The Princeton guide to evolution
(eBooks)

Section I. Introduction. What Is Evolution? -- 1. What is evolution? -- 2. Evolution: Pattern versus process -- 3. Evolution: More than changes in the gene pool -- 4. In the light of evolution -- 5. Critiques and the evidence for evolution -- 6. The pace of evolution -- 7. Evolution, humans, and society -- The History of Evolutionary Thought -- 1. Species and the origins of diversity in the ancient world -- 2. The eighteenth century and ideas of the transmutation of species -- 3. The rise of natural history -- 4. The development of geology in the late eighteenth and nineteenth centuries -- 5. Ideas of transmutation of species before Darwin -- 6. Charles Darwin and On the Origin of Species (1809-1859) -- 7. Post-Darwinian controversies and the eclipse of Darwinism, 1890-1920 -- 8. Heredity and evolution: Mendelism, Darwinism, and the evolutionary synthesis -- 9. Evolutionary theory in the era of molecular biology -- The Evidence for Evolution -- 1. The fossil record -- 2. Comparative biology -- 3. Biogeography -- 4. Evolution in action -- 5. Evolution as fact and theory -- From DNA to Phenotypes -- 1. What is a gene? -- 2. Descriptions of genetic variation -- 3. A multiplicity of forms of inheritance --

Section II. Phylogenetics and the History of Life. Preface -- Interpretation of Phylogenetic Trees -- 1. Introduction to phylogenetic trees -- 2. Misreading trees with species-poor lineages -- 3. Reading trees correctly: Ancestral state reconstruction -- 4. Understanding the process of evolution: We are all cousins -- Phylogenetic Inference -- 1. Logical and statistical inference -- 2. The parsimony approach -- 3. Likelihood-based approaches -- 4. Distance-based approaches -- 5. Computational aspects of tree estimation -- 6. Statistical support for clades -- 7. Bayesian inference -- Molecular Clock Dating -- 1. The molecular evolutionary clock -- 2. Molecular clock dating -- 3. Testing the molecular clock -- 4. Statistical methods for divergence time estimation -- 5. Maximum likelihood estimation of divergence times -- 6. Bayesian estimation of divergence times -- 7. Fossil calibrations -- 8. Relaxed clocks and prior model of rate drift -- 9. Perspectives -- Historical Biogeography -- 1. Early developments -- 2. Cladistic biogeography -- 3. Inferring ancestral areas -- 4. A fresh look at old patterns -- 5. Beyond the standoff -- Phylogeography -- 1. Direct interpretation of single-locus gene genealogies -- 2. Comparative phylogeography -- 3. Lineage sorting and the coalescent -- 4. Multilocus gene genealogies -- 5. Testing models of population history -- Concepts in Character Macroevolution: Adaptation, Homology, and Evolvability -- 1. Darwinism and character variation -- 2. Evolutionary analysis of character homology -- 3. Testing hypotheses of character adaptation -- 4. Character evolvability -- Using Phylogenies to Study Phenotypic Evolution: Comparative Methods and Tests of Adaptation -- 1. Phylogeny and the comparative method -- 2. Ancestral state reconstruction -- 3. Model-based inferences of trait evolution -- 4. Analysis of multiple traits: Correlated evolution and phylogenetic tests of adaptation -- 5. Trait evolution and lineage diversification -- 6. Accuracy and confidence in ancestral inferences -- 7. Future directions for comparative methods -- Taxonomy in a Phylogenetic Framework -- 1. Taxonomy in historical context -- 2. Incorporating an evolutionary perspective -- 3. Species in a phylogenetic framework -- 4. Concerns about and misunderstanding of phylogenetic nomenclature -- 5. The future of phylogenetic nomenclature -- The Fossil Record -- 1. Fossilization and taphonomy -- 2. The nature of the fossil record -- 3. Marine diversity in the Phanerozoic -- 4. The value of the fossil record -- The Origin of Life -- 1. Defining life in evolutionary terms -- 2. Plausible sites for the origin of life -- 3. Conditions required for life's origin -- 4. Self-assembly of boundary membranes and compartments -- 5. Prebiotic polymerization reactions -- 6. How could evolution begin? -- 7. Evolution in the laboratory -- Evolution in the Prokaryotic Grade -- 1. What is a prokaryote? -- 2. Archaea and Bacteria -- 3. Rooting the tree of life -- 4. Symbiosis, syntrophy, and eukaryotic origins -- 5. Horizontal gene transfer in the evolution of prokaryotes -- 6. Darwin's coral of life -- 7. Biased gene transfer -- 8. Sex, recombination, and procreation -- 9. Transfer of genes within and between groups -- 10. Biochemical innovation as a result of horizontal gene transfer -- Origin and Diversification of Eukaryotes -- 1. Origin of eukaryotes -- 2. Timing of the origin and diversification of eukaryotes -- 3. A brief history of eukaryotic classification -- 4. Major clades of eukaryotes -- 5. Distribution of photosynthesis in eukaryotes -- 6. Extant symbioses -- 7. Genome diversity in microbial eukaryotes -- 8. Origins of multicellularity -- Major Events in the Evolution of Land Plants -- 1. Phylogenetic framework -- 2. Origin and diversification of early land plants -- 3. Origin and diversification of vascular plants -- 4. Origin and diversification of seed plants -- 5. Origin and diversification of angiosperms -- 6. Innovation in the land plant body -- 7. Innovation in land plant reproduction -- 8. Coevolution with animals -- 9. Patterns of extinction -- Major Events in the Evolution of Fungi -- 1. Fungi in the tree of life -- 2. Losses of flagella and diversity of the basal fungal lineages -- 3. Evolution of the dikaryon and multicellular fruiting bodies -- 4. Evolution of decayers and plant pathogens -- 5. Evolution of mycorrhizae, lichens, and endophytes -- 6. Evolution of animal pathogens and mutualists -- 7. The age of Fungi -- Origin and Early Evolution of Animals -- 1. The Cambrian explosion and the origin of animal phyla -- 2. Animal phylogeny -- 3. Multicellularity and the origin of sponges (phylum Porifera) -- 4. The origin of the nervous system and the evolution of sensory structures in Cnidaria -- 5. The origins of Bilateria and the phylogenetic placement of Ctenophora, Acoela, Myxozoa, and Placozoa -- 6. Animal diversity -- Major Events in the Evolution of Arthropods -- 1. Arthropod origins -- 2. Phylogenetic framework -- 3. Colonization of land -- 4. Evolution of flight -- 5. Complete metamorphosis -- 6. Life history specializations -- Major Features of Tetrapod Evolution -- 1. Tetrapod ancestry -- 2. The fish-tetrapod transition -- 3. Amniote origins -- 4. Synapsids -- 5. Diapsids: Lepidosaurs and their relatives -- 6. Diapsids: Archosaurs -- Human Evolution -- 1. Origin of the hominins -- 2. Early Homo -- 3. Neanderthals and the origin of modern humans -- 4. Recent human evolution --

