Evolutionary Parasitology. The Integrated Study of Infections, Immunology, Ecology, and Genetics

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Evolutionary Parasitology: The Integrated Study of Infections, Immunology, Ecology, and Genetics
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Preface
Contents
List of common acronyms
Glossary
Chapter 1: Parasites and their significance
	1.1 The Panama Canal
	1.2 Some lessons provided by yellow fever
		1.2.1 Parasites have different life cycles and transmission modes
		1.2.2 Not all host individuals, and not all parasite strains, are the same
		1.2.3 Physiological and molecular mechanisms underlie the infection
		1.2.4 Parasites and hosts are populations
		1.2.5 Parasites can be controlled when we understand them
	1.3 Parasites are not a threat of the past
Chapter 2: The study of evolutionary parasitology
	2.1 The evolutionary process
	2.2 Questions in evolutionary biology
	2.3 Selection and units that evolve
	2.4 Life history
	2.5 Studying adaptation
		2.5.1 Optimality
		2.5.2 Evolutionarily stable strategies (ESS)
		2.5.3 Comparative studies
	Box 2.1 The basic evolutionary forces
	Box 2.2 The disease space
Chapter 3: The diversity and natural history of parasites
	3.1 The ubiquity of parasites
	3.2 A systematic overview of parasites
		3.2.1 Viruses
		3.2.2 Prokaryotes
			3.2.2.1 Archaea
			3.2.2.2 Bacteria
		3.2.3 The basal eukaryotes
		3.2.4 Protozoa
		3.2.5 Fungi
		3.2.6 Nematodes (roundworms)
		3.2.7 Flatworms
		3.2.8 Acanthocephala
		3.2.9 Annelida
		3.2.10 Crustacea
		3.2.11 Mites (Acari), ticks, lice (Mallophaga, Anoplura)
		3.2.12 Parasitic insects (parasitoids)
	3.3 The evolution of parasitism
		3.3.1 Evolution of viruses
		3.3.2 Evolution of parasitism in nematodes
	3.4 The diversity and evolution of parasite life cycles
		3.4.1 Steps in a parasite’s life cycle
		3.4.2 Ways of transmission
		3.4.3 Complex life cycles
		3.4.4 The evolution of complex parasite life cycles
		3.4.5 Example: trypanosomes
		3.4.6 Example: helminths
	Box 3.1 Types of parasites
Chapter 4: The natural history of defences
	4.1 The defence sequence
		4.1.1 Pre-infection defences
			4.1.1.1 Avoidance behaviour
			4.1.1.2 The selfish herd and group-living
			4.1.1.3 Anticipatory defences
			4.1.1.4 ‘Genetic’ defences
		4.1.2 Post-infection defences
			4.1.2.1 Behavioural changes
			4.1.2.2 Physiological responses
		4.1.3 Social immunity
	4.2 Basic elements of the immune defence
		4.2.1 Humoral defences
			4.2.1.1 Immunoglobulins
			4.2.1.2 Complement
			4.2.1.3 Other humoral components
		4.2.2 Cellular defences
			4.2.2.1 Haematopoiesis (cell development)
			4.2.2.2 Phagocytosis
			4.2.2.3 Melanization, encapsulation
			4.2.2.4 Clotting, nodule formation
	4.3 Basic defences by the immune system
		4.3.1 Inflammation
		4.3.2 Innate immunity
		4.3.3 Adaptive (acquired) immunity
		4.3.4 Regulation of the immune response
			4.3.4.1 Regulation by protein–protein interactions
			4.3.4.2 Regulation by miRNAs
			4.3.4.3 Regulation by post-translational modification
			4.3.4.4 Negative regulation
	4.4 Immune defence protein families
		4.4.1 The major families
		4.4.2 Effectors: antimicrobial peptides
	4.5 The generation of diversity in recognition
		4.5.1 Polymorphism in the germline
		4.5.2 Somatic generation of diversity 4.5.2.1 Alternative splicing
			4.5.2.1 Alternative splicing
			4.5.2.2 Somatic DNA modification
			4.5.2.3 Somatic (hyper-)mutation, gene conversion
		4.5.3 Variability and Band T-cells
			4.5.3.1 B-cells
			4.5.3.2 T-cells
	4.6 The diversity of immune defences
		4.6.1 Defence in plants
