| Chapter 1: A case for evolutionary
thinking: Understanding HIV |
Example or Text Reference |
| HIV/AIDS basics (nature of the problem, modes of transmission, geography,
numbers of people infected, etc.) |
pp. 405 |
| HIV life cycle |
Fig 1.3 |
| Defeat of the immune system (especially specificity of cell lineages) |
|
| Consequences of mistakes by HIV reverse transcriptase |
Sections 1.2 |
| Evolution of resistance to AZR |
Section 1.2 |
| Ewald's transmission rate hypothesis |
Figure 1.5 |
| Darwinian scenario to explain evolution of AZT resistance (=evolution
by natural selection) |
p. 9 (end of Section 1.2) |
| Origin of HIV |
Fig. 1.12 |
| Natural resistance to HIV |
Section 1.4 |
| Phylogenetic analysis, cladograms, rapid evolution of HIV's and
SIV's |
Section 1.5, Figure 1.6 |
| Implications of evolutionary biology for the AIDS epidemic |
p. 17 |
| Chapter 2. The Evidence for
Evolution |
Example or Text Reference |
| A static world and a changing world |
Introductory paragraphs |
| Homology |
Fig. 2.1,2.2 |
| Vestigial structures |
Fig. 2.6. Structural, developmental and molecular levels of vestigial
traits. |
| Old earth, uniformitarianism, relative dating, absolute dating, extinction,
environmental change, etc. |
Sections 2.2, 2.3 (which show that earth is changing and is very
old). |
| Transitional forms |
Whales, Fig. 2.10 |
| Direct observation of evolutionary change |
Soapbery bugs, Fig. 2.7 |
| Biogeography of marsupials (correspondence of fossil record and paleomagnetic
datra on continent position) |
Fig. 2.13 |
|
|
| Chapter 3. Darwinian Natural
Selection |
Example or Text Reference |
| Distinguishing between the fact of evolution and the mechanism (natural
selection) which drives it |
Introductory paragraphs |
| Darwin's four postulates |
p. 48 |
| Fitness and adaptation (technical meaning in the context of evolutionary
theory) |
p. 48 |
| Geospiza fortis example |
Section 3.2 |
| The populations are variable |
Fig. 3.3 |
| Some of the variation is heritable |
Heritability (technical meaning), Fig. 3.4, Box 3.1 |
| There is overproduction of young |
Fig 3.5 |
| Non-random survival and reproduction |
Fig. 3.6 |
| The population evovlved a larger mean beak size |
Fig. 3.7, Table 3.2 |
| The Nature of Natural Selection |
Section 3.3 deals with common misconceptions regarding natural selection. |
| Problems with Darwinism |
Source of variation, blending inheritance, age of the earth -- all
discussed in Section 3.4 |
| The modern Synthesis |
Two parts - restates Darwin's postulates in modern genetics language,
and considers macroevolution tro result from microevolution acting over
time (pp. 64-65) |
| "Scientific Creationism" |
You should be familiar with these standard critiques and their resolution. |
| Chapter 4. Mutation and Genetic
Variation |
Example or Text Reference |
| New alleles and new genes (the difference) |
This chapter |
| Types of mutations |
Table 4.1 |
| Point mutations - effect of nucleotide substitutions on protein function |
hemoglobin mutants, pp. 80-81 |
| Mutation rates |
Table 4.2 |
| Factors complicating determination of mutation rates |
pp. 85-85 |
| Gene duplication and unequal crossing over |
Fig. 4.7 |
| Gene families - new genes and pseudogenes |
Globin gene family, Fig. 4.9 |
| New genes from overprinting and reverse transcription of mRNA? |
pp. 88-90 |
| Polyploidy and "overnight" new plant species |
fig. 4.13 |
| Chromosome inversion and linkage |
Fig. 4.11 |
| Measuring genetic variation (at the protein and DNA levels) |
Section 4.4 |
| Calculation of allele frequencies |
Delta 32 example, pp. 98-99 |
