Evolution of Parasitism - A Phylogenetic Perspective (eBook)

Cover 1
CONTENTS 10
Contributors to Volume 54 6
Preface 8
Introduction „ Phylogenies, Phylogenetics, Parasites and the Evolution of Parasitism 14
Chapter 1. Cryptic Organelles in Parasitic Protists and Fungi 22
Abstract 23
1. Introduction 23
2. The Origin of Mitochondria and Plastids by Endosymbiosis 25
3. Cryptic Organelles and How to Find Them 34
4. Case Histories – Mitochondria 37
5. Case Histories – Plastids 51
6. Future Directions 62
Acknowledgements 66
References 67
Chapter 2. Phylogenetic Insights into the Evolution of Parasitism in Hymenoptera 82
Abstract 82
1. Introduction 83
2. Some Questions about Hymenopteran Parasitoid Evolution Addressed using Phylogeny 87
3. Evolution from Parasitism to Other Lifestyles 97
4. The Comparative Method and Parasitoids: Future Prospects 102
5. Conclusion 104
Acknowledgements 104
References 104
Chapter 3. Nematoda: Genes, Genomes and the Evolution of Parasitism 114
Abstract 115
1. Nematode Genomes and the Evolution of Parasitism 116
2. Nematode Parasitism 124
3. Nematode Genomes and Parasitism 139
4. Summary 178
Acknowledgements 180
References 181
Chapter 4. Life Cycle Evolution in the Digenea: a New Perspective from Phylogeny 210
Abstract 211
1. Introduction 211
2. Methods 212
3. Background to the Digenea 216
4. Mapping and Interpreting Life Cycle Traits 222
5. Problems 253
Appendix 257
Acknowledgements 262
References 262
Chapter 5. Progress in Malaria Research: the Case for Phylogenetics 268
Abstract 268
1. The Malaria Phylum: Apicomplexa 269
2. Morphology, Phylogenetics and Plasmodium Systematics 271
3. Evolution and Extant Distribution of Malignant Human Malaria: P. falciparum 279
4. Concluding Remarks 288
References 288
Chapter 6. Phylogenies, the Comparative Method and Parasite Evolutionary Ecology 294
Abstract 295
1. Introduction 295
2. Phylogenetic Effects and Constraints, and the Need for Phylogenies 296
3. The Phylogenetically Independent Contrasts Method 297
4. Diversity and Diversification 300
5. The Phylogenetic Eigenvector Method 303
6. The Study of Host–Parasite Co-adaptation Using the Independent Contrasts Method 305
7. The Study of Host–Parasite Co-adaptation Using PER 306
8. Scepticism about Comparative Methods: Why Bother with Phylogeny? 308
9. Phylogenetically Structured Environmental Variation 309
10. Conclusions 312
Acknowledgements 312
References 312
Chapter 7. Recent Results in Cophylogeny Mapping 316
Abstract 316
1. Introduction 317
2. Cophylogenetic Events 319
3. Cophylogeny Mapping 321
4. Complexity 325
5. Modelling Cophylogeny 329
6. Tests of Significance 335
7. Confounding Cophylogeny 337
8. Discussion 339
Acknowledgements 341
References 341
Chapter 8. Inference of Viral Evolutionary Rates from Molecular Sequences 344
Abstract 345
1. Introduction 345
2. General Linear Regression and Other Distance-based Methods 350
3. Maximum Likelihood Estimation 356
4. Bayesian Inference of Evolutionary Rates 360
5. Discussion 363
Acknowledgements 367
References 368
Chapter 9. Detecting Adaptive Molecular Evolution: Additional Tools for the Parasitologist 372
Abstract 373
1. What is Adaptive Molecular Evolution? 373
2. Methodological Advances 375
3. Example of Adaptive Evolution in the Malaria Rifin Proteins 379
4. Prospects 386
Acknowledgements 389
References 390
Index 394
Contnts of Volumes in This Series 412