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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
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- READINGS:
Lecturenotes (Chapter 1, p. 1-24)
- EXERCISE:
Get to know the UNIX environment. Simple simulation of evolution
- DOWNLOADS:
Slides (PDF)
- LECTURE RECORDINGS:
Lecture part 1 (quicktime, 57 MB),
Lecture part 2 (quicktime, 33 MB)
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February 13 Neutral mutations and genetic drift. Tree reconstruction by parsimony
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- 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)
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February 20 Mini Project 1
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- MINI PROJECT: Tree Quiz + Construct a Tree From Scratch: What are the closest relatives of whales?.
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February 27 Consensus trees. Distance matrix methods
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- 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),
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March 6 Models of DNA and protein evolution
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- READINGS:
Felsenstein: 13 (p. 196-206, 210-211, 213-222) + 14
- EXERCISE:
Models of evolution.
- DOWNLOADS:
Slides (PDF)
Hand-outs
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March 13 Likelihood methods
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- READINGS:
Felsenstein: 16 (p. 248-262, 266-274)
- EXERCISE:
Maximum likelihood.
- DOWNLOADS:
Slides (PDF)
Hand-outs
- LECTURE RECORDINGS:
Part 1
Part 2
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March 20 Mini Project #2
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- MINI PROJECT 2:
Comparison of tree building methods, codon-based alignment - the origin of the SARS virus.
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March 27 No lecture (easter holiday)
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April 3 Bayesian inference of phylogeny
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- READINGS:
Felsenstein: 18
- EXERCISE:
Bayesian inference of phylogeny
- DOWNLOADS:
Slides (PDF)
Hand-outs
- LECTURE RECORDINGS:
Part 1A
Part 1B
Part 2
Part 3
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April 10 Mini Project
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- MINI PROJECT 3:
Protein phylogeny, Bayesian analysis, ancestral reconstruction.
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April 17 Testing hypotheses in a phylogenetic context
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- READINGS:
Felsenstein: 19 (p.307-313, 315-329)
- EXERCISE:
Model selection.
- DOWNLOADS:
Slides (PDF)
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April 24 Bootstrap, jackknife, and permutation tests
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- READINGS:
Felsenstein 20
- EXERCISE:
Bootstrapping.
- DOWNLOADS:
Powerpoints
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May 1 Course overview ("spørgetime")
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- EXAMPLES OF PREVIOUS EXAMS
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