		4.6.2 Defence in invertebrates
			4.6.2.1 Insects
			4.6.2.2 Echinoderms
		4.6.3 The jawed (higher) vertebrates
	4.7 Memory in immune systems
		4.7.1 Memory in the adaptive system
		4.7.2 Memory in innate systems
	4.8 Microbiota
		4.8.1 Assembly, structure, and location of the microbiota
		4.8.2 Mechanisms of defence by the microbiota
	4.9 Evolution of the immune system
		4.9.1 Recognition of non-self
		4.9.2 The evolution of signal transduction and effectors
		4.9.3 The evolution of adaptive immunity
	Box 4.1 Disease space: defences
	Box 4.2 Adaptive immunity in prokaryotes: the CRISPR–Cas system
	Box 4.3 Antiviral defence of invertebrates
	Box 4.4 Priming and memory
Chapter 5: Ecological immunology
	5.1 Variation in parasitism
		5.1.1 Variation caused by external factors
		5.1.2 Variation in immune responses
	5.2 Ecological immunology: The costs of defence
		5.2.1 General principles
		5.2.2 Defence costs related to life history and behaviour
		5.2.3 Cost of evolving an immune defence
			5.2.3.1 Genetic costs associated with the evolution of immune defences
			5.2.3.2 Physiological costs associated with the evolution (maintenance) of immune defences
		5.2.4 Cost of using immune defences 5.2.4.1 Genetic costs associated with the deployment of immune defences
			5.2.4.1 Genetic costs associated with the deployment of immune defences
			5.2.4.2 Physiological costs associated with the deployment of immune defences
			5.2.4.3 Costs due to immunopathology
	5.3 The nature of defence costs
		5.3.1 What is the limiting resource?
			5.3.1.1 Energy
			5.3.1.2 Food and nutrients
		5.3.2 Regulation of allocation
	5.4 Measurement and fitness effects of immune defence
	5.5 Tolerance as defence element
		5.5.1 Defining and measuring tolerance
		5.5.2 Mechanisms of tolerance
		5.5.3 Selection and evolution of tolerance
	5.6 Strategies of immune defence
		5.6.1 General considerations
		5.6.2 Defence and host life span
		5.6.3 Specific vs general defence
		5.6.4 Constitutive vs induced defence
		5.6.5 Robust defence
	Box 5.1 Disease space and costs of defence
	Box 5.2 Measures of host defence
	Box 5.3 Structurally robust immune defencesexogneousdsRNAviraldsRNAtransposon
Chapter 6: Parasites, immunity, and sexual selection
	6.1 Differences between the sexes
		6.1.1 Differences in susceptibility to parasites
		6.1.2 Differences in immune function
		6.1.3 The role of sex hormones
	6.2 Parasitism and sexual selection
		6.2.1 Female mate choice
		6.2.2 Males indicate the quality of resisting parasites
			6.2.2.1 The Hamilton–Zuk hypothesis
			6.2.2.2 The immunocompetence handicap hypothesis
		6.2.3 Male genotypes and benefits for resistance
			6.2.3.1 Heterozygosity advantage
			6.2.3.2 Dissimilar genes
	Box 6.1 Sexual selection
Chapter 7: Specificity
	7.1 Parasite specificity and host range
		7.1.1 Measuring parasite specificity and host range
			7.1.1.1 Observation of infections
			7.1.1.2 Screening with genetic tools
			7.1.1.3 Experimental infections
		7.1.2 Characteristics of a host
		7.1.3 Evolution of parasite specificity and host range
	7.2 Factors affecting the host range
		7.2.1 Biogeographical factors
			7.2.1.1 Parasite geographic distribution
			7.2.1.2 Spatial heterogeneity
		7.2.2 Phylogeny and available time
			7.2.2.1 Constraints by host phylogeny
			7.2.2.2 Phylogenetic age of groups
			7.2.2.3 Constraints by parasite group
		7.2.3 Epidemiological processes
			7.2.3.1 Transmission opportunities
			7.2.3.2 Differences in host predictability
			7.2.3.3 Transmission mode
		7.2.4 Constraints set by life history
