Biology/ Genome Sciences 414 (Molecular Evolution), Winter 2007
Instructor: Willie Swanson. Foege S-143B. wswanson@gs.washington.edu
Willie's office hours are on Fridays from 11-12 in S-143B Foege.
TA: Joanna Kelley: Office hours are from 11-12 in S-143B Foege.
Lectures: Tues/Thurs, 12:00 - 1:20 (BAG 261). Labs: Tues./Thur., 1:30 - 3:20 (Hitchcock 220)
Course website: http://faculty.washington.edu/wjs18/MolEvol.html

1-4: Course Introduction

1-9: Assembly of Genome Sequences (Reading handed out in lecture ¼)
1-11: BLAST (reading is on course website)
Lab: Sequencher Contig assembly

1-16: Models of DNA Evolution
1-18: Multiple Sequence alignment
Lab: Blast and pairwise alignment

1-23: Phylogenetics I, Terminology and distance methods
1-25: Phylogenetics II, Parsimony and Likelihood
Lab: Multiple Sequence alignment

1-30: Adaptive evolution dN/dS ratios
2-1: Adaptive evolution II, variation in dN/dS ratios
Lab: Phylogenetics I, PAUP* and ModelTest

2-6: Gene Duplication, demonstration of sequence retrieval
2-8: Midterm (covers through 2/1/07)
Lab: Phylogenetics II, PAUP*

2-13: Speciation by adaptive evolution of reproductive genes
2-15: Population genetics
Lab: Adaptive evolution

2-20: Human adaptive evolution (Joanna Kelley)
2-22: Convergent evolution: Lysozyme and Antifreeze Proteins
Lab: Work on project

2-27: Evolution of Influenza virus (get a flu shot talk)
3-1: Gene fusions and new gene function
Lab: Work on Project

3-6: Review

3-8: Final (covers whole course, but majority post-midterm)

Lab: Work on Project

Project presentations and papers due:
Thursday, MARCH 15, 2007, 1030-1220 (room to be determined)



Grading: Lab write ups 30% (5 each), Project 35%, Midterm 15%, Final 15%, Participation 5%
Note on cheating: Each lab write up should be your own, although you can get help from people during the lab. Copying the work of others will result in a 0 for both people.