Table of Contents (Drosophila book)

[Jeffrey R. Powell]

Dear Colleagues:
Several of you have responded to the announcement of my book by
requesting a table of contents.  Below is an "expanded table of
contents" which should give you a good idea of what the book is about.

Expanded Table of Contents

Progress and Prospects in Evolutionary Biology: The Drosophila Model
									
Chapter 1. An Overview

	The Problem
	History
		Drosophila in the laboratory
		Drosophila in evolutionary studies
	The Origin of the Flies
	Some Basic Biology
		Life history
		Culturing
	What's in a Name?
	Sources of Information

Chapter 2. Population Genetics--Genes
	The Epistemological Paradox
	Morphological Mutants
		In natural populations
		Implications
	Fitness Variation
		Homozygous chromosomes
		Synthetic lethals
		The load problem
	Selection Experiments
		Laboratory
		Polygenic variation in nature
		The molecular basis of polygenic variation
	Allozymes
		Level of variation
		Geographic homogeneity
		Metabolic function
		Null alleles
	DNA Variation
	Mutation 
		Rates
		Causes of mutations
	Epilog

Chapter 3. Population Genetics--Inversions
	General Features
		Crossover suppression
		Ubiquity of inversion polymorphism
		Origin of Inversions
		Uniqueness of Inversions
	Geographic Distributions
		Geographic heterogeneity
		Geographic homogeneity
		Marginal/Central Patterns
	Temporal changes
		Short-term temporal changes
		Long-term temporal changes
	Other inversions
		Pericentric Inversions
		Sex-Ratio Inversions
		Multiple Inversions
	Allozymes and Inversions
	DNA Studies
	Theory of the Origin of Inversions
	Further Information

Chapter 4. Population Genetics--Laboratory Studies
	Genes
		Morphological mutants
		Allozymes
	Inversions
		Evidence for selection
		The genetic basis of fitness variation among inversions
		Heterosis or frequency dependence?
		Other species
	Fitness components
	The rare male effect
	Sex ratio and segregation distortion
		D. pseudoobscura SR
		SR endosymbionts
		Autosomal meiotic drive
	Heterogeneous environments and habitat choice
	Migration
	Genetic drift
	Epilog

Chapter 5. Ecology
	Breeding sites
		Tropical species
		Temperate woodlands
		Repleta and cacti
		Flowers
		Fungus feeders
		Hawaiian species
		Bizarre Drosophila
	Yeasts and other microbes
	Population structure
		Sex-ratio
		Density
		Dispersal
		Genetical structure
		Age structure
		Overall patterns of population structure
	Interspecific competition
		Natural populations
		Laboratory studies
		Coexistence in the tropics
	Life histories, phenotypic plasticity, acclimation, and aging
	Parasites and symbionts
		Viruses
		Bacteria
		Molds and fungi
		Protozoa
		Nematodes
		Mites
		Hymenoptera
	Epilog

Chapter 6. Ecological Genetics
	Habitat choice
		The obscura group at Mather
		Other studies
		General comments
	Ephemeral and newly founded populations
	Cactus-breeding Drosophila
		Sonoran desert
		Hawaii
		Australia
		South America and elsewhere
	Flower-breeders in South America
	Mycophagous Drosophila
	Male mating success
	Population growth and size

Chapter 7. Speciation
	The taxonomy of species and speciation
	Three caveats
	The first effects
		Premating
		Postmating
	Reinforcement
	Genetic divergence
		Allozymes
		DNA
		General proteins
	Genetics of premating isolation
		Behavior
		Morphology
		Pheromones
		Asymmetry in premating isolation
	Genetics of postmating isolation
		Male sterility
		The Y chromosome
		Female sterility
		Inviability genetics
		Meiotic drive
		Haldane's rule revisited
	Symbionts
		D. paulistorum
		Wolbachia
	Laboratory studies
		Isolation as a byproduct of adaptation
		Founder-flush in the laboratory
	Population processes
	Sexual selection and isolation

Chapter 8. Phylogenetics
	Background
	Basics of phylogenetics
	The larger context
		Drosophilidae within Diptera
		Steganinae
		Drosophilinae
	Genus Drosophila
		DNA-DNA hybridization
		DNA sequences
		Hawaiian drosophilids
		Subgenus Drosophila
		Absolute times
	Individual groups
		The melanogaster group
		The obscura group
		The willistoni group
		The virilis group
		The repleta group
		The Hawaiian Drosophila
	Gene trees-species trees
		Inversion, gene, and species trees
		The simulans/mauritiana/sechellia triad
	Conclusions

Chapter 9. Genome Evolution
	Drosophila genome structure
		Sizes and patterns
		Function
	Genome size evolution
	Karyotype evolution
		Chromosome changes
		The ancestral state
	Linkage
		Conservation
		Non-conservation
		B chromosomes
	Global view of scDNA evolution
		The nature of DNA-DNA hybridization experiments
		Extreme heterogeneity in divergence
		Divergence of functional subclasses
	Heterochromatin
		Functions
		Extreme variation
	The Y chromosome
		Variation
		The D. miranda neo-Y
	Recombination
		Variation
		Sex chromosomes
	Transposable elements
		Some history
		Types of Drosophila TEs
		Population genetics
		Dynamics of spread
		Codon usage in TEs
		Horizontal transfer
		Other species
		Effect of TEs on their hosts
	Genome projects

Chapter 10. Molecular Evolution
	Measures of variation
	Levels of nuclear DNA variation
		D. melanogaster
		Other species
	Pattern of Polymorphism
		Functional differences
		X-linked versus autosomal
		Transitions-transversions
		Silent versus replacement polymorphism
	Insertion/deletions (indels)
	An historical aside
	Recombination and hitchhiking
		Hitchhiking and selective sweeps
		Linkage and balancing selection (HKA)
	Rates of DNA evolution
		Absolute estimates
		Synonymous substitution rates
	Codon usage bias and effects on rates
		Causes of bias
		Codon usage in other species
		Effect on rates
	Between versus within
	Mitochondrial DNA
		Intraspecific mtDNA variation
		Rate of mtDNA evolution
		Pattern of change
		mtDNA in population cages: cytoplasmic-nuclear interactions
	Out of Africa: A reevaluation of D. melanogaster
	DNA variation and inversions: Ancestry and gene conversions
		D. pseudoobscura subgroup
		D. subobscura
		D. melanogaster
	Gene duplications
		Pseudogenes
		Functional duplications
	Gene structure
	Adh: the center of attention
		The big gene tree
		Disequilibrium
		Adhr or Adh-dup
		The origin of Adh 
		Jingwei: A reincarnation?
		Protein polymorphism
		Biochemistry
	Other genes
		Amylases
		Histones
		Chorions
		Opsins
		Transformer--a sex-determining gene
		Genes within genes: Gart, dunce, and sina
		Period
		
Chapter 11. Development
	Gene regulation
		Adh
		Amylase
		Glucose dehydrogenase
		Esterases
		Hawaiian Drosophila
		Egg proteins
	Morphology and embryogenesis
		Drosophila early development
		Variation within Drosophila
		Beyond Drosophila
	Development and phylogeny
	Canalization and genetic assimilation

Chapter 12 Retrospective and prospective
	Integration of information
	Genetic loads
	Whither the selectionist/neutralist debate?
	Scales of analysis
	Development
	Speciation
	Conservation
	The model