			7.2.4.1 Host body size and longevity
			7.2.4.2 Complexity of the life cycle
			7.2.4.3 Selection regimes within the parasite’s life cycle
		7.2.5 Virulence and defence
			7.2.5.1 Virulence of the parasite
			7.2.5.2 Immune defences and defensive symbionts
	7.3 Specific host defences
		7.3.1 Specificity beyond the immune system
			7.3.1.1 Behavioural defences
			7.3.1.2 Other nonimmunological defences
		7.3.2 Specificity of immune systems
	7.4 Memory, transgenerational protection
		7.4.1 Evolution of memory and immune priming
		7.4.2 Transgenerational immune priming (TGIP)
	7.5 Adaptive diversity and crossreactivity
	Box 7.1 Specificity in defence space
	Box 7.2 Host specificity indices
Chapter 8: Parasite immune evasion and manipulation of host phenotype
	8.1 Parasites manipulate their hosts
	8.2 The diversity of immune evasion mechanisms
		8.2.1 Passive evasion
		8.2.2 Active interference
		8.2.3 Functional targets of immune evasion
			8.2.3.1 Escape recognition
			8.2.3.2 Evasion of early responses
			8.2.3.3 Manipulate the signalling network
			8.2.3.4 Avoid bein g killed by effectors
			8.2.3.5 Manipulation of auxiliary mechanisms
			8.2.3.6 Microbiota as a target
	8.3 Manipulation of the host phenotype
		8.3.1 Extending infection life span (parasite survival)
			8.3.1.1 Fecundity reduction
			8.3.1.2 Gigantism
			8.3.1.3 Changes of the social context
		8.3.2 Manipulation of the host phenotype to increase transmission
			8.3.2.1 Transmission site
			8.3.2.2 Transmission to a next host
			8.3.2.3 Transmission by vectors
		8.3.3 Change of host morphology
			8.3.3.1 Colouration and odour
			8.3.3.2 Morphology and feminization
		8.3.4 Affecting transmission routes
		8.3.5 Affecting social behaviour
		8.3.6 Affecting the neuronal system
	8.4 Strategies of manipulation
		8.4.1 Common tactics
		8.4.2 What manipulation effort?
		8.4.3 Multiple infections
	Box 8.1 Immune evasion by Bacillus anthracis
	Box 8.2 Is manipulation adaptive, and for whom?
	Box 8.3 Manipulation and evasion in disease space
	Box 8.4 Manipulation of vertical transmission
Chapter 9: Transmission, infection, and pathogenesis
	9.1 Transmission
		9.1.1 Exit points from the host
		9.1.2 Entry points
		9.1.3 Horizontal vs vertical transmission
		9.1.4 The evolution of transmission
	9.2 Variation in infection outcome
	9.3 Infection
		9.3.1 Infective dose
		9.3.2 Generalized models of infection
			9.3.2.1 Independent action hypothesis (IAH)
			9.3.2.2 Individual effective dose (threshold models)
			9.3.2.3 Host heterogeneity models (HHS)
			9.3.2.4 Withininoculum interaction models
			9.3.2.5 Sequential models
		9.3.3 Processbased models
			9.3.3.1 The lottery model
			9.3.3.2 The manipulation hypothesis
			9.3.3.3 Early infection dynamics
	9.4 Pathogenesis: The mechanisms of virulence
		9.4.1 Impairing host capacities
		9.4.2 Destruction of tissue
		9.4.3 Virulence factors
			9.4.3.1 Adhesion factors (adhesins)
			9.4.3.2 Colonization factors
			9.4.3.3 Invasion factors (Invasins)
			9.4.3.4 Immune evasion factors
		9.4.4 Toxins
		9.4.5 Proteases
		9.4.6 Pathogenesis via the microbiota
		9.4.7 Pathogenesis by coinfections
	9.5 Immunopathology
		9.5.1 Immunopathology associated with cytokines
		9.5.2 Immunopathology caused by immune evasion mechanisms
	Box 9.1 Infection in disease space
	Box 9.2 Definitions of dose
	Box 9.3 Quantitative Microbial Risk Assessment (QMRA)
	Box 9.4 Formalizing infectious dose in general models
Chapter 10: Host–parasite genetics
	10.1 Genetics and genomics of host–parasite interactions
		10.1.1 The importance of genetics
