Preface
Part I. Introduction
1. The Rise of Evolutionary biology
1.1 Evolution means change in living things over long periods of time
1.2 Living things show adaptations
1.3 A short history of evolutionary biology
Summary, Further Reading, Study and Review Questions
2. Molecular and Mendelian Genetics
2.1 Inheritance is caused by DNA molecules, which are physically passed from parent to offspring
2.2 The DNA structurally encodes the information used to build the body's proteins
2.3 The information in the DNA is decoded by transcription and translation
2.4 Mutational errors may occur during DNA replication and repair
2.5 The rates of mutation can be measured and estimated
2.6 Diploid organisms inherit a double set of genes
2.7 Genes are inherited in characteristic Mendelian ratios
2.8 Darwin's theory would probably not work if there was a non-Mendelian blending mechanism of heredity
Summary, Further Reading, Study and Review Questions
3. The Evidence for Evolution
3.1 We distinguish three possible theories of the history of life
3.2 On a small scale, evolution can be observed in nature
3.3 Evolution can also be produced experimentally
3.4 Interbreeding and phenotypic similarity provide two concepts of species
3.5 Ring "species" show that the variation within a species can be extensive enough to produce a new species
3.6 New reproductively distinct species can be produced experimentally
3.7 Small-scale observations can be extrapolated over the long term
3.8 There are homologous similarities between groups of living things
3.9 Different homologies are correlated, and can be hierarchically classified
3.10 There is some fossil evidence for the transformation of species
3.11 The order of the main groups in the fossil record suggests that they have evolutionary relationships
3.12 Summary of the evidence for evolution
3.13 Creationism offers no explanation for adaptation genetic principles
Summary, Further Reading, Study and Review Questions
4. Natural Selection and Variation
4.1 In nature, there is a struggle for existence
4.2 Natural selection operates if some conditions are met
4.3 Natural selection explains both evolution and adaptation
4.4 Natural selection can be directional, stabilizing, or disruptive
4.5 Variation in natural populations is widespread
4.6 Organisms in a population vary in reproductive success
4.7 New variation is generated by mutation and recombination
4.8 The variation created by recombination and mutation is random with respect to the direction of adaptation
Summary, Further Reading, Study and Review Questions
PART II. EVOLUTIONARY GENETICS
5. The Theory of Natural Selection
5.1 Population genetics is concerned with genotype and gene frequencies
5.2 An elementary population genetic model has four main steps
5.3 Genotype frequencies in the absence of selection go to the Hardy-Weinberg equilibrium
5.4 We can test, by simple observation, whether genotypes in a population are at the Hardy-Weinberg equilibrium
5.5 The Hardy-Weinberg theorem is important conceptually and historically, and in practical research and the workings of theoretical models
5.6 The simplest model of selection is for one favored allele at one locus
5.7 The model of selection can be applied to the peppered moth
5.8 Pesticide resistance in insects is an example of natural selection
5.9 Finesses are important numbers in evolutionary theory and can be estimated by three main methods
5.10 Natural selection operating on a favored allele at a single locus is not meant to be a general model of evolution
5.11 A recurrent disadvantageous mutation will evolve to a calculable equilibrial frequency
5.12 Heterozygous advantage
5.13 The fitness of a genotype may depend on its frequency
5.14 Multiple niche polymorphism can evolve in a heterogeneous environment
5.15 Subdivided populations require special population generic principles
Summary, Further Reading, Study and Review Questions
6. Random Events in Population Genetics
6.1 Successive generations are a random sample from the parental gene pool
6.2 The frequency of alleles with the same fitness will change at random through time in a process called genetic drift
6.3 A small founder population may have a nonrepresentative sample of the ancestral population's genes
6.4 One gene can be substituted for another by random drift
6.5 The Hardy-Weinberg "equilibrium" is not an equilibrium in a small population
6.6 Neutral drift over time produces a march to homozygosity
6.7 A calculable amount of polymorphism will exist in a population because of neutral mutation
6.8 Population size and effective population size
Summary, Further Reading, Study and Review Questions
7. Molecular Evolution and the Neutral Theory
7.1 Neutral drift and natural selection can both hypothetically explain molecular evolution
7.2 The rates of molecular evolution and amounts of genetic variation can be measured
7.3 A population in which not all individuals have the optimal genotype is said to have a genetic load
7.4 Haldane described a "cost" of natural selection
7.5 Test 1 (part 1) : the rates of molecular evolution were argued to be too fast to be explained by natural selection because the implied cost of selection would be too high
7.6 Test 1 (part 2) : the degree of genetic variation in populations was argued to be too high to be explained by natural selection because the implied segregational load would be too high
