Here is the course arrangement of EvoGen. Please make sure you are ready before class, and related materials could be found in lectures and references.
| 11/27/06 |
Introduction: A brief description of the course (LM)
The goal and plan, reference materials, schedule and registration, etc.
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Lecture 1-2. Species: Typological and Population Concepts (DZ)
Basic concepts and theories: Origin of Population genetics
Anthony J.F. Griffiths, William M. Gelbart, Richard C. Lewontin, and Susan R. Wessler.
Introduction to Genetic Analysis. 8th ed New York: W. H. Freeman & Co. 2005.
Chapter 19, Population Genetics.
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| 11/29/06 |
Lecture 3-4. Species: Typological and Population Concepts (DZ)
Basic concepts and theories: Microevolution
Changes of Genes and Genotype Frequencies
Anthony J.F. Griffiths, William M. Gelbart, Richard C. Lewontin, and Susan R. Wessler.
Introduction to Genetic Analysis. 8th ed New York: W. H. Freeman & Co. 2005.
Chapter 19, Population Genetics.
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| 12/01/06 |
Lecture 5-6. Species: Typologial and Population Concepts (DZ)
Basic concepts and theories: Fitness and selection
The target of natural selection
Anthony J.F. Griffiths, William M. Gelbart, Richard C. Lewontin, and Susan R. Wessler.
Introduction to Genetic Analysis. 8th ed New York: W. H. Freeman & Co. 2005.
Chapter 19, Population Genetics.
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| 12/03/06 |
Lecture 7-8. Species: Typological and Population Concepts (DZ)
Basic concepts and theories: inbreeding coefficient
Measure of genetic relationship among individuals
Anthony J.F. Griffiths, William M. Gelbart, Richard C. Lewontin, and Susan R. Wessler.
Introduction to Genetic Analysis. 8th ed New York: W. H. Freeman & Co. 2005.
Chapter 19, Population Genetics.
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| 12/04/06 |
Lecture 9-10: Neutral Theory of Molecular Evolution (LM)
Kimura M, 1983. The neutral theory of molecular evolution Theory: Page 34-36; Evidence and Features: Page 98-116; Fixation Probability of neutral alleles: Page 43-46.
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| 12/06/06 |
Lecture 11. Molecular Clock: theories and observations (LM)
Kimura M, 1968. Evolutionary rate at the molecular level. Nature 217: 624-626
Gillespie J, 1993. The Causes of Molecular Evolution. Oxford Univ Press.
Chapter 3: Page 105-121.
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Minilecture: History and issues about molecular clock
Student presentation 1: Molecular Clock
Zuckerkandl, E. and Pauling, L, 1965, Evolutionary divergence and convergence in proteins. In: Evolving genes and proteins. Ed. Bryson V and Vogel HJ: 97-166. Academic, New York.
Kumar S. (2005) Molecular Clock: Four Decades of evolution, Nature Reviews Genetics. |
| 12/08/06 |
Lecture 12. Make sense of single nucleotide polymorphism (LM)
Waterson G (1970s): Measure and Significance of SNPs
Stochastic Process - Basic concept and theory
Convolution and Generating Functions
Waterson theory of nucleotide polymorphisms
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Minilecture 2: History and issues about Gene Duplication (GH)
Student Presentations 2: Gene Duplication
Kimura M, 1983, The neutral theory of molecular evolution, page 104-113.
Force A et al.. Preservation of duplicate genes by complementary, degenerative mutations... Genetics. 1999 Apr;151(4):1531-45. Review.
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| 12/10/06 |
Lecture 13. Make sense of single nucleotide polymorphism (LM)
Waterson G (1970s): Measure and Significance of SNPs
Stochastic Process - Basic concept and theory
Convolution and Generating Functions
Waterson theory of nucleotide polymorphisms
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Minilecture 3: History and issues about genome duplication (LJ)
Students Presentations 3: Genome duplication
Wolfe KH, Shields DC. 1997. Molecular evidence for an ancient duplication of the entire yeast genome. Nature. 387:708-713.
Yu J, et al., 2005. The Genomes of Oryza sativa: A History of Duplications. PLoS Biol. 3(2):e38.
Wang et al., 2005. Duplication and DNA segmental loss in the rice genome: implications for diploidization. 165: 937-946.
Wang et al., 2006. Statistical inference of chromosomal homology based on gene colinearity and applications to Arabidopsis and rice. BMC Bioinformatics. 2006 Oct 12;7:447.
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| 12/11/06 |
Lecture 14: Make sense of single nucleotide polymorphism (LM)
Waterson G (1970s): Measure and Significance of SNPs
Stochastic Process - Basic concept and theory
Convolution and Generating Functions
Waterson theory of nucleotide polymorphisms
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Minilecture 4: History and issues about the gene orders
Students presentation 4: Evolution of gene orders
Hurst LD, Pal C, Lercher MJ. 2004.The evolutionary dynamics of eukaryotic gene order.