Section III. Natural Selection and Adaptation. Natural Selection, Adaptation, and Fitness: Overview -- 1. Natural selection explains adaptation -- 2. Concepts are tools -- 3. Definitions and complications -- 4. Fitness and units of selection -- 5. Connecting selection to fitness in hierarchies -- 6. Polished adaptations or rough history -- 7. Adaptationist storytelling -- 8. How to recognize selection and adaptation -- 9. Can we do without these concepts? Absolutely not. -- Units and Levels of Selection -- 1. The group selection controversy -- 2. Kin selection, inclusive fitness, and the gene's-eye view -- 3. Species selection -- 4. Major evolutionary transitions -- Theory of Selection in Populations -- 1. An example of natural selection -- 2. Fisher's fundamental theorem of natural selection -- 3. Patterns of selection -- 4. Components of selection -- 5. Maintenance of polymorphism -- 6. Selection and other processes -- 7. Synthesis and conclusions -- Kin Selection and Inclusive Fitness -- 1. The problem of altruism -- 2. Inclusive fitness and Hamilton's rule -- 3. Kinds of social selection -- 4. Comparative evidence in social insects -- 5. Experimental evidence in microbes -- 6. Kin recognition -- 7. Challenges to kin selection -- Phenotypic Selection on Quantitative Traits -- 1. How selection works -- 2. Selection is a statistical process -- 3. The genetic response to selection -- 4. Modes of selection -- 5. The multidimensional phenotype -- 6. Indirect selection and misleading covariances -- 7. Genetic correlations and correlated response to selection -- Responses to Selection: Experimental Populations -- 1. Will adaptation evolve? -- 2. How fast will adaptation evolve? -- 3. Does sex accelerate adaptation? -- 4. Is adaptation gradual or saltational? -- 5. What is the limit to adaptation? -- 6. Is adaptation based on gain or loss of function? -- 7. Is adaptation repeatable? -- 8. Is adaptation predictable? -- 9. Is adaptation reversible? -- 10. How do ancestry, selection, and chance contribute to adaptation? -- 11. How can selection maintain diversity? -- 12. What limits the extent of specialization? -- Responses to Selection: Natural Populations -- 1. Measuring selection in natural populations -- 2. Strength and patterns of phenotypic selection -- 3. Microevolution in natural populations -- 4. Local adaptation and population divergence -- 5. Limits to selection and evolutionary responses -- Evolutionary Limits and Constraints -- 1. Lack of genetic variation as a limit and constraint -- 2. Trade-offs -- 3. Multivariate selection -- 4. Gene flow in marginal populations limiting range expansion -- 5. Limits and constraints: biodiversity and conservation -- Evolution of Modifier Genes and Biological Systems -- 1. Evolution of biological systems -- 2. Evolution of dominance -- 3. Direct versus indirect selection -- 4. The evolution of genetic transmission -- 5. The evolution of the mutation rate -- 6. The evolution of sex and recombination -- 7. The evolution of haploidy versus diploidy -- 8. On evolution and optimization -- Evolution of Reaction Norms -- 1. Two major features of the genotype-phenotype map -- 2. Induced responses: Examples of adaptive plasticity -- 3. Robust traits: Examples of canalization -- 4. Reaction norms: Phenotypic plasticity and canalization -- 5. The evolutionary significance of plasticity and canalization -- 6. The Baldwin effect and genetic assimilation -- Evolution of Life Histories -- 1. What is the life history and why is it of interest? -- 2. The theory of life history evolution: A sampler -- 3. Other aspects of life history evolution -- 4. What have we learned? -- 5. Future research -- Evolution of Form and Function -- 1. Form and function in organismal design -- 2. Measuring the evolution of form and function -- 3. Key features of life's functional systems: Multi-functionality, genes, and complexity -- 4. General principles of the evolution of complex functional systems -- Biochemical and Physiological Adaptations -- 1. Physiological diversity -- 2. How do we know that physiological variation is adaptive? -- 3. Biochemical mechanisms inform models of physiological adaptation -- 4. Adaptive variation in tolerance -- 5. Adaptive variation in regulation -- 6. Adaptive acclimation -- 7. Constraints on physiological adaptation -- 8. Implications for global change biology -- Evolution of the Ecological Niche -- 1. Natural history, niches, and evolution -- 2. What is an ecological "niche"? -- 3. Complexities in the niche concept -- 4. The issue of genetic variation in niches -- 5. Demographic constraints on niche evolution -- 6. Niches evolving in communities -- Adaptation to the Biotic Environment -- 1. Defining adaptation to the biotic environment -- 2. Differences between adaptation to biotic versus abiotic environments -- 3. Factors that influence adaptation to the biotic environment, and our ability to detect them -- 4. Conflicting selection and community complexity complicate detection of biotic adaptation -- 5. Lessons from introduced species -- 6. Changing relative abundances of species may alter selection from the biotic environment --

