Semester of Instruction
Autumn. The course runs only if enough students enrol.
Objectives and Content
The course provides a theoretical introduction to phylogenetic methods with topics that deal with different data types, characteristics of phylogenetic trees, models of evolutionary change, phylogenetic signal, model testing, parsimony, "likelihood, Bayesian methods, character reconstruction and phylogenetic hypothesis testing. Through practical exercises the student will gain experience with some of the most frequently used software application in phylogenetic research, including the Paup *, MrBayes and BEAST. Participants will learn to prepare their data, explore the characteristics of data, to perform various forms of tree search and how to present their results with various graphics programs.
The course aims to enable students to be able to reproduce key parts of a phylogenetic analysis of a given research publication and to evaluate results and conclusions of such work. Having completed the course, a student is expected to be able to prepare and perform phylogenetic analysis by:
- using appropriate software to align and compile DNA sequence data
finding and using relevant "Gene Bank" information about homologous DNA sequences
- finding the reading frame for a protein coding gene with a relevant codon table
- concatenating different data sets in one file and defining different partitions of data
- writing command files to include / exclude parts of the data in various operations
- finding the best evolutionary models for different data sets and defining these models for use in the applied computer program
- calculating the tree length and the "likelihood" of a given phylogenetic tree
- using optimal methods for tree search with parsimony and "likelihood"
- applying Bayesian methods to search for tree topology, calculation of the clade probability, branch lengths, and parameter values ¿¿for a given model
using different molecular clocks
- applying various digital graphic formats of phylogenetic trees for publication
- demonstrating a good understanding of how different phylogenetic tree structures are interpreted as signatures of different evolutionary processes
Required Previous Knowledge
Bachelor degree in Biology or the equivalent
The grading scale used is A to F. Grade A is the highest passing grade in the grading scale, grade F is a fail.
Type of assessment: Portfolio assesment
- Withdrawal deadline