		10.1.2 Genomics and host–parasite genetics
			10.1.2.1 Diagnostics
			10.1.2.2 Reading the genome
			10.1.2.3 Association with a phenotype
			10.1.2.4 Changing the genotype
	10.2 Genetics of host defence
	10.3 Parasite genetics
		10.3.1 Viral genetics
		10.3.2 Genetics of pathogenic bacteria
			10.3.2.1 Pathogenicity islands
			10.3.2.2 PICIs and genetransfer agents
	10.4 Genetic variation
		10.4.1 Individual genetic polymorphism
		10.4.2 Genetic variation in populations
		10.4.3 Gene expression
			10.4.3.1 Expression profile and transcriptome
			10.4.3.2 Copy number variation
			10.4.3.3 Phase variation and antigenic variation
		10.4.4 Heritability of host and pathogen traits
	10.5 Host–parasite genetic interactions
		10.5.1 Epistasis
		10.5.2 Models of genotypic interactions
			10.5.2.1 Geneforgene interaction (GFG)
			10.5.2.2 Matching specificities (matching alleles)
		10.5.3 Role of the microbiota
	10.6 Signatures of selection
		10.6.1 Selection by parasites in animal populations
		10.6.2 Selection by parasites in human populations
		10.6.3 Signatures of selection in parasites
	10.7 Parasite population genetic structure
		10.7.1 Determinants of structure
		10.7.2 Genetic exchange in parasites
	Box 10.1 Host–parasite interaction in disease space
	Box 10.2 Sequencing technologies
	Box 10.3 Quantitative genetic effects
	Box 10.4 Cross- infection experiments
	Box 10.5 Genetic interaction models
	Box 10.6 Signatures of selection
Chapter 11: Betweenhost dynamics (Epidemiology)
	11.1 Epidemiology of infectious diseases
	11.2 Modelling infectious diseases
		11.2.1 The SIR model
		11.2.2 Thresholds and vaccination
		11.2.3 Stochastic epidemiology
		11.2.4 Network analysis of epidemics
		11.2.5 Spatial heterogeneity
		11.2.6 The epidemic as an invasion process
	11.3 Endemic diseases and periodic outbreaks
	11.4 Epidemiology of vectored diseases
	11.5 Epidemiology of macroparasites
		11.5.1 Distribution of macroparasites among hosts
		11.5.2 Epidemiological dynamics of macroparasites
	11.6 Population dynamics of host–parasitoid systems
	11.7 Molecular epidemiology
	11.8 Immunoepidemiology
		11.8.1 Effects of immunity on disease dynamics
		11.8.2 Inferences from disease dynamics
		11.8.3 Immunological markers in epidemiology
	Box 11.1 Bernoulli’s theory of smallpox
	Box 11.2 The basic epidemiological model (SIR)
	Box 11.3 Calculating R0
	Box 11.4 Epidemics and disease space
	Box 11.5 Epidemiology of macroparasites
	Box 11.6 Phylodynamics
	Box 11.7 Coronavirus outbreaks
Chapter 12: Withinhost dynamics and evolution
	12.1 Primary phase of infection
	12.2 Withinhost dynamics and evolution of parasites
		12.2.1 Target celllimited models
		12.2.2 Dynamics in disease space
		12.2.3 Strategies of withinhost growth
		12.2.4 Modelling immune responses
			12.2.4.1 Computational immunology
			12.2.4.2 Systems immunology
	12.3 Withinhost evolution
		12.3.1 Evolutionary processes in infecting populations
			12.3.1.1 Processes of diversification
			12.3.1.2 Evolution of bacteria
			12.3.1.3 Evolution of viruses
		12.3.2 Antigenic variation
		12.3.3 Antibiotic resistance
		12.3.4 Evolutionary perspectives of antibiotic resistance
	12.4 Multiple infections
		12.4.1 Competition within the host
		12.4.2 Cooperation within hosts
	12.5 Microbiota within the host
	12.6 Withinvs betweenhost episodes
	Box 12.1 Signalling theory and infection
	Box 12.2 Target cell- limited models
	Box 12.3 Predictions for infections from disease space
	Box 12.4 Mechanisms of antibiotic resistance in bacteria
	Box 12.5 Quorum sensing in bacteria
Chapter 13: Virulence evolution
