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Computational Evolutionary Biology

Graduate · Historical course

Fall 2005

Topics

  • Introduction: The Basic Dynamical Systems of Evolution
  • Forces of Evolution I: Complications
  • Forces of Evolution II: Optimization
  • Forces of Evolution III: Mutation, Migration
  • Forces of Evolution IV: Genetic Drift
  • Evolution at The Molecular Level I
  • Evolution at The Molecular Level II
  • Evolution at The Molecular Level III
  • The Algebra of Evolution: Price’s Theorem I
  • The Algebra of Evolution: Price’s Theorem II
  • Detecting Selection
  • Detecting Selection: A Case Study
  • Codon Volatility
  • Coalescent Theory and Phylogenetics
  • Evolutionary Phylogenetics
  • Evolutionary Phylogenetics (cont.)
  • Quantitative Genetics I
  • Quantitative Genetics II
  • Host-parasite Interactions and Disease Models
  • Evolutionary Stable Strategies
  • Developmental Evolution
  • Final Project Presentations
  • Finale: The Future of Evolution

Readings

  • The reading assignments for the course refer to chapters in the following textbooks:
    Listed reading
  • Rice, Sean. Evolutionary Theory: Conceptual and Mathematical Foundations . Sunderland, MA: Sinauer, 2004. ISBN: 9780878937028 .
    Listed reading
  • Hall, Barry. Phylogenetic Trees Made Easy . Sunderland, MA: Sinauer, 2004. ISBN: 9780878933129 .
    Listed reading
  • LEC #: 1 · TOPICS: Introduction: The Basic Dynamical Systems of Evolution · READINGS: Rice: Chapter 1
    Reading assignment
  • LEC #: 2 · TOPICS: Forces of Evolution I: Complications · READINGS: Rice: Chapters 1 and 2
    Reading assignment
  • LEC #: 3 · TOPICS: Forces of Evolution II: Optimization · READINGS: Rice: Chapters 1 and 2
    Reading assignment
  • LEC #: 4 · TOPICS: Forces of Evolution III: Mutation, Migration · READINGS: Rice: Chapter 3
    Reading assignment
  • LEC #: 5 · TOPICS: Forces of Evolution IV: Genetic Drift · READINGS: Rice: Chapter 3
    Reading assignment
  • LEC #: 6 · TOPICS: Evolution at The Molecular Level I · READINGS: Rice: Chapters 3 and 4
    Reading assignment
  • LEC #: 7 · TOPICS: Evolution at The Molecular Level II · READINGS: Rice: Chapters 3 and 4
    Reading assignment
  • LEC #: 8 · TOPICS: Evolution at The Molecular Level III · READINGS: Rice: Chapter 6
    Reading assignment
  • LEC #: 9 · TOPICS: The Algebra of Evolution: Price’s Theorem I · READINGS: Rice: Chapter 6
    Reading assignment
  • LEC #: 13 · TOPICS: Codon Volatility · READINGS: Hall: Chapters 1 and 2
    Reading assignment
  • LEC #: 14 · TOPICS: Coalescent Theory and Phylogenetics · READINGS: Hall: Chapters 1 and 2
    Reading assignment
  • LEC #: 15 · TOPICS: Evolutionary Phylogenetics · READINGS: Hall: Chapters 2 and 3
    Reading assignment
  • LEC #: 16 · TOPICS: Evolutionary Phylogenetics (cont.) · READINGS: Hall: Chapters 2 and 3
    Reading assignment
  • LEC #: 17 · TOPICS: Quantitative Genetics I · READINGS: Rice: Chapter 7
    Reading assignment
  • Host-parasite Interactions Rice: Chapter 7
    Listed reading
  • LEC #: 19 · TOPICS: Host-parasite Interactions and Disease Models · READINGS: Rice: Chapter 9
    Reading assignment
  • LEC #: 20 · TOPICS: Evolutionary Stable Strategies · READINGS: Rice: Chapter 9
    Reading assignment
  • Hartl, D., and A. Clark. Principles of Population Genetics . 3rd ed. Sunderland, MA: Sinauer, 1997. ISBN: 9780878933068 .
    Recommended
  • Futuyma, D. Evolutionary Biology . 3rd ed. Sunderland, MA: Sinauer, 1997. ISBN: 9780878931897 .
    Recommended
  • Felsenstein, J. Inferring Phylogenies . Sunderland, MA: Sinauer, 2003. ISBN: 9780878931774 .
    Recommended
  • Ewens, W. Mathematical Population Genetics . 2nd ed. Vol. 1. New York, NY: Springer-Verlag, 2004. ISBN: 9780387201917 .
    Recommended
  • Weiss, K., and A. Buchanan. Genetics and the Logic of Evolution . New York, NY: Wiley-Liss, 2004. ISBN: 9780471238058 .
    Recommended
Sources