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Description of Individual Course Units

Course Unit Code Course Unit Title Type Of Course D U L ECTS BYL 5050 MOLECULAR SYSTEMATICS ELECTIVE 2 2 0 6

Offered By

Graduate School of Natural and Applied Sciences

Level of Course Unit

Second Cycle Programmes (Master's Degree)

Course Coordinator

ASSOCIATE PROFESSOR KAMIL CANDAN

Offered to

Ph.D. in Biology Biology

Course Objective

It aims to teach the identification of genetic lineages, revealing inter-species relationships, and patterns of speciation through the detection of genetic lineages.

Learning Outcomes of the Course Unit

1   Grasping systematic arrangement based on molecular markers. 2   Learning the logic of phylogenetic inference. 3   Recognizing molecular markers. 4   Processing DNA datasets using bioinformatics methods. 5   Applying phylogenetic analysis methods. 6   Tracking the evolutionary patterns of species.

Mode of Delivery

Face -to- Face

Prerequisites and Co-requisites

None

Recomended Optional Programme Components

None

Course Contents

Week Subject Description 1 Fundamental principles of molecular systematics 2 Structure and organization of the genome 3 Molecular markers 4 DNA sequencing techniques 5 Generation and editing of DNA data files 6 Detection of nucleotide substitution models 7 Calculation of genetic distances 8 Midterm exam 9 Phylogenetic analyses: Neighbor-Joining, Maximum Likelihood 10 Phylogenetic analyses: Maximum Parsimony, Bayesian Inference 11 Species delimitation analyses 12 Construction of haplotype distributions through network analysis 13 Calculation of species divergence times 14 Molecular systematics of reptile species in Türkiye

Recomended or Required Reading

- Yang Z. 2014, Molecular Evolution: A Statistical Approach, Oxford University Press - Lemey P., Salemi M., and Vandamme A. 2009, The Phylogenetic Handbook, Cambridge University Press. -Scientific articles

Planned Learning Activities and Teaching Methods

The course will consist of lectures, class discussions, presentations.

Assessment Methods

SORTING NUMBER SHORT CODE LONG CODE FORMULA 1 MTE MIDTERM EXAM 2 FIN FINAL EXAM 3 FCG FINAL COURSE GRADE MTE * 0.40 + FIN * 0.60 4 RST RESIT 5 FCGR FINAL COURSE GRADE (RESIT) MTE * 0.40 + RST * 0.60

Further Notes About Assessment Methods

None

Assessment Criteria

mid-term and final exams

Language of Instruction

Turkish

Course Policies and Rules

To be announced.

Contact Details for the Lecturer(s)

kamil.candan@deu.edu.tr

Office Hours

To be announced.

Work Placement(s)

None

Workload Calculation

Activities Number Time (hours) Total Work Load (hours) Lectures 14 2 28 Tutorials 14 2 28 Preparations before/after weekly lectures 14 2 28 Preparation for midterm exam 1 12 12 Preparation for final exam 1 17 17 Preparing assignments 6 6 36 Preparing presentations 1 6 6 Final 1 3 3 Midterm 1 2 2 TOTAL WORKLOAD (hours) 160

Contribution of Learning Outcomes to Programme Outcomes

PO/LO PO.1 PO.2 PO.3 PO.4 PO.5 PO.6 PO.7 PO.8 PO.9 PO.10 PO.11 PO.12 LO.1 5 5 5 4 5 3 4 5 5 LO.2 5 5 5 4 5 3 4 5 5 LO.3 5 5 5 4 5 3 4 5 5 LO.4 5 5 5 4 5 3 4 5 5 LO.5 5 5 5 4 5 3 4 5 5 LO.6 5 5 5 4 5 3 4 5 5