Molecular Evolution 27615 - 2016

Lecture Schedule 2016

Week 1 (February 3): Introduction to evolutionary theory and population genetics. Models of growth, selection and mutation

Online lectures

• Common descent (11:52)
• Natural selection (14:57)
• Evidence for evolution (part 1) (9:34)
• Evidence for evolution (part 2) (20:54)
• Population growth and selection (18:13)

Course material

• Lecture notes
• Slides, week 1

Computer exercise

• Population Growth, Fitness, and Selection

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Week 2 (February 10): Neutral mutations and genetic drift. Tree reconstruction by parsimony

Online lectures

• Neutral Theory of Molecular Evolution (11:28)
• Genetic Drift (9:35)
• Trees: Terminology and Representation (9:41)
• Homology and Homoplasy (9:07)
• Maximum Parsimony (7:48)
• The Fitch Algorithm (10:31)
• Searching Tree Space (14:01)

Course material

• Slides, week 2

Computer exercise

• Phylogenetic Analysis using Parsimony

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Week 3+4 (February 17+24): Mini project 1

Building a tree from scratch: What are the closest relatives of whales?

The mini project should be submitted and assessed via the peergrade.io interface.

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Week 5 (March 2): Consensus trees. Distance matrix methods

Online lectures

• Consensus Trees (16:27)
• Distance Matrix Methods, part 1 (6:07)
• Distance Matrix Methods, part 2 (22:28)
• Neighbour Joining (15:28)

Course material

• Handout exercise: Consensus Trees
• Handout exercise: Distance Matrix Methods
• Slides, week 5

Computer exercises

• Consensus Trees
• Distance Matrix Methods

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Week 6 (March 9): Models of sequence evolution. Likelihood methods

Online lectures

• Models of evolution (28:48)
• Maximum likelihood (22:06)
• Ancestral reconstruction (10:45)

Course material

• Handout exercise: Real, Observed, and Expected Change
• Handout exercise: Computation of Likelihood
• Slides, week 6

Computer exercises

• Models of Evolution
• Maximum Likelihood

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Week 9 (April 6): Bayesian inference of phylogeny

Online lectures

• Bayesian Inference (23:48)
• Markov chain Monte Carlo (19:54)

Course material

• Handout exercise: Bayesian estimation of model parameter value
• Slides, week 9
• Background reading: "An Introduction to Bayesian Statistics Without Using Equations"
• Background reading: "What is Bayesian statistics?"
• Background reading: "Bayesian computation: a statistical revolution"

Computer exercise

• Bayesian Phylogeny

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Week 10 (April 13): Testing hypotheses in a phylogenetic context

Online lectures

• Model selection, part 1 (15:19)
• Model selection, part 2 (17:20)
• Introduction to exercise (15:24)

Course material

• Slides, week 10

Computer exercise

• Model selection

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Old exam sets

• Mini project exam
• Exam 2004 (Answers)
• Exam 2005
• Exam 2006
• Exam 2007
• Exam 2008
• Exam 2009 (Answers)
• Exam 2015 (Answers)