Meret Oppenheim, 1936, Object, fur covered cup, saucer,
and spoon
Molecular Evolution
Dr. Dan Graur
Lecture and Exam Schedule for Spring 2008
Study Guide #1
Study Guide #2
Study Guide #3
Midterm I (with answers)
Midterm I (explanations to questions with a low success rate)
Midterm I (grades)
Study Guide #4
Study Guide #5
Study Guide #6
Midterm II (with answers)
Midterm II (explanations to questions with a low success rate)
Midterm 2 (Grades + Bonus points)
Study Guide #7
Final exam (with answers)
Final grades
Powerpoint Presentations
1. Administrative stuff
2. What is Molecular Evolution?
3. Evolution as a Play
4. A Short History of DNA
5. DNA and RNA
6. Proteins and Translation
7. Mutation
8. Dynamics of Genes in Populations
9. Weak Forces of Evolution
10. Selection
11. Introduction to Probability
12. Random Genetic Drift
13. Gene Substitution
14. Genetic Variability
15. Mutationism, Neutralism, Selectionism
16. Evolutionary Change in Nucleotide Sequences
17. Number of Substitutions between two Protein-Coding Genes
18. Alignment of amino-acid and nucleotide sequences
19. Rates of nucleotide substitutions
20. Positive Darwinian Selection
21. Male Driven Evolution
22. Patterns of Nucleotide Substitution
23. Codon Usage
24. Iconography of Evolution
25. Clocks
26. Introduction to Phylogenetics
27. Phylogenetic Terminology
28. Methods of Phylogenetic Reconstruction
29. Processing and Testing of Phylogenetic Trees
30. Human Phylogeny
31. Cetacean Phylogeny
32. Molecular Archeology
33. Early Divergence Events
34. Segmental & Contextual Changes
35. Post-duplication Evolutionary Processes
36. Exon Shuffling
37. Concerted Evolution
38. Transposable Elements
39. SINEs and LINEs
40. Horizontal Gene Transfer
41. Genome Size
42. Prokaryotic Genomes
43. The C-Value Paradox
44. Gene Geography
45. GC Content
46. Experiemental Evolution
Gabriel Germain Joncherie. ca. 1829-1844. Still Life of Eggs Cooking on a Stove. Oil on canvas
GLOSSARY OF TERMS
A
B
C
D
E
F
G
H
I
J
K
L
M
N
O
P
Q
R
S
T
U
V
W
X
Y
Z
Tim Noble and Sue Webster. 2007. Metal Fucking Rats with Shaped Tail
(Version 1). Welded scrap metal and light projector
Additional Reading (Optional)
1. Terry L. Erwin. 1982. Tropical forests: their richness in coleoptera and other arthropod species.
2. Sniegowski, et.al. 1985. Mutation and Adaption: The Directed Mutation Controversy in Evolutionary Perspective.
3. Cargill, et.al. 1999. Characterization of single-nucleotide polymorphisms in coding regions of human genes.
4. Gillooly, et.al. 2005. The rate of DNA evolution: Effects of body size and temperature on the molecular clock.
5. Li WH, Yi S, and Makova K. 2002. Male-driven Evolution.
6. dos Reis M, et.al. 2004. Solving the riddle of codon usage preferences: A test for translational selection.
7. Massingham T and Goldman N. 2005. Detecting amino acid sites under positive selection and purifying selection.
Links
SAMPLE TEST QUESTIONS
1. The rate of neutral mutation is affected by the effective size of the population. (YES/NO)
2. In a population of infinite size, an overdominant mutation will generate stable equilibrium. (YES/NO)
3. If the rate of nucleotide substitution in sequence A is higher than the rate of nucleotide substitution in sequence B, then one possible inference may be that purifying selection on A is more intense than that on B. (YES/NO)
ANSWERS
1. (NO); 2. (YES); 3. (NO)