Genetics and Evolution of Infectious Diseases

1. Recent Developments in the Definition and Official Names of Virus Species

• 1. Introduction
• 2. The Logic of Hierarchical Virus Classification
• 3. Bionominalism: Are Species Classes or Individuals?
• 4. The Virus Species Problem
• 5. Properties Used for Defining Virus Species and Identifying Individual Viruses
• 6. A Virus Species Cannot Be Defined Solely by the Properties of Viral Genomes
• 7. The New ICTV Definition of Virus Species
• 8. Non-Latinized Binomial Names for Virus Species
• 9. Discussion

2. A Theory-Based Pragmatism for Discovering and Classifying Newly Divergent Species of Bacterial Pathogens

• 1. Introduction
• 2. Ecological Breadth of Recognized Species
• 3. The Stable Ecotype Model of Bacterial Speciation
• 4. Demarcating Putative Ecotypes From Sequence Data
• 5. Ecological Diversity Within Putative Ecotypes
• 6. Models of Frequent Speciation
• 7. Other Models Where Ecotypes Are Not Discernible as Sequence Clusters
• 8. Are Bacterial Ecotypes Cohesive?
• 9. Incorporating Ecology Into Bacterial Systematics

3. Population Structure of Pathogenic Bacteria

• 1. Introduction
• 2. Recombination in Bacterial Populations
• 3. Evolutionary Processes Shape Intra- and Interhost Bacterial Population Structure
• 4. Genomic Analysis Tools for Studying Bacterial Population Structure
• 5. Conclusions

4. Epidemiology and Evolution of Fungal Pathogens in Plants and Animals

• 1. Introduction
• 2. New and Emerging Mycoses
• 3. Plant Pathogenic Fungi
• 4. New and Emerging Plant Diseases
• 5. Modern Molecular Epidemiological Tools for Investigating Fungal Diseases
• 6. Population Genetics of Pathogenic Fungi
• 7. Genomics of Fungi: What Makes a Fungus Pathogenic?
• 8. Conclusion

5. Clonal Evolution

• 1. Introduction
• 2. Definitions
• 3. The Origin of Life, the Origin of Propagation, and Recombination
• 4. Clonal Modes
• 5. Quantifying the Importance of Asexuality in the Biosphere
• 6. Genetic Consequences of Asexuality
• 7. Evolution and the Paradox of Sex
• 8. Clonal Microevolution
• 9. Conclusions
• Abbreviation List

6. Coevolution of Host and Pathogen

• 1. Coevolution of Host and Pathogen
• 2. The Process of Antagonistic Coevolution
• 3. Testing for Host–Pathogen Coevolution
• 4. Implications of Coevolution
• 5. Summary/Future Outlook

7. Microbes as Tracers of Past Human Demography and Migrations

• 1. Introduction
• 2. Using Pathogens as Genetic Tracers for Host History
• 3. Candidates
• 4. Conclusion
• Abbreviations

8. Phylogenetic Analysis of Pathogens

• 1. Introduction
• 2. The Uses of Phylogenies
• 3. The Logic of Phylogeny Reconstruction
• 4. Characters and Samples
• 5. The Practice of Phylogeny Reconstruction
• 6. Choosing a Method
• 7. Representing Phylogenies: Trees
• 8. Phylogenetic Networks

9. Evolutionary Responses to Infectious Disease

• 1. Introduction
• 2. Parasites as Our Friends
• 3. Demography and Parasites
• 4. Agriculture
• 5. Some Lessons From Malaria
• 6. Disease and Standard of Living in Preindustrial Societies: A Simple Model
• 7. Population Limitation
• 8. Disease, Mating, and Reproductive Strategy
• 9. Prosperity and the Postindustrial Era Mortality Decline

10. Infectious Disease Genomics

• 1. Introduction
• 2. Vaccine Target
• 3. New Drug Discovery
• 4. Drug Target
• 5. Therapeutic Response and Drug Resistance
• 6. Vector Control
• 7. Clinical Application
• 8. Conclusion

11. Proteomics and Host–Pathogen Interactions: A Bright Future?

• 1. Introduction
• 2. Interest of Proteomics to Study Host–Pathogen Interactions
• 3. Retrospective Analysis of Previous Proteomics Studies
• 4. Toward New Conceptual Approaches to Decipher the Host–Parasite Interactions for Parasites With Simple or Complex Life Cycle
• 5. Population Proteomics: An Emerging Discipline to Study Host–Parasite Interactions
• 6. Conclusion

12. The Evolution of Antibiotic Resistance

• 1. Introduction
• 2. Mechanisms and Sources of Antibiotic Resistance
• 3. Evolution of Antibiotic-Resistance Genes
• 4. Limitations to Adaptation and the Cost of Resistance
• 5. Can the Evolution of Antibiotic Resistance be Predicted?
• 6. Conclusions and Perspectives
• Glossary
• List of Abbreviations

13. Modern Morphometrics of Medically Important Arthropods

• 1. Introduction
• 2. Landmark-Based Geometric Morphometry
• 3. Pseudo-Landmark-Based Shape
• 4. Allometry
• 5. Measurement Error
• 6. Some Considerations About the Genetics of Metric Change
• 7. Phenotypic Plasticity
• 8. A Special Case of Shape Change: the Character Displacement
• 9. The Regulation of Phenotype
• 10. Applications in Medical Entomology
• Glossary