7.7 Some possible answers to the genetic load problem
7.8 The first test, using observations of the absolute rates of evolution and levels of polymorphism, is indecisive
7.9 Test 2 : the rates of molecular evolution are arguably too constant for a process controlled by natural selection
7.10 The generation time effect in the molecular clock
7.11 Evolutionary rate and functional constraint
7.12 DNA sequences provide strong evidence for natural selection on protein structure
7.13 Test 4 : are the rates of evolutionary change of molecules correlated with their heterozygosities?
7.14 The analysis of DNA sequences is only the most recent stage in a long controversy
Summary, Further Reading, Study and Review Questions
8. Two-Locus and Multi-Locus Population Genetics
8.1 Mimicry in Papilio is controlled by more than one genetic locus
8.2 The genotypes at different loci in Papilio memnon are coadapted
8.3 Mimicry in Heliconius is controlled by more than one gene, but not by a supergene
8.4 Two-locus genetics is concerned with haplotype frequencies
8.5 The frequencies of haplotypes may or may not be in linkage equilibrium
8.6 The human HLA genes are a multi-locus gene system
8.7 Linkage disequilibrium can exist for several reasons
8.8 Two-locus models of natural selection can be built
8.9 Hitchhiking occurs in two-locus selection models
8.10 Linkage disequilibrium can be advantageous, neutral, or disadvantageous
8.11 Why does the genome no congeal?
8.12 Wright invented the influential concept of an adaptive topography
8.13 The shifting balance theory of evolution
Summary, Further Reading, Study and Review Questions
9. Quantitative Genetics
9.1 Climatic changes have driven the evolution of beak size in one of Darwin's finches
9.2 Quantitative genetics is concerned with characters controlled by large numbers of genes
9.3 Variation is first divided into genetic and environmental effects
9.4 The variance of a character is divided into genetic and environmental effects
9.5 Relatives have similar genotypes, producing the correlation between relatives
9.6 Heritability is the proportion of phenotypic variance that is additive
9.7 A character's heritability determines its response to artificial selection
9.8 The relation between genotype and phenotype may be non-linear, producing remarkable responses to selection
9.9 Selection reduces the genetic variability of character
9.10 Characters in natural populations subject to stabilizing selection show genetic variation
9.11 Selection-mutation balance is one possible explanation, but there are two models for it
9.12 The rate of slightly deleterious mutations can be observed in experiments in which selection against them is minimized
9.13 Conclusion
Summary, Further Reading, Study and Review Questions
10. Genome Evolution
10.1 Non-Mendelian processes must be added to classical population genetics to explain the evolution of the whole genome
10.2 Genes are arranged in gene clusters
10.3 Gene clusters probably originated by gene duplication
10.4 The genes in a gene family often evolve in concert
10.5 Not all DNA codes for genes
10.6 Repetitive DNA other than in gene clusters may be selfish DNA
10.7 Minisatellites are sequences of short repeats, found scattered through the genome
10.8 Scattered repeats may originate by transposition
10.9 Selfish DNA may explain the C-factor paradox
10.10 Conclusion
Summary, Further Reading, Study and Review Questions
Part III. Adaptation and Natural Selection
11. The Analysis of Adaptation
11.1 The way organisms are adapted may not be obvious
11.2 Three main methods are used to study adaptation
11.3 Example 1 : the function of sex
11.4 Example 2 : sexual selection
11.5 Example 3 : the sex ratio
11.6 Different adaptations are understood in different levels of detail
Summary, Further Reading, Study and Review Questions
12. The Units of Selection
12.1 For the benefit of which level in the biological hierarchy of levels of organization does natural selection produce adaptations?
