Bi6447 Evoluční analýzy

Faculty of Science
Autumn 2012
Extent and Intensity
2/1. 3 credit(s) (fasci plus compl plus > 4). Type of Completion: zk (examination).
Teacher(s)
doc. Mgr. Natália Martínková, Ph.D. (lecturer)
prof. RNDr. Miloš Macholán, CSc. (lecturer)
prof. Mgr. et Mgr. Josef Bryja, Ph.D. (lecturer)
Guaranteed by
prof. RNDr. Ladislav Dušek, Ph.D.
RECETOX – Faculty of Science
Contact Person: doc. Mgr. Natália Martínková, Ph.D.
Supplier department: RECETOX – Faculty of Science
Timetable
Fri 9:00–11:50 F01B1/709; and Fri 21. 9. 9:00–11:50 B11/235
Prerequisites (in Czech)
Studenti musí mít základní znalosti z evoluční biologie a molekulární genetiky. Doporučuje se absolvovat Bi0999 Molekulární ekologie nebo Bi7492 Analýza sekvencí DNA. Část studijních materiálů je v angličtině.
Course Enrolment Limitations
The course is offered to students of any study field.
Course objectives
After completing the course, the student should be able to:
- analyze genetic data at individual and population level;
- formulate a hypothesis and test it;
- design an analytical workflow to test the hypothesiss;
- assess validity of the model;
- interpret results of evolutionary analyses.
Syllabus
  • The exact composition of the course changes according to which modules students choose upon applying for the course. The modules are chosen using the ROPOT system in the IS. Modules will be included in the course according to the students' choice up to the capacity of the semester.
  • 1. Phylogeny reconstruction (3 weeks) – alignment, substitution model, parsimony networks, maximum likelihood, Bayesian inference.
  • 2. Molekular dating (2 weeks) – mutation rate, detection of temporal signal in DNA sequence data, branch length transformation, Bayesian dating, coalescent dating.
  • 3. Spatial structure in populations (2 weeks) – spatially explicit models of population structure, Bayesian analysis of spatial structure, MCMC.
  • 4. Selection (1 week) – codon-based models, analysis of population structure comparing neutral markers and markers under selection.
  • 5. Population genetics (3 weeks) – detection of Hardy-Weinberg equillibrium, linkage disequilibrium, estimation of effective population size, genetic diversity indices, gene-flow, bottleneck detection.
  • 6. Whole-genome sequencing (2 weeks) – flowgram analysis, quantification of polymorphism.
  • 7. Co-divergence (1 week) – phylogenetic representation, comparison of genetic distance matrices.
  • 8. Hybrid zones (1 week) – cline detection.
Teaching methods
Lectures, discussion, in-class data analysis.
Assessment methods
Short tests after each module, final project based on student's design, verbal interpretation of the project for the final exam, final written test. Modules that the student chose will be weighed in the final assessment.
Language of instruction
Czech
Further Comments
Study Materials
The course is taught annually.
The course is also listed under the following terms Autumn 2013.
  • Enrolment Statistics (Autumn 2012, recent)
  • Permalink: https://is.muni.cz/course/sci/autumn2012/Bi6447