INTERNATIONAL BURCH UNIVERSITY
Graduate Study - Faculty of Engineering and Natural Sciences
Genetics and Bioengineering PhD
2015-2016

SYLLABUS
Code Name Level Year Semester
GBE 603 Phylogenetics Graduate 1 Spring
Status Number of ECTS Credits Class Hours Per Week Total Hours Per Semester Language
Area Elective 6 3 150 English

Instructor Assistant Coordinator
Serkan DOĞAN, Assist. Prof. Dr. Serkan Dogan Serkan DOĞAN, Assist. Prof. Dr.
[email protected] [email protected] no email

Phylogenetics is a modern-era area of science that is offered to our doctorate students as an elective course. The first goal of the course is to distinguish between basic terms: phylogenesis, phylogeny, and phylogenetics. The course is utilizing sequencing data to discover and analyze evolutionary relationships between species and populations. Furthermore, approximations of an evolutionary history of specific taxonomic groups are made according to sequence analyses. The ultimate goal of the course is to make the graduate student familiar with the theoretical and practical aspects of phylogenetic analysis.

COURSE OBJECTIVE
The cognitive, affective and behavioral objectives of this course are following:
• Introduction to the basics of bioinformatics needed to study phylogenetics.
• Explaining various software used for the study of phylogenetics.
• Teaching graduates to construct phylogenetic trees.

COURSE CONTENT
Week
Topic
  1. Basic concepts of molecular evolution
  2. Sequence databases and database searching
  3. Multiple sequence alignment
  4. Genetic distances and nucleotide substitution models
  5. Phylogenetic inference based on distance models
  6. Phylogenetic inference using maximum likelihood methods
  7. Bayesian phylogenetic analysis using MRBAYES
  8. MID-TERM EXAM
  9. Phylogeny inference based on parsimony and other methods using PAUP
  10. Phylogenetic analysis using protein sequences
  11. Selecting models of evolution
  12. Molecular clock analysis
  13. Testing tree topologies
  14. Natural selection and adaptation of molecular sequences
  15. Estimating selection pressures on alignment of coding sequences

LABORATORY/PRACTICE PLAN
Week
Topic

    TEACHING/ASSESSMENT
    Description
    • Interactive Lectures
    • Presentation
    • Discussions and group work
    Description (%)
    Method Quantity Percentage (%)
    Midterm Exam(s)130
    Presentation130
    Final Exam140
    Total: 100
    Learning outcomes
    • Illustrate the basics of sequence analysis needed for phylogenetic studies
    • Analyze phylogenetic trees
    • Create phylogenetic trees
    • Interpret phylogenetic trees
    • Apply knowledge of bioinformatics in phylogenetic research
    TEXTBOOK(S)
    • Lemey, P., Salemi, M. & Vandamme, A.-M. (2009). The phylogenetic handbook: A practical approach to phylogenetic analysis and hypothesis testing, 2nd ed. Cambridge, UK: Cambridge University Press.

    ECTS (Allocated based on student) WORKLOAD
    Activities Quantity Duration (Hour) Total Work Load
    Lecture (14 weeks x Lecture hours per week)15345
    Laboratory / Practice (14 weeks x Laboratory/Practice hours per week)15230
    Midterm Examination (1 week)122
    Final Examination(1 week)122
    Preparation for Midterm Examination11010
    Preparation for Final Examination12020
    Assignment / Homework/ Project12121
    Seminar / Presentation12020
    Total Workload: 150
    ECTS Credit (Total workload/25): 6