Practical course on phylogenetic analysis, spring 2008

Lecturer

dos. Sirkka-Liisa Varvio

Scope

6-8 cu.

Type

Advanced studies.

Prerequisites

For the optional practical work you should be familiar with sequence databases, BLASTing etc., and aligning sequences

Lectures

Period IV, Monday 14-16 in room C124, Tuesday 14-16 in room B120,

First lecture Monday 10.3,

Outline of the course

Lectures (handouts), three review papers to be read for the examination, seven home-exercises, of which four must be resolved and returned 28. April (the answers will be send by e-mail on Thursday 2. May), resolving all seven exercises gives an additional 1 op

• 10.3
   A short expedition to sequence databases, how to find and collect sequences, to define a working plan, to align them and build up own databases which form the basis and input for phylogeny programs. Introduction to the vast constellation of phylogeny programs, of which the free PHYLIP, MrBayes, and MEGA packages are recommended for own practical work during (or after) this course.

• 17-18.3
   (Handout 1) Methods of tree reconstruction, markov process and parametrization of the problem, bootstrapping as tool for confidence, modelling evolutionary change in nucleotide sequences, phylogenetic trees: basic concepts and terminology, rooted and unrooted trees, reconstructing histories of character change, species vs. gene phylogenies.
   (Handout 2) Phylogenetic inference: the parsimony method and philosophy.

• 31.3-1.4
   Examples from literature, utilization of phylogenetic inference for tracing the origins, histories, events, etc. in viruses and animals.
   (Handout 3) Virus phylogenies, phylodynamics.

• 7-8.4
   (Handout 4) Phylogenetic inference: maximum likelihood methods.

• 14-15.4
   (Handout 5) Bayesian inference of phylogenies.
  (Handout 6)Distance matrix methods for phylogenetic trees. Synonymous and non-synonymous substitutions and the evolutionary path method.

• 21-22.4
   (Handout 7) Rates and patterns of nucleotide substitution, evolutionary rates.
   (Handout 8) Positive selection, the PAML program package. Biased phylogenetic tree branch lengths and sites. Examples from literature, human genes, integrating phylogenetic inference, trees and character evolution, picking up positive selection from human genome databases.

• 28.4
   (Handout 9) Network phylogenies, bacteria as examples.

• 5.5
   Examination, 16-18 in room C124