12.2 Natural selection has produced adaptations that benefit various levels of organization
12.3 Another sense of "unit of selection" is the entity whose frequency is adjusted directly by natural selection
12.4 The two senses of "unit of selection" are compatible; one specifies the entity that generally shows phenotypic adaptations, the other specifies the entity whose frequency is generally adjusted by natural selection
Summary, Further Reading, Study and Review Questions
13. Adaptive Explanation
13.1 Natural selection is the only known explanation for adaptation
13.2 Pluralism is appropriate in the study of evolution, not of adaptation
13.3 Natural selection can, in principle, explain all known adaptations
13.4 Adaptation can be defined either historically or by current function
13.5 The function of an organ should be distinguished from the effects it may have
13.6 Adaptations in nature are not perfect
13.7 Adaptations may be imperfect because of time lags
13.8 Genetic constraints may cause imperfect adaptation
13.9 Developmental constraints may cause imperfect adaptation
13.10 Historical constraints may cause adaptive imperfection
13.11 An organism's design may be a trade-off between different adaptive needs
13.12 Conclusion : constraints on adaptation
13.13 How can we recognize adaptations?
Summary, Further Reading, Study and Review Questions
Part IV. Evolution and Diversity
14. Evolution and Classification
14.1 Biologists classify species into a hierarchy of groups
14.2 There are phenetic and phylogenetic principles of classification
14.3 There are phenetic, cladistic, and evolutionary schools of classification
14.4 A method is needed to judge the merit of a school of classification
14.5 Phenetic classification uses distance measures and cluster statistics
14.6 Phylogenetic classification uses inferred phylogenetic relations
14.7 Evolutionary classification is a synthesis of the phenetic and phylogenetic principles
14.8 The principle of divergence explains why phylogeny is hierarchical
14.9 Conclusion
Summary, Further Reading, Study and Review Questions
15. The Idea of a Species
15.1 In practice, species are recognized and defined by phenetic characters
15.2 Some species concepts define species at a point in time; others define species through evolutionary time
15.3 The cladistic species concept defines species throughout their evolutionary history
15.4 Taxonomic concepts may be nominalist or realist
15.5 Conclusion
Summary, Further Reading, Study and Review Questions
16. Speciation
16.1 How can one species split into two reproductively isolated groups of organisms?
16.2 A newly evolving species could theoretically have an allopatric, parapatric, or sympatric geographical relation with its ancestor
16.3 Geographic variation is widespread and exists in all species
16.4 Allopatric speciation
16.5 Parapatric speciation
16.6 Sympatric speciation
16.7 Some plant species have originated by hybridization and polyploidy
16.8 Reinforcement is suggested by greater sympatric than allopatric prezygotic isolation between a pair of species
16.9 A study of speciation in Drosophila, by Coyne and Orr, provides evidence about reinforcement and other interesting results
16.10 Chromosomal changes could potentially lead to speciation
16.11 Conclusion
Summary, Further Reading, Study and Review Questions
17. The Reconstruction of Phylogeny
17.1 Phylogenies are inferred from characters shared between species
17.2 The parsimony principle works if evolutionary change is improbable
17.3 Phylogenetic inference uses tow principles : parsimony and distance statistics
17.4 In most real cases, not all characters suggest the same phylogeny
17.5 Homologies are more reliable for phylogenetic inference than are analogies
17.6 Homologies can be distinguished from analogies by several criteria
17.7 Derived homologies are more reliable indicators of phylogenetic relations than are ancestral homologies
17.8 The polarity of character states can be inferred by three main techniques
17.9 Any residual character conflict can be resolved by parsimony
17.10 Molecular sequences are becoming increasingly important in phylogenetic inference, and they have distinct properties
17.11 Molecular sequences can be used to infer an unrooted tree for a group of species
17.12 Different molecules evolve at different rates, and molecular evidence can be tuned to solve particular phylogenetic problems
17.13 Molecular phylogenetic research encounters difficulties when the number of possible trees is large and not enough informative evidence exists
17.14 Unrooted trees can be inferred from other kinds of evidence, such as chromosomal inversions in Hawaiian fruitflies or comparative anatomy in the mammal-like reptiles
