotypes, and Variation 523
INTRODUCTION 523
I. MECHANISM VERSUS VARIATION 526
II. FROM GENOTYPE TO PHENOTYPE: MECHANISM 527
III. FROM GENOTYPE TO PHENOTYPE: VARIATION 534
IV. SUMMARY 541
ACKNOWLEDGMENTS 542
REFERENCES 542
The Study of Phenotypic Variability: An Emerging Research Agenda for Understanding the Developmental Ò Genetic Architecture Underlying Phenotypic Variation 549
INTRODUCTION 550
I. VARIABILITY AND THE BIOLOGICAL HIERARCHY 551
II. COMPONENTS OF VARIABILITY 553
III. CURRENT APPROACHES TO UNDERSTANDING THE DEVELOPMENT Ò GENETIC ARCHITECTURE OF VARIABILITY 555
IV. A DEVELOPMENTAL SYSTEMS APPROACH TO PHENOTYPIC VARIABILITY 565
V. CONCLUSION 571
REFERENCES 572
Index 577