Cover -- Half-title -- Title -- Copyright -- Contents -- Contributors -- Publications of R. C. Lewontin -- Preface -- Introduction -- PART I HISTORICAL FOUNDATIONS AND PERSPECTIVES -- 1 Building a science of population biology -- 1.1 Natural selection and demography -- 1.2 The determination of components of fitness -- 1.3 The evolution of population ecological processes -- 1.4 What is to be done? -- REFERENCES -- 2 Toward a population biology, still -- 2.1 The genotype and the whole organism -- 2.1.1 The norm of reaction revisited -- 2.1.2 Schmalhausen's Law -- 2.1.3 Shades of Lamarck -- 2.1.4 The phenotypes of populations -- 2.1.4.1 Population/environment feedback -- 2.1.5 The role of history -- 2.2 A biological definition of environment -- 2.2.1 Patchiness -- 2.2.2 Variance of life factors -- 2.2.3 Temperature -- 2.2.4 Opposing demands -- 2.2.5 Predictability -- 2.3 Selection in variable environments -- 2.3.1 Selection of complex physiological systems -- REFERENCES -- PART II GENOTYPES TO PHENOTYPES: NEW GENETIC AND BIOINFORMATIC ADVANCES -- 3 Genetic dissection of quantitative traits -- 3.1 Introduction -- 3.2 Identifying genes affecting quantitative traits -- 3.2.1 Mutagenesis -- 3.2.2 QTL mapping -- 3.2.2.1 Genome scans -- 3.2.2.2 High-resolution mapping -- 3.2.3 From QTL to gene -- 3.2.4 From gene to QTN -- 3.3 Properties of genes affecting quantitative traits -- 3.3.1 Additive effects -- 3.3.2 Interaction effects -- 3.3.3 Pleiotropy -- 3.4 Future prospects -- 3.5 Acknowledgments -- REFERENCES -- 4 Gene expression profiling in evolutionary genetics -- 4.1 Introduction -- 4.2 Déj`a vu all over again? -- 4.3 DNA microarrays and their applications -- 4.4 Statistical analysis -- 4.5 DNA microarrays in evolutionary genetics: some specific examples -- 4.5.1 Molecular evolution of genes expressed early and late in nematode development.

4.5.2 Expression profiling of natural isolates of vineyard yeast -- 4.5.3 Variation in gene expression in Drosophila -- 4.5.4 Interspecific comparisons in Drosophila -- 4.6 Concluding remarks -- 4.7 Acknowledgments -- REFERENCES -- 5 Population biology and bioinformatics -- 5.1 Introduction -- 5.2 Background -- 5.3 Population-level bioinformatics -- 5.4 Biodiversity -- 5.5 Comparative biology and population bioinformatics -- 5.6 Environmental microbial bioinformatics -- 5.7 The shift toward environmental genomics and bioinformatics -- REFERENCES -- 6 Beyond beanbag genetics: Wright's adaptive landscape, gene interaction networks, and the evolution of new genetic systems -- 6.1 Introduction -- 6.2 Wright's shifting balance theory -- 6.2.1 Shifting balance theory: critical assumptions -- 6.2.2 Shifting balance theory: critics and defenders -- 6.2.3 Shifting balance theory: an alternative to mass selection? -- 6.2.4 Shifting balance theory: linking microevolution to macroevolution -- 6.3 The problem of epistasis: two views of developmental complexity -- 6.4 Epistasis in fitness, phenotypes and molecular traits -- 6.4.1 The nature of newly arising mutations -- 6.4.2 Evidence from linkage disequilibrium and complex polymorphisms -- 6.4.3 Evidence from species hybrids -- 6.4.4 Epistasis and sexual traits -- 6.5 Is shifting balance theory more relevant to speciation and macroevolution? -- 6.6 Alternative views of epistasis and stability -- 6.6.1 Functional redundancy -- 6.6.2 Interacting genetic networks -- 6.6.3 Network stability -- 6.7 Evolution of new genetic systems -- 6.7.1 Gene transfer -- 6.7.2 Gene loss -- 6.7.3 Gene addition -- 6.8 Conclusions -- REFERENCES -- PART III PHENOTYPES TO FITNESS: GENETICS AND ECOLOGY OF POPULATIONS -- 7 Density-dependent selection -- 7.1 Introduction -- 7.2 The origin -- 7.3 Nonoverlapping generations.