14. Evolution of Resistance to Insecticide in Disease Vectors

• 1. Introduction
• 2. Insecticide Resistance: Definition and History
• 3. Mechanisms of Resistance
• 4. Conclusion

15. Genetics of Major Insect Vectors

• 1. Introduction
• 2. Genetics of Tsetse Flies and African Trypanosomiasis
• 3. Genetics of the Triatominae (Hemiptera, Reduviidae) and Chagas Disease
• 4. The Anopheles gambiae Complex
• 5. Genetics of the Order Ixodida
• Glossary

16. Multilocus Sequence Typing of Pathogens: Methods, Analyses, and Applications

• 1. Introduction
• 2. Molecular Design and Development of Multilocus Sequence Typing
• 3. Multilocus Sequence Typing Databases
• 4. Advantages and Disadvantages of Multilocus Sequence Typing
• 5. Analytical Approaches
• 6. Applications of Multilocus Sequence Typing
• 7. Conclusions and Prospects

17. Next-Generation Sequencing, Bioinformatics, and Infectious Diseases

• 1. Analyzing Big Data
• 2. Comparative Genomics
• 3. Transcriptomics
• 4. Single-Cell Technologies
• 5. High-Throughput Sequencing
• 6. De Novo Genome Assembly
• 7. Whole-Genome Sequence Analysis
• 8. RNA-Seq (Transcriptomics)
• 9. Concluding Remarks

18. Genomics of Infectious Diseases and Private Industry

• 1. Introduction
• 2. Technologies and Instrument Platforms
• 3. Customers and Their Needs
• 4. Industry Landscape
• 5. Conclusion

19. Current Progress in the Pharmacogenetics of Infectious Disease Therapy

• 1. Introduction
• 2. Pharmacogenetics of HIV Therapy
• 3. Pharmacogenetics of Antimalarial Therapy
• 4. Pharmacogenetics of Antituberculous Therapy
• 5. Summary and Perspective

20. Genetic Exchange in Trypanosomatids and Its Relevance to Epidemiology

• 1. Introduction
• 2. Trypanosoma brucei
• 3. Trypanosoma cruzi
• 4. Leishmania
• Abbreviations

21. Genomic Insights Into the Past, Current, and Future Evolution of Human Parasites of the Genus Plasmodium

• 1. Introduction
• 2. Evolution of Plasmodium: The Last 10Million Years
• 3. Evolution of Plasmodium: The 21st Century in Three Courses
• 4. Evolution of Plasmodium, and the Eradication Agenda

22. Integrated Genetic Epidemiology of Chagas Disease

• 1. What Is Integrated Genetic Epidemiology?
• 2. Chagas Disease: A Major Health Problem in Latin America and Other Countries
• 3. The Chagas Disease Cycle
• 4. Host Genetic Susceptibility to Chagas Disease
• 5. Vector Genetic Diversity
• 6. Parasite Genetic Diversity
• 7. Concluding Remarks
• Glossary

23. Adaptive Evolution of the Mycobacterium tuberculosis Complex to Different Hosts

• 1. Overview: Disease and Mycobacterial Genetics
• 2. Host–Pathogen Coevolution of the Tubercle Bacillus
• 3. Evolution of the Mycobacterium tuberculosis Complex From a Genomic Perspective
• 4. Evolution in the Laboratory Environment and In Vitro Attenuation of Bacteria From the Mycobacterium tuberculosis Complex
• 5. Short-Term Evolution of Mycobacterium tuberculosis During Infection, Drug Treatment, and Disease
• 6. Adaptive Cues of the Mycobacterium tuberculosis Complex As the Most Successful Pathogens
• 7. Pending Questions and Concluding Remarks

24. The Evolution and Dynamics of Methicillin-Resistant Staphylococcus aureus

• 1. Introduction
• 2. The Staphylococcal Cassette Chromosome mec
• 3. Evolution of Staphylococcus aureus and MRSA
• 4. Molecular Epidemiology of MRSA
• 5. Conclusion

25. Origin and Emergence of HIV/AIDS

• 1. History of AIDS
• 2. Human Immunodeficiency Viruses Are Closely Related to Simian Immunodeficiency Virus From Nonhuman Primates
• 3. HIV-1 Is Derived From Simian Immunodeficiency Viruses Circulating Among African Apes
• 4. Origin of HIV-2: Another Emergence, Another Epidemic
• 5. Ongoing Exposure of Humans to a Large Diversity of Simian Immunodeficiency Viruses: Risk for a Novel HIV?
• 6. Conclusion

26. Evolution of SARS Coronavirus and the Relevance of Modern Molecular Epidemiology

• 1. A Brief History of SARS
• 2. SARS Coronavirus
• 3. The Animal Link
• 4. Natural Reservoirs of SARS-CoV
• 5. Molecular Evolution of SARS-CoV in Humans and Animals
• 6. Coronavirus Surveillance in Wildlife Animals
• 7. Concluding Remarks

27. Ecology and Evolution of Avian Influenza Viruses

• 1. Introduction to Influenza A Virus
• 2. Influenza Viruses in Birds
• 3. Evolutionary Genetics of Avian Influenza Viruses
• 4. Future Perspective