Section IV. Evolutionary Processes. Genetic Drift -- 1. Genetic drift -- 2. Effective population size -- 3. Neutral theory -- 4. Coalescence -- 5. Future directions -- Mutation -- 1. The meaning of mutation -- 2. Types of mutations -- 3. Causes of mutation -- 4. Mutation and evolution: Basic principles -- 5. How random is mutation? -- 6. Variation in mutation rate: Among taxa -- 7. Variation in mutation rate: Within the genome -- 8. The mutational spectrum and mutational bias -- 9. Mutation, genome size, and genomic complexity -- 10. Mutation and extinction -- 11. Mutation and evolution: Other long-term consequences -- Geographic Variation, Population Structure, and Migration -- 1. The causes of spatial structure in genetic diversity -- 2. Individuals and their genes move around -- 3. Gene flow shapes patterns of spatial genetic structure -- 4. Evolution in spatially structured populations -- 5. Implications for conservation -- Recombination and Sex -- 1. Molecular recombination -- 2. Rates of recombination -- 3. Linkage disequilibrium -- 4. What generates linkage disequilibria? -- 5. Recombination facilitates selection -- Genetic Load -- 1. Genetic load -- 2. Mutation load -- 3. Other types of load -- 4. Consequences of load -- Inbreeding -- 1. Inbreeding -- 2. Measuring the degree of inbreeding -- 3. Measuring inbreeding coefficients and rates of self-fertilization and other inbreeding -- 4. Long- and short-term consequences of inbreeding -- 5. Consequences of inbreeding for molecular evolution and genome evolution -- 6. Inbreeding depression, heterosis, and purging -- Selfish Genetic Elements and Genetic Conflict -- 1. What are selfish genetic elements? -- 2. Diversity of selfish genetic elements -- 3. Selfish genetic elements and genome evolution -- 4. Selfish genetic elements and population variation -- 5. Selfish genetic elements and speciation -- 6. Applied uses of selfish genetic elements -- Evolution of Mating Systems: Outcrossing versus Selfing -- 1. Definitions and measurement -- 2. Variation in mating patterns -- 3. Evolution of self-fertilization -- 4. Mechanisms of selection -- 5. The problem of mixed mating -- 6. Evolutionary history --

