Front Cover; Advances in Parasitology; Copyright Page; Contributors to Volume 54; Preface; CONTENTS; Introduction -- Phylogenies, Phylogenetics, Parasites and the Evolution of Parasitism; Chapter 1. Cryptic Organelles in Parasitic Protists and Fungi; Abstract; 1. Introduction; 2. The Origin of Mitochondria and Plastids by Endosymbiosis; 3. Cryptic Organelles and How to Find Them; 4. Case Histories -- Mitochondria; 5. Case Histories -- Plastids; 6. Future Directions; Acknowledgements; References; Chapter 2. Phylogenetic Insights into the Evolution of Parasitism in Hymenoptera; Abstract

1. Introduction2. Some Questions about Hymenopteran Parasitoid Evolution Addressed using Phylogeny; 3. Evolution from Parasitism to Other Lifestyles; 4. The Comparative Method and Parasitoids: Future Prospects; 5. Conclusion; Acknowledgements; References; Chapter 3. Nematoda: Genes, Genomes and the Evolution of Parasitism; Abstract; 1. Nematode Genomes and the Evolution of Parasitism; 2. Nematode Parasitism; 3. Nematode Genomes and Parasitism; 4. Summary; Acknowledgements; References; Chapter 4. Life Cycle Evolution in the Digenea: a New Perspective from Phylogeny; Abstract; 1. Introduction

2. Methods3. Background to the Digenea; 4. Mapping and Interpreting Life Cycle Traits; 5. Problems; Appendix; Acknowledgements; References; Chapter 5. Progress in Malaria Research: the Case for Phylogenetics; Abstract; 1. The Malaria Phylum: Apicomplexa; 2. Morphology, Phylogenetics and Plasmodium Systematics; 3. Evolution and Extant Distribution of Malignant Human Malaria: P. falciparum; 4. Concluding Remarks; References; Chapter 6. Phylogenies, the Comparative Method and Parasite Evolutionary Ecology; Abstract; 1. Introduction

2. Phylogenetic Effects and Constraints, and the Need for Phylogenies3. The Phylogenetically Independent Contrasts Method; 4. Diversity and Diversification; 5. The Phylogenetic Eigenvector Method; 6. The Study of Host-Parasite Co-adaptation Using the Independent Contrasts Method; 7. The Study of Host-Parasite Co-adaptation Using PER; 8. Scepticism about Comparative Methods: Why Bother with Phylogeny?; 9. Phylogenetically Structured Environmental Variation; 10. Conclusions; Acknowledgements; References; Chapter 7. Recent Results in Cophylogeny Mapping; Abstract; 1. Introduction

2. Cophylogenetic Events3. Cophylogeny Mapping; 4. Complexity; 5. Modelling Cophylogeny; 6. Tests of Significance; 7. Confounding Cophylogeny; 8. Discussion; Acknowledgements; References; Chapter 8. Inference of Viral Evolutionary Rates from Molecular Sequences; Abstract; 1. Introduction; 2. General Linear Regression and Other Distance-based Methods; 3. Maximum Likelihood Estimation; 4. Bayesian Inference of Evolutionary Rates; 5. Discussion; Acknowledgements; References; Chapter 9. Detecting Adaptive Molecular Evolution: Additional Tools for the Parasitologist; Abstract