Exercises contents for 2024 Autumn Evolutionary Thinking course, Aarhus University
Bjarke Meyer Pedersen bjarke@birc.au.dk
Janek Sendrowski sendrowski.janek@birc.au.dk
Special Thanks to Moisès Coll Macià who structured the exercise materials and Jilong Ma from whom I forked (stole) the repository.
Session 1 Reading the Tree and Installing MEGA
Short Intro
Basic concepts in reading phylogeny trees.
Terminology
Session 2 MEGA exercises - Retrieve Sequences, Alignments, and Distance Matrix
Short review on alignments algorithms
Distance matrix, how do we define "distance"
Session 1 Substituion models
Observed pairwise difference and substitutions.
Jukes and Cantor's model and Kimura's model
Paper Discussion: Modeltest: testing the model of DNA substitution
Session 2 MEGA exercises - choosing substitution model and building phylogeny trees.
Distance based phylogeny tree building algorithms - UPGMA and NJ
Finding the best fitted substitution model using MEGA
Building your own phylogeny tree using MEGA.
- Maximum likelihood
- Maximum Parsimony
- Distance based methods
Session 1 Molecular clock - dates the time since divergence
How does molecular clock work ?
Calibraton of molecular clock.
Assumptions of molecular clock.
Relaxation for the assumptioms.
Session 2 Handin 1 - Phylogeny Trees
Working on handin 1
Session 1 Paper Discussion: HIV transmission in dental practice
Review and practice on the phylogenetics from previous weeks.
Session 1 Basis of Population Genetics
Terminology in Population Genetics
Hardy-Weinberg Equilibrium
Wright-Fisher model and Genetic Drift
Session 2 Simulations of Wright-Fisher model and coalescence
R exercises
Coalescence Theory
Coalescence time and exponential distribution
Genetic Drift
Genetic drift and population size
Session 1 Population Subdivision, Demography Inference, LD
Session 1 Selection
Vialility difference and selection coefficient
Type of selections
Trajectories of mutation under selection
Genetic hitchhiking and selection sweep
Methods of selection detection
Session 2 Testing for selection using dn/ds
Paper discussion on selection
HAND-IN II
Session 2 Work on hand-in II
Paper discussion on Gene duplication
MEGAX and gene duplication
Session 2 MEGAX exercise
Paper discussion on the Y-chromosome
R exercise and data from Wednesdays paper by Skov L. Et al.
Session 2 R exercise
Paper discussion on Phylogenetic incongruences
MEGAX and Incongruences
Session 2 MEGAX exercise
Paper discussion on Ancient Selection
R exercise and the infamous PCA
Session 2 R exercise
Hand-in-III Hand-in III
Hand-in III correction
Evaluation and talk about the entire semester (maybe even cake)