Section V. Genes, Genomes, Phenotypes. Molecular Evolution -- 1. What is molecular evolution and why does it occur? -- 2. Origins of molecular evolution, the molecular clock, and the neutral theory -- 3. Predictions of the neutral theory for variation within and between species -- 4. The impact of natural selection on molecular variation and evolution -- 5. Biological insights from the study of molecular evolution -- 6. Conclusions -- Genome Evolution -- 1. Evolution of genome architecture -- 2. Genome expansion and restructuring -- 3. Drivers of genome evolution -- Comparative Genomics -- 1. Comparative genomics and genome evolution -- 2. Evolution of gene number -- 3. Identifying regulatory regions -- 4. Copy number variation -- 5. Rapidly evolving regions -- 6. Ultraconserved elements -- 7. The future of comparative genomics -- Evolution of Sex Chromosomes -- 1. Origin of sex chromosomes -- 2. Y (W)-chromosome degeneration -- 3. Dosage compensation of the X -- 4. Gene content evolution of sex chromosomes -- 5. Diversity of sex determination -- Gene Duplication -- 1. Mechanisms of gene duplication -- 2. Fixation of duplicate genes -- 3. Pseudogenization after duplication -- 4. Stable retention of duplicate genes -- 5. Rate of gene duplication -- 6. Determinants of gene duplicability -- 7. Functional redundancy among duplicate genes -- 8. Functional diversification of duplicate genes -- 9. Future directions in the study of gene duplication -- Evolution of New Genes -- 1. Mutational mechanisms to generate new genes -- 2. Rates of new gene origination -- 3. Patterns of new gene evolution -- 4. Evolutionary forces acting on new genes -- 5. Functions and phenotypic effects of new genes -- Evolution of Gene Expression -- 1. The importance of regulatory evolution: A historical perspective -- 2. Finding expression differences within and between species -- 3. Genomic sources of regulatory evolution -- 4. Enhancer evolution -- 5. Evolution of transcription factors and transcription factor binding -- 6. Evolutionary forces responsible for expression divergence -- Epigenetics -- 1. The concept of epigenetics -- 2. The history of epigenetics -- 3. Epigenetics and gene regulation -- 4. Molecular epigenetics -- 5. Epigenetic processes -- 6. Transgenerational epigenetic effects -- 7. Lamarckism and neo-Lamarckism -- 8. Epigenetics and evolution -- 9. Plasticity and assimilation -- 10. Epilogue -- Evolution of Molecular Networks -- 1. Network representations of biological data -- 2. Global organization of biological networks -- 3. Evolution of global network organization -- 4. Local organization and dynamics of biological networks -- 5. Evolution of local network organization -- 6. The future of evolutionary systems biology -- Evolution and Development: Organisms -- 1. Evolution of form and function -- 2. The rise of evolutionary developmental biology -- 3. Evolutionary constraints and patterns of allometry -- 4. Patterns of parallel evolution -- 5. The paradox of morphological stasis -- 6. Opportunities for future research -- Evolution and Development: Molecules -- 1. The goals of molecular studies in evolutionary developmental biology -- 2. Mapping genotype to phenotype during development -- 3. Mapping genotype to phenotype during evolution -- 4. The evolution of novel traits and their underlying gene regulatory networks -- 5. Future areas of research in evolutionary developmental biology -- Genetics of Phenotypic Evolution -- 1. Genetic architecture of phenotypic evolution -- 2. Molecular basis of phenotypic evolution -- 3. Using genotypes to test whether phenotypes are adaptive -- 4. Genetic basis of repeated phenotypic evolution -- 5. Prospects for future research -- Dissection of Complex Trait Evolution -- 1. Genetic variation in complex traits -- 2. Using laboratory crosses to map the mutations responsible for phenotypic evolution -- 3. Using association testing to map the mutations responsible for phenotypic evolution -- 4. Current challenges and prospects for future research -- Searching for Adaptation in the Genome -- 1. Evolution as mutation and change in allele frequencies -- 2. The neutral theory of molecular evolution -- 3. The McDonald-Kreitman test -- 4. Population genomics approaches for detecting and quantifying adaptation -- 5. Remaining challenges -- Ancient DNA -- 1. Beginnings -- 2. The importance of being clean -- 3. Name that bone: Inserting extinct species into molecular phylogenies -- 4. Ancient population genetics and phylogeography -- 5. Ancient genomics -- 6. The future of ancient DNA --

