Contents -- 1. An Overview -- The Problem -- History -- The Origin of the Flies -- Some Basic Biology -- What's in a Name? -- Sources of Information -- 2. Population Genetics-Genes -- The Epistemological Paradox -- Morphological Mutants -- Fitness Variation -- Selection Experiments -- Allozymes -- DNA Variation -- Mutation -- Epilog -- 3. Population Genetics-Inversions -- General Features -- Geographic Distributions -- Temporal Changes -- Other Inversions -- Allozymes and Inversions -- DNA Studies -- Theory of the Origin of Inversions -- Further Information -- 4. Population Genetics-Laboratory Studies -- Genes -- Inversions -- Fitness Components -- The Rare Male Effect -- Sex Ratio and Segregation Distortion -- Heterogeneous Environments and Habitat Choice -- Migration -- Genetic Drift -- Epilog -- 5. Ecology -- Breeding Sites -- Yeasts and Other Microbes -- Population Structure -- Interspecific Competition -- Life Histories, Phenotypic Plasticity, Acclimation, and Aging -- Parasites and Symbionts -- Epilog -- 6. Ecological Genetics -- Habitat Choice -- Ephemeral and Newly Founded Populations -- Cactus-Breeding Drosophila -- Flower-Breeders in South America -- Mycophagous Drosophila -- Male Mating Success -- Population Growth and Size -- 7. Speciation -- The Taxonomy of Species and Speciation -- Three Caveats -- The First Effects -- Reinforcement -- Genetic Divergence -- Genetics of Premating Isolation -- Genetics of Postmating Isolation -- Symbionts -- Laboratory Studies -- Population Processes -- Sexual Selection and Isolation -- 8. Phylogenetics -- Background -- Basics of Phylogenetics -- The Larger Context -- Genus Drosophila -- Individual Groups -- Gene Trees-Species Trees -- Conclusions -- 9. Genome Evolution -- Drosophila Genome Structure -- Genome Size Evolution -- Karyotype Evolution -- Linkage -- Global View of scDNA Evolution.

Heterochromatin -- The Y Chromosome -- Recombination -- Transposable Elements -- Genome Projects -- 10. Molecular Evolution -- Measures of Variation -- Levels of Nuclear DNA Variation -- Pattern of Polymorphism -- Insertion/Deletions (Indels) -- An Historical Aside -- Recombination and Hitchhiking -- Rates of DNA Evolution -- Codon Usage Bias and Effects on Rates -- Between Versus Within -- Mitochondrial DNA -- Out of Africa: A Reevaluation of D. melanogaster -- DNA Variation and Inversions: Ancestry and Gene Conversions -- Gene Duplications -- Gene Structure -- Adh: The Center of Attention -- Other Genes -- 11. Development -- Gene Regulation -- Morphology and Embryogenesis -- Development and Phylogeny -- Canalization and Genetic Assimilation -- 12. Retrospective and Prospective -- Integration of Information -- Genetic Loads -- Whither the Selectionist/Neutralist Debate? -- Scales of Analysis -- Development -- Speciation -- Conservation -- The Model -- References -- Index -- Subject Index -- A -- B -- C -- D -- E -- F -- G -- H -- I -- K -- L -- M -- N -- O -- P -- R -- S -- T -- V -- Y -- Taxonomic Index -- A -- B -- C -- D -- E -- F -- G -- H -- I -- L -- M -- N -- O -- P -- Q -- R -- S -- T -- V -- W -- Y -- Z.