Syllabus for Molecular Evolution and Phylogenetics

Molekylär evolution och fylogenianalys


  • 10 credits
  • Course code: 1MB446
  • Education cycle: Second cycle
  • Main field(s) of study and in-depth level: Technology A1F, Bioinformatics A1F
  • Grading system: Fail (U), Pass (3), Pass with credit (4), Pass with distinction (5)
  • Established: 2010-03-16
  • Established by: The Faculty Board of Science and Technology
  • Applies from: week 27, 2010
  • Entry requirements: 120 credits inclusive Methods in bioinformatics and genomics – experimental methods, Genome Biology
  • Responsible department: Biology Education Centre

Learning outcomes

The course will give the student knowledge about molecular evolutionary processes, knowledge and skills in phylogenetic analysis and how this can be used to study (molecular) evolution.

After the course, the student shall be able to

  • describe evolutionary process at the molecular level

  • apply molecular methods to study genetic variation within and between species

  • explain and justify different models of sequence evolution

  • explain and evaluate different phylogenetic optimality criteria, and select adequate criterion to solve a given problem

  • sketch and apply the process to do and evaluate a phylogenetic analysis , and explain the different steps

  • select and apply, for the problem area, existing software on a given biological problem


Mutational processes, evolution of mutation rates, evolution of DNA sequences, the molecular clock, selection and genetic drift on the molecular level, nucleotide composition, polymorphism and SNPs.

Phylogenetic trees and other models, optimality criteria for selecting phylogenetic hypothesis. Substitution models for DNA and other data types. Super trees, consensus trees, tree compatibility. Algorithms for evaluating the tree space; Markov Chain Monte Carlo, genetic algorithms. Evaluation of results from phylogentic analyses, phylogenetic dating.


Instruction will be given as lectures and computer assignments.


To pass the course it is required that all computer exercises equivalent to 4 credits and project assignment equivalent to 2 credits has been presented in writing and is passed. The theory part is examined by a written examination equivalent to 4 credits.

Reading list

Reading list

Applies from: week 01, 2012

  • Yang, Ziheng Computational molecular evolution

    Oxford: Oxford University Press, 2006

    Find in the library