Section VI. Speciation and Macroevolution. Species and Speciation -- 1. Species concepts and definitions -- 2. Speciation as the evolution of intrinsic barriers to gene exchange -- 3. Classifying barriers to gene exchange -- 4. Studying speciation -- Speciation Patterns -- 1. Testing the nature of species -- 2. Speciation patterns in sexual eukaryotes -- 3. Speciation patterns in asexuals -- 4. Speciation patterns in prokaryotes -- 5. Speciation and global diversity patterns -- 6. Linking patterns with process -- Geography, Range Evolution, and Speciation -- 1. Geographic patterns of species and speciation -- 2. The geography of speciation -- 3. Island patterns and their implications -- 4. Speciation and area -- 5. Geographic and geological triggers of speciation -- 6. Challenges and prospects -- Speciation and Natural Selection -- 1. Types of natural selection contributing to reproductive isolation -- 2. Types of reproductive barriers and the effect of selection on their evolution -- 3. Considerations when studying natural selection and speciation -- 4. Reinforcement -- 5. Future directions -- Speciation and Sexual Selection -- 1. Can sexual selection generate diversity? -- 2. Patterns of speciation by sexual selection -- 3. The mechanisms of sexual selection that cause speciation -- 4. Sexual selection and postmating isolation -- Gene Flow, Hybridization, and Speciation -- 1. Gene flow leads to species cohesion -- 2. Gene flow and the origin of species -- 3. Hybridization: A common phenomenon -- 4. Evolutionary outcomes of hybridization -- 5. How to think about species in the context of gene flow and hybridization -- Coevolution and Speciation -- 1. Coevolution and the divergence of species interactions -- 2. Speciation with character displacement -- 3. Predators, parasites, and diversification -- 4. Mutualistic networks and speciation -- 5. Coevolved symbionts and speciation -- 6. Escape-and-radiate coevolution -- 7. Cospeciation -- 8. Conclusions -- Genetics of Speciation -- 1. Genetics of prezygotic isolation -- 2. Genetics of postzygotic isolation -- 3. Summary -- Speciation and Genome Evolution -- 1. From beanbags to genomes -- 2. Geography and gene flow -- 3. Primary versus secondary geographic contact -- 4. Selection-recombination antagonism and genomic heterogeneity -- 5. Empirical data and patterns -- 6. Chromosomal rearrangements and speciation -- 7. Polyploidy and speciation -- 8. Sex chromosomes and speciation -- Adaptive Radiation -- 1. Biodiversity -- 2. Origin and development of the concept -- 3. The ecological theory -- 4. Speciation -- 5. Ecological opportunity -- 6. Species interactions -- 7. Intrinsic factors: Key innovations -- 8. Hybridization -- 9. Testing the ideas -- 10.Future prospects -- Macroevolutionary Rates -- 1. How fast is evolution? -- 2. Rates of speciation and extinction -- 3. Rates of trait evolution -- 4. Are there relationships between rates of trait evolution and diversification? -- Macroevolutionary Trends -- 1. Directionality in evolution -- 2. The scope of trends -- 3. Trend mechanisms -- 4. Examples of trend hypotheses -- Causes and Consequences of Extinction -- 1. Species extinction -- 2. Some definitions: Extinction styles and magnitudes -- 3. Mass extinctions -- 4. Declining extinction risk and resetting the clock -- 5. Extinction and the drivers of macroevolution -- Species Selection -- 1. Concepts and consequences -- 2. History and controversy -- 3. Empirical tests -- Key Evolutionary Innovations -- 1. Key innovation concepts in evolutionary biology -- 2. Where do key evolutionary innovations originate? -- 3. How do key innovations lead to evolutionary diversity? -- 4. Testing hypotheses of key innovation -- 5. Problems with the idea of key innovations -- Evolution of Communities -- 1. What are communities? -- 2. Microevolutionary change and community evolution -- 3. Macroevolutionary change and community evolution -- 4. Geography of speciation and extinction --

