Phylogenetic Methods

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 students will gain experience with some of the most frequently used software applications in phylogenetic research. Students will learn to prepare their data and explore its characteristics. They will learn to actively assess alternative methods strengths and weakness and how to design and carry out phylogenetic and comparative studies including various forms of tree search and comparative analyses. Further, students will learn how to present their results with various graphics programs. Finally, students will actively apply learned skills to analyze a dataset, interpret the results and write a comprehensive scientific report.

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

Autumn.

This course has a limited capacity, enrolment is based on application. The application deadline is Wednesday in week 33 for the autumn semester. Please see this page for more information. You will receive confirmation of whether you received a seat in Studentweb no later than Monday the week after the deadline.

It is compulsory to attend the first lecture/orientation meeting, or you risk losing your seat. If you are unable to attend the first lecture, you must contact the Study Section (studie.bio@uib.no). The time of the first lecture/orientation meeting can be found in the schedule on the course website or on Mitt UiB.