| Populations tend to be polymorphic |
Fig. 4.16 |
| Chapter 5. Mendelian genetics
in populations I: Selection and Mutation |
Example or Text Reference |
| Allele and genotype frequencies - how they are determined, p and q |
Don't confuse them with genotype frequencies in crossing experiments! |
| Hardy Weinberg model as null model (Conclusions 1 and 2) |
p. 117 |
| Effects of directional selection on allele frequency (loss and fixation) |
Fig. 5.10 |
| Experiment on directional selection Cavenor and Clegg, Drosophila ADH
alleles) |
Fig. 5.11 |
| Selection on dominant and recessive alleles. (Selection can't "see"
recessive alleles) |
Fig. 5.14 |
| Selection against homozygotes. (Equilibrium allele frequencies result;
neither allele becomes fixed/extinct) |
Fig.5.16 |
| Selection against heterozygotes. (Populations become fixed for one
or another of the alleles). |
Fig 5.17 (this is an exceptionally complicated example - don't worry
about the details of the "compound chromosomes, etc.). |
| Frequency dependent selection (Hori, left- and right-handed fish) |
Fig. 5.19, 5.20 |
| "Mutation by itself is generally not a potent evolutionary force" |
Section 5.4, pp. 142-143 |
| Mutation-selection balance |
Equation on p. 145, spinal muscular atrophy, cystic fibrosis |
| Regeneration of variation through mutation |
Fig. 5.24 |
| Chapter 6. Mendelian Genetics
in Populations II: Migration, Genetic Drift and Nonrandom Mating |
Example or Text Reference |
| Migration (gene flow): the one island model |
Fig. 6.4 |
| Migration: example (Lake Erie snakes) |
Fig. 6.6, 6.7 |
| Interaction of migration and drift in archipelagoes (Gills and Goudet,
red bladder campaign). Founder effect. |
Fig. 6.9 |
| Genetic drift and the random fixation of alleles - computer and laboratory
simulations |
Fig 6.13, 6.14 (Notice how these show the same result) |
| Genetic drift and the random fixation of alleles - examples from nature |
Ozark lizards, Fig. 6.16; Flowering plants, Fig. 6.17 |
| You can skip (for now) the discussion of "neutralist" and "selectionist"
positions on pp.177-179 |
|
| Inbreeding - reduces frequency of heterozygotes |
Fig. 6.19 (a similar argument was presented in lecture) |
| Example of inbreeding from nature: Malarial parasite |
Fig. 6.20, Table 6.2, 6.3. Note the use of sex ratio theory to
conclude that populations are descended from single foundress |
| Inbreeding depression - occurs if inbreeding results in more deleterious
recessive alleles being exposed to selection |
Humans, Fig. 6.22, plants, Fig. 6.23 |
| F, the coefficient of inbreeding, can be calculated in two ways |
pp. 185-186 |
| Conservation genetics of the Prairie Chicken ties all of these
concepts together |
Chapter introduction and conclusion |
| Chapter 7, Section 7.2. The
Adaptive Significance of Sex |
Example or Text Reference |
| Maynard Smith's model - this clearly shows that there is a problem
with sexual reproduction |
pp. 214-215 (especially Fig. 7.13) |
| Genetic recombination - what it is, how it happens, its consequences |
p. 216, also see your Genetics text |
| Muller's ratchet |
Fig. 7.15 |
| Andersson and Hughes experiment (they subjected bacterial populations
to bottlenecks) and Muller's hypothesis. |
pp. 220-221 |
| Lambert and Moran study (they compared mutation incidence in endosymbiotiv
bacteria and free living bacteria) and Muller's hypothesis. |
pp. 220-221 |
| Host-parasite coevolution |
Fig. 7.17 |
| Parasitism as a selective force favoring sexual reproduction |
Snails and trematode parasites, Fig. 7.18 |
| Chapter 8. Adaptation |
Example or Text Reference |