7.4 Exploitative competition -- 7.5 Density-independent selection -- 7.6 Structured habitats -- 7.7 Population dynamics and selection -- 7.8 Acknowledgments -- REFERENCES -- 8 Nonsynonymous polymorphisms and frequency-dependent selection -- 8.1 Introduction -- 8.2 How many nonsynonymous polymorphisms are there? -- 8.3 How many of these polymorphisms are maintained by natural selection? -- 8.3.1 Genetic load -- 8.3.2 Polymorphism and recombination -- 8.3.3 Polymorphism and constraint -- 8.3.4 The problem of testing for selection -- 8.4 Is the selection balancing? -- 8.4.1 Detecting selective agents -- 8.4.2 The ecology of selective agents -- 8.4.2.1 Predators -- 8.4.2.2 Parasites -- 8.4.2.3 Competitors -- 8.4.2.4 Self-incompatibility -- 8.5 Heterozygous advantage -- 8.6 Balance between selection and migration -- 8.7 Conclusions -- 8.8 Envoi -- 8.9 Acknowledgments -- REFERENCES -- 9 Why k = 4Nus is silly -- 9.1 Introduction -- 9.2 TIM and the house-of-cards model -- 9.3 Related models -- 9.4 Faster fluctuations -- 9.5 Conclusions -- 9.6 Acknowledgments -- REFERENCES -- 10 Inferences about the structure and history of populations: coalescents and intraspecific phylogeography -- 10.1 Introduction -- 10.1.1 Population genetics history -- 10.1.2 Phylogenetics and intraspecific phylogeography -- 10.2 Gene genealogies and the coalescent -- 10.3 The axes of genealogical variation: tree size and branching pattern -- 10.4 The effects of population structure and population history on genealogies -- 10.4.1 Population growth -- 10.4.2 Population decline -- 10.4.3 Equilibrium migration -- 10.4.4 Isolation without gene flow -- 10.5 Domains of application: coalescents and phylogeography -- 10.5.1 Measures of variation in tree size -- 10.5.2 Measures of correlation in branching pattern -- 10.5.3 Simulations of population structure and population history.

10.6 Conclusions -- 10.7 Acknowledgments -- REFERENCES -- 11 The population genetics of life-history evolution -- 11.1 Introduction -- 11.2 Constructing a model of selection -- 11.2.1 Demographic parameters -- 11.2.2 Genetic parameters -- 11.3 Determining the effects of selection -- 11.3.1 The selection equations -- 11.3.2 Equilibrium conditions -- 11.3.3 Stability analyses -- 11.3.4 Weak selection -- 11.3.5 Reconciling the fitness measures -- 11.3.6 Sex differences and nonrandom mating -- 11.3.7 Multiple loci and quantitative traits -- 11.3.8 Variable environments -- 11.4 Conclusions -- 11.4.1 Measuring fitness -- 11.4.2 Dependence of fitness on demography -- 11.4.3 Life-history evolution -- 11.5 Acknowledgments -- REFERENCES -- 12 Gene-environment complexities: what is interesting to measure and to model? -- 12.1 Preamble - 1974 -- 12.2 "Environment" in the age of DNA -- 12.3 Five approaches to gene-environment complexities -- 12.3.1 Gestational programming -- 12.3.2 Life events and difficulties -- 12.3.3 Behavioral genetics -- 12.3.4 Scientific criticism of biological determinism -- 12.3.5 Models of reciprocal causation of any individual's developing traits and environment -- 12.4 Some ways that the approaches challenge each other -- 12.4.1 Gestational programming -- 12.4.2 Life events and difficulties research -- 12.4.3 Reciprocal causation models -- 12.5 From commentary to engagement -- 12.6 Acknowledgments -- REFERENCES -- 13 Genus-specific diversification of mating types -- 13.1 Introduction -- 13.2 Determination of specificity -- 13.3 Pattern of divergence -- 13.4 Process of divergence -- 13.4.1 Population and sample genealogies -- 13.4.2 Wright's diffusion model of GSI -- 13.4.3 Bifurcation rate and homozygosity -- 13.4.3.1 Rate of origin -- 13.4.3.2 Rate of extinction -- 13.4.4 Scaling factor -- 13.5 Divergence among haplotypes.

13.5.1 Spectrum of descendant number -- 13.5.2 Process of bifurcation -- 13.5.2.1 Relative rate of bifurcation -- 13.5.2.2 Relative population sizes and allele numbers -- 13.6 Conclusions -- 13.7 Acknowledgments -- REFERENCES -- PART IV GENES, ORGANISMS, AND ENVIRONMENT: EVOLUTIONARY CASE STUDIES -- 14 Adaptation, constraint, and neutrality: mechanistic case studies with butterflies and their general implications -- 14.1 Introduction -- 14.2 The adaptation concept and its role in the study of evolution -- 14.3 Evolutionary generality via mechanistic specificity: bioenergetically based studies -- 14.3.1 Thermoregulatory adaptations and thermal constraints on butterfly flight -- 14.3.2 Adaptation, constraint, and neutrality in variants of a specific gene: molecular mechanisms to fitness effects -- 14.3.3 Molecular aspects of the lowland Colias PGI polymorphism -- 14.3.4 Adaptive complexities of PGI variation among taxa -- 14.3.5 Epistasis in metabolism - a feasible new level of analyzable complexity -- 14.4 Conceptual questions in evolution: some empirical answers -- 14.4.1 The feasibility of mechanistic evolutionary study -- 14.4.2 "Genic selectionism" vs. the genotypic level of selection -- 14.4.3 The continuity of adaptation from passive to constructionist emphases -- 14.4.4 The coincidence and coimportance of adaptation and constraint -- 14.4.5 Barring some holds: the dysfunction of "neutralism" and "selectionism" -- 14.4.6 The evolutionary importance of strongly selected variants at major genes -- 14.5 Mechanistic evolutionary study in social context - initial suggestions and speculations -- 14.6 Acknowledgments -- REFERENCES -- 15 Evolution in hybrid zones -- 15.1 Introduction -- 15.2 The 1920s and 1930s -- 15.3 The 1940s and 1950s -- 15.4 The 1960s and 1970s -- 15.5 The 1980s to present -- 15.6 Concluding remarks -- 15.7 Acknowledgments.

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