Section VII. Evolution of Behavior, Society, and Humans. Genes, Brains, and Behavior -- 1. Genes and behavior -- 2. Nature versus nurture -- 3. What is a behavioral gene? -- 4. Analyzing behavior: Natural variations versus mutations -- 5. Genomes and systems genetics -- 6. The future of behavioral genetics: The behavioral epigenome -- Evolution of Hormones and Behavior -- 1. Hormonal mechanisms and phenotypic variation -- 2. Hormones and phenotypic integration -- 3. Hormones and microevolution -- 4. Hormones and macroevolution -- 5. Summary and future directions -- Game Theory and Behavior -- 1. The basic ideas -- 2. Examples -- 3. Issues for consideration -- 4. Applications -- 5. Future directions -- Sexual Selection and Its Impact on Mating Systems -- 1. What are mating systems and why are they important? -- 2. Measures of mating systems -- 3. Plastic, continuous mating systems and the evolution of behavior -- 4. Mating systems and evolutionary potential -- 5. Applied relevance of the study of the evolution of mating systems -- Sexual Selection: Male-Male Competition -- 1. Why are males most often the competing sex and females the choosy sex? -- 2. The processes of sexual selection -- 3. Male-male competition in the big and small -- 4. Weapon evolution -- 5. Additional forms of male-male competition -- 6. Male-male competition in plants -- 7. Total sexual selection -- 8. Sexual selection and ecological context -- Sexual Selection: Mate Choice -- 1. Why does mate choice fascinate evolutionary biologists? -- 2. What counts as mate choice? -- 3. Choosiness lowers the breeding rate, and there are other costs -- 4. The rewards of being choosy -- 5. Why do the sexes differ in choosiness? -- Evolution of Communication -- 1. Elements of animal communication -- 2. What communication is -- 3. How does communication originate and how does it evolve? -- 4. Evolutionary trajectories: Four examples -- 5. On the reliability of animal communication -- Evolution of Parental Care -- 1. Natural diversity in forms of parental care -- 2. Origin and evolution of parental care -- 3. Evolutionary maintenance of parental care -- 4. Genetics and epigenetics of parental care -- 5. Sociality beyond family -- Cooperation and Conflict: Microbes to Humans -- 1. What is cooperation and why is it so important? -- 2. Fraternal and egalitarian cooperation -- 3. Fraternal cooperation is explained by kin selection -- 4. Egalitarian cooperation requires direct benefits -- 5. Conflict and control of conflict in fraternal cooperative systems -- 6. Conflict and control of conflict in egalitarian cooperative systems -- 7. Organismality results from high cooperation and low conflict -- Cooperative Breeding -- 1. Ecology and evolution of cooperative breeding -- 2. The evolution of helping -- 3. Individual differences in helping behavior -- 4. Reproductive conflict -- Human Behavioral Ecology -- 1. Development of human behavioral ecology -- 2. Problems and criticism -- 3. New focus on evolution in the modern societies -- 4. What can human behavioral ecology contribute to the general study of evolution? -- Evolutionary Psychology -- 1. The Darwinian background for evolutionary psychology -- 2. The modern-day program of evolutionary psychology -- 3. Psychological evidence -- 4. The application of evolutionary models in evolutionary psychology -- 5. Evolutionary alternatives -- Evolution of Eusociality -- 1. Eusociality: A highly integrated form of social organization -- 2. What drives eusociality? -- 3. Working together -- 4. Intragroup conflicts and their resolution -- Cognition: Phylogeny, Adaptation, and By-Products -- 1. What are we measuring? -- 2. The space of possibilities -- 3. Novel possibilities and unanticipated outcomes -- 4. Evolving limitless options -- Evolution of Apparently Nonadaptive Behavior -- 1. What is apparently nonadaptive behavior? -- 2. Behavior as a transaction -- 3. Random mutation versus adaptation: Cannibalism -- 4. Manipulation: Imposter birds and zombie snails -- 5. Evolution does not equal perfection: Sexual cannibalism -- 6. Same-sex sexual behavior: A case study -- 7. Insights from apparently nonadaptive behavior -- Aging and Menopause -- 1. A natural history of aging -- 2. Theories for the evolution of aging -- 3. Menopause -- 4. Pressing questions on the evolution of aging --