| "The adaptationist program": Goals and problems |
Polar bear and giraffe examples, Section 8.1 |
| Adaptations to the physical environment: temperature regulation by
ectotherms |
Desert iguanas, Fig. 8.1
Garter snakes, Fig. 8.8,8.10, Table 8.2 |
| Phenotypic plasticity can be adaptive |
Phototactic behavior of Daphnia, Fig. 8.17 |
| Constraints on adaptation: tradeoffs |
Lecture material will include quantity/quality of offspring, costs/benefits
of thermoregulatory strategies in animals. |
| Constraints on adaptation: development |
Fuchsia flower color change, Fig. 8.24, Table 8.3 |
| Constraints on adaptation: lack of genetic variation |
Text example (host shifts by phytophagous beetles) is too complicated! |
| Chapter 12. Mechanisms of
Speciation |
Example or Text Reference |
| Species concepts (especially the morphological species concept and
biological species concept) |
Section 9.1, red wolf example (pp. 316-318) |
| Mechanisms of isolation: since migration (=gene flow) inhibits divergence,
isolation through dispersal or vicariance is essential for (allopatric)
speciation. |
Section 9.2, Figures 9.4, 9.6 |
| Mechanisms of divergence: genetic drift (founder effect), natural selection,
mutation (polyploidy in plants) |
Section 9.3 |
| Allopatric vs. sympatric speciation. Don't worry about parapatric
speciation. |
Rhagoletis as example of sympatric speciation (Figure 9.8) |
| Secondary contact, hybridization, effect of hybrid fitness, reinforcement,
pre- and post-zygotic isolation |
Section 9.4, Figure 9.13 (evolution of pre-zygotic isolation leading
to reinforcement), Figure 9.15 and Table 9.1 (show stable hybrid zone).
Table 9.2 is a good summary of the outcomes of secondary contact and hybridization. |
| Rates of speciation: Cichlid fishes in East Africa |
Section 9.7, Figures 9.21,22, Table 9.4 |
| Rates of speciation: patterns across taxa |
Section 9.7, Figure 9.24, 9.25 (Lyellian curves), 9.26. |
| Chapter 14. The Origin of
Life and Precambrian Evolution |
Example or Text Reference |
| Cenancestor |
Fig. 11.1 |
| Inferring ancestral traits using phylogeny of extant organisms |
Fig 11.3 and accompanying discussion to determine that common ancestor
had four legs and was ectothermic, Fig 11.6 (for Bacteria, Archaea, Eucarya |
| Phylogeny of all living things based on small unit rRNA gene |
Fig. 11.5 (don't memorize it!) |
| Characteristics of the cenancestor |
pp. 406-407 |
| When did the cenancestor live? |
Section 11.2 |
| Oparin-Haldane model |
Model stated succinctly on p. 421, Section 11.3 is a discussion of
efforts to fill in the model by adding the necessary steps. |
| Non biological synthesis of monomers |
ditto |
| Assembly of polymers |
ditto |
| Self replication, rybozmes |
ditto |
| Evolution of eucarya 1 - organelles |
Section 11.4, Figs. 11.24-26 |
| Evolution of eucarya 2 - introns |
Section 11.4, Figs 11.28,29 |
| Chapter 16. Human Evolution |
Example or Text Reference |
| Phylogenetic position of humans |
Section 14.1, Figure 14.1, 14.3d. Don't worry about the details
of the human-chimp-gorilla clade. I presented the relationship in
Fig. 14.3d as a reasonable hypothesis |
| Fossil evidence: Australopithecus and Homo, major anatomical differences |
Section 14.2, homine
chronology (but don't try to memorize this!) |
| Models for evolution of modern humans: single replacement vs. multiregional
evolution |
Section 14.3,Table 14.12, Figures 14.12, 16,17,18 |
| Development of bipedal locomotion |
Lecture notes |
| Development of large brains, language, culture |
Lecture notes, Figure 14.23 |
| Future evolution of humans |
Section 18.3 |