	13.1 The meaning of virulence
	13.2 Virulence as a nonor maladaptive phenomenon
		13.2.1 Virulence as a side effect
		13.2.2 Shortsighted evolution
		13.2.3 Virulence as a negligible effect for the parasite
		13.2.4 Avirulence theory
	13.3 Virulence as an evolved trait
	13.4 The standard evolutionary theory of virulence
		13.4.1 The basic principle
		13.4.2 The recovery–virulence tradeoff
		13.4.3 The transmission–virulence tradeoff
	13.5 The ecology of virulence
		13.5.1 Transmission mode
		13.5.2 Host population dynamics
	13.6 Host population structure
		13.6.1 Spatial structure
		13.6.2 Variation in host types
		13.6.3 Social structure
	13.7 Nonequilibrium virulence: Invasion and epidemics
	13.8 Withinhost evolution and virulence
		13.8.1 Withinhost replication and clearance of infection
		13.8.2 Withinhost evolution: Serial passage
		13.8.3 Withinhost evolution and virulence in a population
	13.9 Multiple infections and parasite interactions
		13.9.1 Virulence and competition among parasites
			13.9.1.1 Resource competition
			13.9.1.2 Apparent competition
			13.9.1.3 Interference competition
		13.9.2 Cooperation among coinfecting parasites
			13.9.2.1 Kinship among parasites
			13.9.2.2 Cooperative action
	13.10 Additional processes
		13.10.1 Medical intervention and virulence
		13.10.2 Castration and obligate killers
	13.11 Virulence and life history of infection
		13.11.1 The timing of benefits and costs
		13.11.2 Sensitivity of parasite fitness
	Box 13.1 Virulence in disease space
	Box 13.2 Extensions to the standard theory
	Box 13.3 Virulence evolution with immunopathology
	Box 13.4 Serial passage
	Box 13.5 Kin selection and virulence
Chapter 14: Host–parasite coevolution
	14.1 Macroevolution
		14.1.1 The adapted microbiota
		14.1.2 Cospeciation
		14.1.3 Host switching
	14.2 Microevolution
		14.2.1 Coevolutionary scenarios
			14.2.1.1 Selective sweeps
			14.2.1.2 Arms races
			14.2.1.3 Antagonistic, timelagged fluctuations (Red Queen)
			14.2.1.4 ‘Evolutionproof’ strategies
		14.2.2 Parasites and maintenance of host diversity
			14.2.2.1 Host–parasite asymmetry
			14.2.2.2 Red Queen and host diversity
			14.2.2.3 Transspecies polymorphism
	14.3 Parasites, recombination, and sex
		14.3.1 Theoretical issues
		14.3.2 Empirical studies
	14.4 Local adaptation
	Box 14.1 Co- evolution and disease space
	Box 14.2 History of the Red Queen hypothesis
	Box 14.3 The masterpiece of nature: Sex and recombination
Chapter 15: Ecology
	15.1 Host ecology and life history
		15.1.1 Host body size
		15.1.2 Host reproductive patterns
		15.1.3 Host group living and sociality
		15.1.4 Regulation of host populations by parasites
		15.1.5 Host population decline and extinction
	15.2 Host ecological communities
		15.2.1 Parasite effects on host competition
		15.2.2 Communities of hosts
		15.2.3 Food webs
		15.2.4 Dilution effect
		15.2.5 The value of parasites for hosts
	15.3 Parasite ecology
		15.3.1 Geographical patterns
			15.3.1.1 Relation to area size
			15.3.1.2 Latitudinal gradients
		15.3.2 Parasite community richness and diversity
	15.4 Migration and invasion
		15.4.1 Host migration
		15.4.2 Host invasion
			15.4.2.1 Enemy release (parasite loss)
			15.4.2.2 Parasite spillover
			15.4.2.3 Parasite spillback
			15.4.2.4 Facilitation
	15.5 Zoonoses and disease emergence
		15.5.1 Reservoirs
		15.5.2 Emergence
		15.5.3 Zoonotic human diseases
	15.6 Climate change and parasitism
	Box 15.1 Basic population ecology
	Box 15.2 The African rinderpest epidemic
	Box 15.3 Spill- over and disease space
Bibliography
Subject index
Taxonomic index