Section VIII. Evolution and Modern Society. Evolutionary Medicine

1. Evolution and medicine

2. Pathogens

3. Defense mechanisms

4. Trade-offs in human traits

5. Mismatches to modernity

6. Implications of evolutionary medicine

Evolution of Parasite Virulence

1. Defining virulence

2. The phase model of virulence

3. The trade-off model

4. Vertically transmitted parasites

5. How well do optimality models predict virulence?

Evolution of Antibiotic Resistance

1. A medical miracle - and how to ruin it

2. Origins of antibiotics and antibiotic-resistance mechanisms

3. Transmission of resistant bacteria

4. Persistence and reversibility of resistance

5. Can resistance evolution be slowed or even stopped?

6. Will antibiotics become a footnote to medical history?

Evolution and Microbial Forensics

1. Evolutionary thinking, molecular epidemiology, and microbial forensics

2. The uses of DNA in human and microbial forensics

3. Genetic technology and the significance of a match

4. The Kameido Aum Shinrikyo anthrax release

5. The Ames strain and the 2001 anthrax letters

6. From molecular epidemiology to microbial forensics and back

Domestication and the Evolution of Agriculture

1. Domestication

2. Evolution under domestication

3. Agriculture as a mutualism

4. Agriculture in ants

5. Conclusions

Evolution and Conservation

1. Evolution, genetics, and conservation

2. Process versus pattern and why both matter

3. The enemies to watch out for

4. What genomics brings to the table

5. Concluding thoughts and prospectus

Directed Evolution

1. Directed evolution of nucleic acids

2. Directed evolution of proteins

3. Directed evolution of cells

4. The future of directed evolution

Evolution and Computing

1. Unexpected links and shared principles

2. How evolutionary biology joined forces with computer science

3. How evolutionary computation is helping evolutionary biology

4. Evolutionary computation takes off

5. The future of evolution and computing

Linguistics and the Evolution of Human Language

1. What is language?

2. When did language evolve?

3. Why did language evolve?

4. The evolution of human languages

5. Languages adapt to speakers

6. The future of language evolution

Cultural Evolution

1. What cultural evolution is not

2. Memetics

3. Cultural evolution

4. Nonhuman animal cultural evolution

5. Defining culture

Evolution and Notions of Human Race

1. The biological meaning of race

2. Do biological races exist in chimpanzees?

3. Do biological races exist in humans?

4. Do adaptive traits define human races?

5. Do human races exist: The answer

The Future of Human Evolution

1. Can we predict how humans will evolve?

2. Has human evolution stopped?

3. Future nonadaptive evolution

4. Future adaptive evolution

5. Eugenics and genetic engineering

Evolution and Religion

1. Natural theology and the Bridgewater Treatises

2. Darwin's revolution

3. Evolution and the Bible

4. The problem of evil

5. Evolution: Imperfect design, not intelligent design

6. Evolution and religion: Coda

Creationism and Intelligent Design

1. What kind of creationist?

2. The creation-evolution continuum

3. Intelligent design

4. What does the future hold?

Evolution and the Media

1. Evolution and the birth of modern science communication

2. Evolution and creationism: The dangers of false balance

3. Evolution and the rise of new media

4. The Darwinius affair: A cautionary tale

5. Conclusion.