Nat Rev Genet. 5:299-310
Pevzner P, Tesler G. (2003) Genome rearrangements in mammalian evolution: lessons from human and mouse genomes. Genome Res. 2003 Jan;13(1):37-45.
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| 12/13/06 |
Lecture 15: Make sense of single nucleotide polymorphism (LM)
Waterson G (1970s): Measure and Significance of SNPs
Stochastic Process - Basic concept and theory
Convolution and Generating Functions
Waterson theory of nucleotide polymorphisms
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Lecture 1-2. Species: Typological and Population Concepts (DZ)
Minilecture 5: History and issues about gene expression
Students presentation 5: Evolution of gene expression.
K?rn et al. 2005. Stochasticity in gene expression: from theories to phenotypes. Nature Reviews Genetics 6, 451-464
Rifkin SA, Kim J, White KP. 2003. Evolution of gene expression in the Drosophila melanogaster subgroup. Nat Genet. 33:138-144.
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| 12/15/06 |
Minilecture 6:History and Issues about the "silenced" portion of genomes (LM)
Student presentation 6: evolution of non-coding regions and synonymous sites
Llopart et al. 2002.? Intron presence-absence polymorphism in Drosophila driven by positive Darwinian selection. Proc Natl Acad Sci U S A 99:8121-8126.
Andolfatto P. 2005. Adaptive evolution of non-coding DNA in Drosophila. Nature. 437:1149-1152.
Chamary JV, Parmley JL, Hurst LD. 2006. Hearing silence: non-neutral evolution at synonymous sites in mammals. Nat Rev Genet. 2006 Feb;7(2):98-108.
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Minilecture 7: History and issues about evolution of sex-related traits (LM)
Student presentation 7: evolution of sex chromosomes and unidirectional gene movement.
Kaiser VB, Ellegren H. 2006. Nonrandom distribution of genes with sex-biased expression in the chicken genome. Evolution. 60:1945-1951.
Emerson J.J., H. Kaesmann, E. Betran and M. Long 2004. Extensive gene traffic on the human X chromosome. Science 303: 537-540.
Betran E, Thornton K, Long M. 2002. Retroposed new genes out of the X in Drosophila. Genome Res. 12:1854-1859.
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| 12/17/06 |
Minilecture 8: History and Issues about transposable elements (LM)
Student Presentation 8: Evolution of transposable elements
Jiang et al. 2004. Pack-MULE transposable elements mediate gene evolution in plants. Nature. 2004 Sep 30;431:569-573.
Aminetzach YT, Macpherson JM, Petrov DA "Pesticide resistance via transposition-mediated adaptive gene truncation in Drosophila." Science? 2005; 309: 5735: 764-7.
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Minilecture 9: History and issues about the gene networks (WL)
Student Presentation 9: Gene Networks and Evolution
Garcia-Fernandez J.2005. The genesis and evolution of homeobox gene clusters. Nature Reviews Genetics 6, 881-892.
Wagner A (2003) How the global structure of protein interaction networks evolves. Proc R Soc Lond B 270: 457-466.
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| 12/18/06 |
Debate: Systems Biology: A real science? (LM, WL)
Kitano, H. 2004. Biological robustness. Nature Reviews Genetics5, 826 - 837.
Mitchell P. Levesque and Philip N. Benfey, 2004. Systems biology. Current Biology 2004 14: R179-R180.
Mitchison G. 2004. Happy days here again? Current Biology 2004 14: R97-R98.
Stevens CF, 2004. Systems biology versus molecular biology. Current Biology 2004 14: R51-R52.
Bork P. 2005. Is there biological research beyond Systems Biology? A comparative analysis of terms. Mol Syst Biol. 1:2005.0012. Attention: Both first prize and second prize will be awarded to two teams and the most articulate students.
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| 12/20/06 |
?Minilecture 10: History and Issues about gene evolution (LM)
Student Presentation 10: Evolution of new genes and gene structures
Wang et al., 2006. High rate of chimeric gene origination by retroposition in plant genomes. Plant Cell. 18:1791-1802
Arguello et al. 2006. An X-linked Testes Chimeric Gene by Illegitimate Recombination in Drosophila. PLoS Genetics 2(5): e77.
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Minilecture 11: History and issues (LM)
Student Presentation 11: The way scientists think - Not only philosophy (LM)
Rzhetsky A, Iossifov I, Loh JM, White KP. (2006). Microparadigms: chains of collective reasoning in publications about molecular interactions. Proc Natl Acad Sci U S A. 103:4940-4945.
Jacob, F. 1977, Evolution and Tinkering. Science, 196: 1161-1166.
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| 12/22/06 |
Summary: Students present term papers
Term paper writing: Evolutionary genomics: What did we learn?
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