Molecular Evolution - #27615

Course Programme - Spring 2013

Teacher: Anders Gorm Pedersen

The course starts Wednesday, February 6, 2013, and runs each Wednesday from 13:00 to 17:00 (except for April 17th which is easter holiday). Lectures and exercises will take place at the Center for Biological Sequence Analysis at the Technical University of Denmark, building 208, auditorium 062 (in the basement below CBS). Participation in the weekly lectures/exercises is required (since it counts as part of the exam).

Classes will be a mixture of lectures, problem solving (bring a pocket calculator), computer exercises (bring your laptop - requires wireless network and some software), and micro projects done in groups of two.

Textbook:   Inferring Phylogenies by Joseph Felsenstein, Sinauer Associates, Inc., 2003. The book can be bought at Polyteknisk Boghandel, DTU. It is a good idea to check the online list of typos and comments when reading.

Please note: the program may change slightly along the way. The required readings for a class can be trusted from one week prior to the class. The exact content of powerpoint slides and handouts may change up to the last minute!

Recordings: To view recorded lectures you will need the (free) Quicktime Player (Mac or Windows).

February 6   Brief introduction to evolutionary theory. Population genetics: models of growth, selection and mutation
READINGS:  Lecturenotes (Chapter 1, p. 1-24)
EXERCISE:  Get to know the UNIX environment. Simple simulation of evolution
LECTURE RECORDINGS:  Lecture part 1 (quicktime, 57 MB),   Lecture part 2 (quicktime, 33 MB)

February 13  Neutral mutations and genetic drift. Tree reconstruction by parsimony
READINGS:  Lecture notes (Chapter 2, p. 24-31), Evolutionary trees (PDF),   Felsenstein: 1 + 2 (p. 11-16) + 3 (p. 19-25) + 4 + 5.
EXERCISE:  Introduction to PAUP* phylogeny software. Reconstruction of phylogenies.
DOWNLOADS:  Slides (PDF) Slides (PDF)
LECTURE RECORDINGS:  Neutral theory/genetic drift (MP4, 128 MB),   Phylogenetic Reconstruction: Parsimony (MP4, 241 MB)

February 20  Mini Project 1
MINI PROJECT: Tree Quiz + Construct a Tree From Scratch: What are the closest relatives of whales?.

February 27  Consensus trees. Distance matrix methods
READINGS:  Felsenstein: 11 (p. 147-153, 155-161, 166-171, 174-175)
EXERCISE:  Consensus trees. Phylogenetic reconstruction using distance-based methods.
DOWNLOADS:  Slides (PDF)  Hand-outs Slides (PDF)   Hand-outs  
LECTURE RECORDINGS:  Consensus trees (MP4, 46 MB),   Distance part I (MP4, 58 MB),   Distance part II (MP4, 45 MB),   Distance part III (MP4, 65 MB),  

March 6  Models of DNA and protein evolution
READINGS:  Felsenstein: 13 (p. 196-206, 210-211, 213-222) + 14
EXERCISE:  Models of evolution.
DOWNLOADS:  Slides (PDF)  Hand-outs  

March 13  Likelihood methods
READINGS:  Felsenstein: 16 (p. 248-262, 266-274)
EXERCISE:  Maximum likelihood.
DOWNLOADS:  Slides (PDF)   Hand-outs

March 20  Mini Project #2
MINI PROJECT 2: Comparison of tree building methods, codon-based alignment - the origin of the SARS virus.

March 27  No lecture (easter holiday)

April 3  Bayesian inference of phylogeny
READINGS:  Felsenstein: 18
EXERCISE:  Bayesian inference of phylogeny
DOWNLOADS:  Slides (PDF)  Hand-outs
LECTURE RECORDINGS:  Part 1A   Part 1B   Part 2   Part 3

April 10  Mini Project
MINI PROJECT 3: Protein phylogeny, Bayesian analysis, ancestral reconstruction.

April 17  Testing hypotheses in a phylogenetic context
READINGS:  Felsenstein: 19 (p.307-313, 315-329)
EXERCISE:  Model selection.

April 24  Bootstrap, jackknife, and permutation tests
READINGS:  Felsenstein 20
EXERCISE:  Bootstrapping.
DOWNLOADS:  Powerpoints

May 1  Course overview ("spørgetime")