Teacher: Sirkka-Liisa Varvio 

Scope: 5-10 cr

Type: intermediate / advanced studies

Teaching: lectures and working in computer class

Teaching schedule: intensive teaching period in August, computer class C128, 12-16 in Thu 25.8, Fri 28.8, Mon 29.8, Wed 31.8, and additional times to be negotiated.
Assignments during the intensive period => 5 cr option of the course. Additional assignments/project after this period => another 5 cr.

Topics: The goal is to provide understanding of life through statistical and computational analyses of molecular information. Models of molecular evolution and phylogeny inference, distance matrix methods, maximum likelihood, bayesian and network inference. Past, or traditional, practice on phylogenetics has been to describe relationships among species within the disciplines systematics and taxonomy. Today the scope is much wider. Phylogenetics is used as a necessary tool in all kind of bioscience research questions: relationships among genes, gene families, alleles, cell lines, various genomic components, histories of populations, evolutionary and epidemiological dynamics of bacteria and viruses, etc.  Phylomics is the natural extension of genomics and metagenomics, phylotyping the current way of understanding ecosystems within and outside organisms (environments) and evolutionary thinking is a complementary framework to medical genetics. Statistical and computational approaches, based on predictions derived from population genetics theory, aim at dissecting neutral (stochastic) and selected (darwinian natural selection) components of genetic diversity.
Course assignments will be from human, animal, virus, bacteria data.

Prerequisites: At least intermediate level of probability and statistical inference courses. No familiarity with bio-studies expected as prerequisites.

Moodle-area

This is the area for exercise and assignment submissions, for request of help and all kind of questions and discussion.

Lecture material and literature

Lecture material (edited version added 28.8)

 _{e-books in HU-library}

•  _{Z Yang, Computational molecular evolution}
• _{P Lemey et al, The phylogenetic handbook}
• _{M Nei and S Kumar, Molecular evolution and phylogenetics}
• 
  

_{Articles of note}

• _{Short tutorial article}, _{Phylogenetics - Principles and practice}
• _{Original NJ-algorithm paper}
• _{Traditional and Bayesian phylogeny estimation}
•    
• _{Confidence limits on phylogenies}
  

Software and necessary links

• NCBI, NCBI BLAST

• Collection of phylogeny software
  • These programs have been installed in computer class C128 and you can also freely download them to your own computer. Note the manuals behind the links, as well as other tutorial material, inluding discussion areas:
    • 
      
      • MEGA7. This link goes to the most recent version (MEGA7). The computer class version is MEGA5, MEGA5 original paper

• 
  
  • 
    
    • 
      
      • mrBayes, Original MrBayes paper,  MCMCMC

• 
  
  • 
    
    • 
      
      • SplitsTree
      • Network
      • Clustal. This is not a phylogeny program (it makes so called guide trees), it is the the classical software for aligning sequences and useful for many purposes. Multiple sequence alignment.pdf

• 
  
  • 
    
    • 
      
      • DnaSP. This is not a phylogeny program but you may use it for some exercises.
  • You will also need this: MAFFT-server, for aligning sequences.
  • Link to choosing a model (note also model choice option in MEGA5)  Modeltest, This is useful, AIC
  •  

Exercises and assignments

• Exercise set 1 (mainly pen-and-paper -type exercises) and phylogeny Assignment 1 (computer work) are based on lecture and tutorial which will be given during Thu 25.8 and Fri 26.8 sessions.

• 
  
  • All students should perform these and submit solutions to Moodle on Sunday 11.9 at the latest.

• In addition to Exercise set 1 and Assignment 1, there are five alternative assignments (2-6 in the table below). You are supposed to select three out of them in order to get the 5 credit option. There is also the possibility to write three essays instead of these three computer assignments (or one computer assignment, two essays, two computer assignments, one essay).
  • Time schedule: You can work according your own time schedule during the I-teaching period (i.e. till 23.10). This means that you have a possibility to complete the course (5 cr) in two about weeks ---- in about two months. 
• You can choose: grade 1-5 or pass/fail. You can also choose to work as a group of 2-4 students. A group will get pass/fail, not a grade. In case you choose to work alone, you cannot replicate other students results, i.e. you must submit only your own results in your submissions. This does not mean that you cannot discuss with other students and ask for help from other students, of course you can! The results which you submit must represent your own performance. Essays cannot be group work, but it is possible to work as group for other assignments, and write the essays alone.

Essay topics 

 Instructions for writing essays: tba  

• _{mammals_1 mammals_2}
• _{virus_1, virus_2}
• _{bacteria_1, bacteria_2, lateral gene transfer_1, lateral_gene_transfer_2}
• _languages
• _{cancer_1, cancer_2, cancer_3, cancer_4, celltypes},
• _{history_1, history_2}
• _{Protein_evolution_1, Protein_evolution_2, Protein_evolution_3, Protein_evolution_4, Protein_evolution_5}
• _{metagenomics_methods, human_metagenomics_1, human_metagenomics_2},
• _{env_metagenomics_1, env_metagenomics_2}
• _{statistics_1, statistics_2, HMM_2}
• _...
• _...
• _...

Registration

Did you forget to register? What to do? 

Course feedback

Course feedback can be given at any point during the course. Click here.