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 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 analyse a dataset, interpret the results and write a comprehensive report.
Learning Outcomes
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
- 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
Each student is expected to bring a laptop with preinstalled software (detailed instructions will be sent before the course to the admitted students).
Credits. 5 ECTS for a passed take-home exam (to be distribute electronically in early November 2023). Participants will receive a certificate issued by ForBio.
The course is taught by Dimitar Dimitrov (University of Bergen), invited teachers will be announced later.
Quota
The course is organized jointly by ForBio and the University of Bergen (UiB). Total number of students 20. Maximum 10 students can apply via ForBio. UiB students must apply for a place in the BIO332 course through UiB. ForBio applicants will be evaluated based on the registration form, which includes a paragraph for motivation and importance of the course for their study/work.
Financial support: ForBio has limited funds to support a number selected PhD or MSc students affiliated with a Norwegian institution to cover travel and/or accommodation expenses during the course. Please note that no automatic coverage will be provided this year based on Norwegian affiliation. The decision will be made based on the information provided in the application form and provided funding may cover only part of the course-associate expenses.
Application deadline: September 6th 2024
Please apply here.
Contact Dimitar Dimitrov (Dimitar.Dimitrov@uib.no) for questions about the content of the course or Nataliya Budaeva (Nataliya.Budaeva@uib.no) for more information about ForBio and course logistics.