Note: This syllabus is from 1996, and will be extensivelyrevised for the Spring 2001 offering of the course!

Zoology/Genetics 715/815
Molecular Evolution
Wed 1:10-2:00pm, Fri 1:10-5:00pm
Room G17 and elsewhere, Rudman Bioscience

Instructor: Tom Kocher (tdk@hopper.unh.edu)
Office hours: by appointment, room 216 Rudman
Text: Fundamentals of Molecular Evolution by Li & Graur
Optional text: Molecular Evolutionary Genetics by Nei
Prerequisites: Introductory Genetics is strongly recommended

Tentative Lecture/Lab Schedule

Sep 4 - Orientation; "What is molecular evolution?"
6 - Gene structure and regulation (L&G pp. 1-19)
LAB: The Blind Watchmaker

11- Mutation and the genetic codes
13- Basic Population Genetics I: Selection (L&G pp. 20-25)
LAB: The Time Machine - Selection

18- Basic Population Genetics II: Mutation (L&G pp. 25-30)
20- Basic Population Genetics III: Population size and geneticdrift
LAB: The Time Machine - Mutation and drift

25- Neutral expectations (L&G pp. 31-41)
27- Techniques for measuring evolutionary change (L&G pp.58-64)
LAB: Lab tour & methods of sequence alignment

Oct 2- Mutational pathways and sequence divergence (L&G pp.42-55)
Independent project proposals due!
4- Patterns of nucleotide substitution (L&G 67-79)
LAB: Appointments to discuss project proposals

9- Evolution of mitochondrial DNA - base composition
11- Evolution of mitochondrial DNA - patterns of selective constraint
LAB:Estimation of sequence divergence

16 - Varying rates of molecular evolution (L&G pp. 79-98)
18 - Problems with relative rate tests
LAB: Help prepare for NEMEB meetings at UNH
19 - Attend New England Molecular Evolutionary Biologists meeting!!

23- Theory of phylogenetic reconstruction (L&G pp. 99-106,113-117)
Hand out take-home mid-term.
25- Phylogenetic reconstruction I: Distance methods (L&Gpp. 106-111)
LAB: The MEGA computer package

30- Phylogenetic reconstruction II: Parsimony methods (L&Gpp. 111-113)
Mid-term exam due!
Nov 1- Phylogenetic reconstruction III: Evaluating significanceand support
Preliminary project reports due!
LAB: The PAUP computer package

6- Phylogenetic reconstruction IV: Maximum likelihood methods
8- Phylogenetic reconstruction V: Comparison of methods (L&G113-135)
LAB: Maximum likelhood

13- Evolution by gene duplication (L&G pp. 136-161)
15- Evolution of multigene families (L&G pp. 162-171)
LAB: Gene trees and species trees

20- Transposable elements and adaptation (L&G pp. 172-192)
22- Hybrid dysgenesis L&G pp. 193-203)
LAB: Searching the genome databases on the WWW

27- Evolution of genome size (L&G pp. 204-214
LAB: Turkey dissection

Dec 4- Project Presentations
6- Molecular evolution and AIDS
LAB: Project Presentations
11- Project Presentations

20- Final Exam (8AM)

 

Grading policy -

Class participation (10%) - Ask questions as we go!
Lab exercises (20%) - Fill out the lab worksheets.
Individual project (30%) - A project of your choosing.
Written report and presentation to class.
Midterm (20%) - Midsemester reality check (take-home exam).
Final (20%) - An opportunity to synthesize the semester