Avian Molecular Evolution and Systematics (eBook)

Front Cover 1
Avian Molecular Evolution and Systematics 4
Copyright Page 5
Contents 6
Contributors 14
Preface 18
Part I: Molecular Sequences and Evolutionary History in Birds 22
Chapter 1. Molecular Evolution of the Mitochondrial Genome 24
I. Introduction 25
II. Mitochondria: An Ancient Legacy 25
III. The Vertebrate Mitochondrial Genome 26
IV. Avian Mitochondrial Genomes 27
V. Major Genomic Features as Characters for Phylogenetic Analysis 32
VI. Intergenomic Transfer of Mitochondrial Sequences 38
VII. Conclusion 44
References 44
Chapter 2. DNA Microsatellites as Genetic Markers at Several Scales 50
I. Introduction 51
II. Technical Overview 51
III. The Range of Scales 55
IV. Cautions for Data Analysis 60
V. Case Histories 62
VI. Summary and Conclusions 64
References 64
Appendix I 70
Chapter 3. Mitochondrial Control Region Sequences as Tools for Understanding Evolution 72
I. Introduction 72
II. Sequence Organization and Evolution 74
III. Population Structure and Intraspecific Taxonomy 85
IV. Higher Level Systematics 98
References 100
Chapter 4. The Window of Taxonomic Resolution for Phylogenies Based on Mitochondrial Cytochrome b 104
I. Introduction 105
II. Materials and Methods 108
III. Results 109
IV. Discussion 126
References 130
Appendix I 135
Appendix II 136
Chapter 5. Phylogeny and Evolution of 12S rDNA in Gruiformes (Aves) 142
I. Introduction 142
II. Methods 148
III. Phylogenetic Inferences 155
IV. Molecular Evolution 163
V. Implications of 12S Evolution for Phylogenetic Inference 173
VI. Summary 174
References 175
Chapter 6. Phylogeny of the Pelacaniformes: Molecular Systematics of a Privative Group 180
I. Introduction 180
II. Methods 185
III. Results 187
IV. Discussion 188
References 191
Chapter 7. The Phylogeny of Ratite Birds: Resolving Conflicts between Molecular and Morphological Data Sets 194
I. Introduction 194
II. Materials and Methods 197
III. Results 202
IV. Discussion 207
V. Conclusions 211
References 213
Appendix I 217
Appendix II 230
Chapter 8. Phylogenetic Relationships among and within Select Avian Orders Based on Mitochondrial DNA 234
I. Introduction 235
II. Issues in Phylogenetic Analyses 236
III. Methods 240
IV. Results and Discussion 246
V. Conclusions 262
References 264
Part II: Applying Phylogeny and Population Genetics to Broader Issues 270
Chapter 9. Relevance of Microevolutionary Processes to Higher Level Molecular Systematics 272
I. Introduction 272
II. Molecular Variability 274
III. Population Processes 283
IV. Conclusion 294
References 295
Chapter 10. Phylogeny in Studies of Bird Ecology, Behavior, and Morphology 300
I. Introduction 300
II. Accurate Phylogenetic Estimates and Historical Ecology 302
III. Application of the Comparative Approach to Classic Problems of Evolution 306
IV. Summary 315
References 317
Chapter 11. Phylogeographic Studies of North American Birds 322
I. Introduction 322
II. Allozymic Studies of Avian Geographic Variation 323
III. The DNA Revolution in Intraspecific Studies 324
IV. Phylogeographic Studies in Birds 326
V. Comparative Phylogeography 335
VI. Prospectus 341
References 342
Chapter 12. The Speciation of South American and African Birds in Montane Regions 346
I. Introduction 346
II. The Model Hypothesis 347
III. Old and New Species in South America 349
IV. Old and New Species in Africa 351
V. Implications for the Model 353
VI. Case Studies of Biogeographic Patterns in Tropical Mountains 354
VII. Discussion and Summary 360
References 362
Chapter 13. Studies of Avian Ancient DNA: From Jurassic Park to Modern Island Extinctions 366
I. Introduction 366
II. Review of Ancient DNA Research 367
III. Systematics and Paleoecological Applications 370
IV. Summary 389
V. Future Research 389
References 390
Index 396