17.15 Some molecular evidence can only be used to infer phylogenetic relations with distance statistics
17.16 Comparing molecular evidence and paleontological evidence
17.17 Conclusion
Summary, Further Reading, Study and Review Questions
18. Evolutionary Biogeography
18.1 Species have defined geographic distributions
18.2 The ecological characteristics of a species limit its geographic distribution
18.3 Geographic distributions are influenced by dispersal
18.4 Geographic distributions are influenced by climate, such as in the Ice Age
18.5 Geographic distributions are influenced by vicariance events, such as continental drift and speciation
18.6 The Great American Interchange
18.7 Conclusion
Summary, Further Reading, Study and Review Questions
Part V. Paleobiology and Macroevolution
19. The Fossil Record
19.1 Fossils are remains of organisms from the past, and are preserved on sedimentary rocks
19.2 Geological time is conventionally divided into a series of eras, epochs, and periods
19.3 The history of life
19.4 The completeness of the fossil record can be expressed by various quantitative measures
Summary, Further Reading, Study and Review Questions
20. Rates of Evolution
20.1 How to measure the rate of evolution of horse teeth
20.2 How do population genetic and fossil evolutionary rates compare?
20.3 Why do evolutionary rates vary?
20.4 The theory of punctuated equilibrium originally applied the idea of allopatric speciation to predict the pattern of change in the fossil record
20.5 What is the evidence for punctuated equilibrium and for phyletic gradualism?
20.6 The theory of punctuated equilibrium has developed since 1972
20.7 Darwin was not a phyletic gradualist
20.8 The theory of punctuated equilibrium does no t render the modern synthesis "effectively dead;" the relation between microevolution and macroevolution is an open question
20.9 Evolutionary rates can be measured for non-continuous character changes, as illustrated by the evolution of "living fossil" lungfish
20.10 Taxonomic data can be used to describe the rate of evolution of higher taxonomic groups
20.11 Conclusion
Summary, Further Reading, Study and Review Questions
21. Macroevolutionary Change
21.1 The mammals evolved form the reptiles in a long series of small changes
21.2 The mammal-like reptiles illustrate the neo-Darwinian theory of macroevolution
21.3 Morphological transformations are generally accomplished by developmental changes
21.4 Examples exist of the different types of heterochronic evolution
21.5 The question of the relative frequencies of the different types of developmental change is interesting but not yet answered
21.6 Heterochronic change can occur between different somatic cell lines as well as between the timing of reproductive and somatic development
21.7 Changes in the genes controlling development can produce macromutational monsters
21.8 Conclusions : developmental change and evolution
21.9 Higher taxa rise, fall, and replace one another
Summary, Further Reading, Study and Review Questions
22. Coevolution
22.1 Coadaptation alone suggests, but is not conclusive evidence for, coevolution
22.2 Coevolution should be distinguished from sequential evolution
22.3 Coevolutionary relations will often be diffuse
22.4 Parasites and hosts coevolve
22.5 The evolution of parasitic virulence
22.6 The phylogenetic branching of parasites and hosts may be simultaneous
22.7 Coevolution can proceed in an "arms race"
22.8 Coevolutionary arms races can result in evolutionary escalation
22.9 The probability that a species will go extinct is approximately independent of how long it has existed
22.10 Antagonistic coevolution can have various forms
22.11 The Red Queen hypothesis can be tested by plotting extinction rates against absolute time
22.12 Both biological and physical hypotheses should be tested on macroevolutionary observations
22.13 Competition may have driven some grand scale trends in the history of life
Summary, Further Reading, Study and Review Questions
23. Extinction
23.1 The diversity of life in the fossil record is due to a balance of extinction and speciation
23.2 Real extinction should be distinguished from pseudoextinction
23.3 The characters that evolve within taxa may influence extinction and speciation rates, as is illustrated by snails with planktonic and direct development
23.4 Differences in the persistence of ecological niches will influence macroevolutionary patterns
23.5 The factors that control macroevolution may differ from those that control microevolution
23.6 Mass extinction
23.7 Several theories have been suggested to explain why mass extinctions happen
23.8 Summary for mass extinctions
23.9 Some kinds of species may survive mass extinctions more effectively than other species
23.10 A two-geared engine of macroevolution?
Summary, Further Reading, Study and Review Questions
Glossary
References
Answers to Study and Review Questions
Index
