6.891 Computational Evolutionary Biology
   The Course

Lecture slides and notes

Additional notes for lectures, slides, etc... will be posted here. Color slides are for viewing. Don't print them if you value your printer...

Viewable/printable slides
Lecture 1 Intro color slides pdf / Printable bw pdf Notes1&2
Lecture 2 Evol forces I color slides pdf / Printable bw pdf Notes 1&2
Lecture 3 Evol forces II color slides pdf / Printable bw pdf Notes 3
Lecture 4 Evol forces III color slides pdf / Printable bw pdf Notes 4


Before and after every lecture we will post questions for further discussion and reflection.

  1. September 8, Intro, Rice Ch 1.
    1. Why do organisms require evolutionary theory? What is it about organisms that requires an evolutionary accounting?
    2. Do all historical processes require a selectionist account?
    3. What are the major features of organic diversity?
    4. What other classes of objects, besides organisms, are conditioned by history?
    5. Describe the organization of morphospace. How is it clustered?
    6. How is individuality (variation within each type) like/unlike that found in minerals?
    7. What about the distribution of forms in morphospace encourages an historical explanation?
    8. Does perfection of organic design require evolutionary explanation?
    9. What is the principle of historical inference?
    10. How are the "quirks" within adaptations "signs of the past"?
    11. Distinguish transformational and variational evolution.
    12. How are changes in an ensemble different in biological evolution than in stellar evolution?
    13. Why is sieving useless with out heritability of traits?
  2. additional readings; Gould, S. J. (1980) Panda's Thumb.
  3. September 13, Population genetics, Rice Ch 1 & 2.
    1. Describe the way variation, heritability and differential reproduction convert individual variation to population variation.
    2. Why does every population have differential reproduction? Does this always imply natural selection?
    3. How do we find out if variation is heritable? Why this especially difficult with animal behavior?
    4. Are chromosome number and shape invariant in a population? (Discuss supernumerary chromosomes, inversion loops, ...)
    5. How much protein variation is there for sexually reproducing species? What are poly-morphic loci?
    6. How big does a population have to be to realize Hardy Weinberg assumptions?
    7. Contrast continuous and discrete population growth models.
    8. Compare fitness as defined in terms of contribution to the succeeding generation and fitness in terms of optimalilty.
    9. What are Mendel's laws? In what way are they laws?
    10. Is simple dominance common? Do all loci assort independently?
    11. Describe segregation distortion. How is the t-allele retained by the population?
    12. Define; endogamy, planktonic mating, gene frequency (allele frequency), and gamete distribution.
    13. How do we move from phenoptypic to genotypic frequency.
    14. Derive the Hardy-Weinberg equilibrium. What assumptions must be made?
    15. What does the following table illustrate? Focus on the assumptions that have to be made to apply this model.
        pA qa
      pA p*p p*q
      qa p*q q*q

    16. What happens to the allele frequency after one round of random mating? How does this show that heritable variation is conserved?
    17. Can simple blending be simulated by having a trait that is the result of many loci? How does this difference reinvigorate Darwin's whole argument? (This is a critical point, make sure you can answer this.)
    18. Descuss the relationship between environment, genetics and development.
    19. In what ways is DNA 'self-reproducing'?
    20. Discuss the following;
      1. differential reproduction is not equivalent to natural selection
      2. natural selection operating at various levels (e.g. group and kin selection with respect to altruism).
      3. How does vegetative growth make the evaluation of fitness by "counting heads" difficult?
      4. What are some causes of differential reproduction?
      5. Discuss the fitness of phenotypic classes and the fitness of genotypic classes.
    21. Define; allele, genotype, fitness, relative fitness, absolute fitness, mean population fitness, marginal fitness, viability selection, sexual selection, fertility selection, adaptive landscape, Darwinian extinction, mutation-selection equilibrium, mutational load, segregation load, outcrossing, additive genetic variance, fundamental theorem of natural selection,norms of reaction.
    22. additional readings; Binomial distribution can be found in any introductory statistics book, e.g.
      Kachigan, S. K. (1986) Statistical Analysis Radius Press: NY. 122-12
      Dupré, John (Editor) (1987) The Latest on the Best: Essays on Evolution and Optimality, Cambridge: MIT Press.
  4. September 15, Neutralism
  5. September 20, Diffusion
  6. September 22, Price's Thm
  7. September 27, QTL
  8. September 29, Development
  9. October 4, Game theory
  10. October 6, Multilevel selection
  11. October 13, Detecting selection
  12. October 18, Phylogeny/Cladistics
  13. October 20, Genome evolution
  14. October 25, Codon Volatility
  15. October 27, Species & Speciation
  16. November 1, Extinctions/Above the spp.
  17. November 3, Disease




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