6.877J | Fall 2005 | Graduate
Computational Evolutionary Biology

Readings

The reading assignments for the course refer to chapters in the following textbooks:

Rice, Sean. Evolutionary Theory: Conceptual and Mathematical Foundations. Sunderland, MA: Sinauer, 2004. ISBN: 9780878937028 .

Hall, Barry. Phylogenetic Trees Made Easy. Sunderland, MA: Sinauer, 2004. ISBN: 9780878933129 .

LEC # TOPICS READINGS
1 Introduction: The Basic Dynamical Systems of Evolution Rice: Chapter 1
2 Forces of Evolution I: Complications Rice: Chapters 1 and 2
3 Forces of Evolution II: Optimization Rice: Chapters 1 and 2
4 Forces of Evolution III: Mutation, Migration Rice: Chapter 3
5 Forces of Evolution IV: Genetic Drift Rice: Chapter 3
6 Evolution at The Molecular Level I Rice: Chapters 3 and 4

Hall: Appendix 1

7 Evolution at The Molecular Level II Rice: Chapters 3 and 4

Hall: Appendix 1

8 Evolution at The Molecular Level III Rice: Chapter 6
9 The Algebra of Evolution: Price’s Theorem I Rice: Chapter 6
10 The Algebra of Evolution: Price’s Theorem II  
11 Detecting Selection  
12 Detecting Selection: A Case Study  
13 Codon Volatility Hall: Chapters 1 and 2
14 Coalescent Theory and Phylogenetics Hall: Chapters 1 and 2
15 Evolutionary Phylogenetics Hall: Chapters 2 and 3
16 Evolutionary Phylogenetics (cont.) Hall: Chapters 2 and 3
17 Quantitative Genetics I Rice: Chapter 7
18 Quantitative Genetics II

Host-parasite Interactions

Rice: Chapter 7
19 Host-parasite Interactions and Disease Models Rice: Chapter 9
20 Evolutionary Stable Strategies Rice: Chapter 9
21 Developmental Evolution  
22 Quantitative Genetics II  
23-25 Final Project Presentations  
26 Finale: The Future of Evolution