COURSE UNIT TITLE

: MOLECULAR PHYLOGENETIC

DEGREE PROGRAMMES

Description of Individual Course Units

Course Unit Code Course Unit Title Type Of Course D U L ECTS
BIY 4120 MOLECULAR PHYLOGENETIC ELECTIVE 2 2 0 5

Offered By

Biology

Level of Course Unit

First Cycle Programmes (Bachelor's Degree)

Course Coordinator

ASSOCIATE PROFESSOR KAMIL CANDAN

Offered to

Biology

Course Objective

To reveal the relationships between species by following the changes at molecular level. It also aims to determine the extent of evolutionary change, and to reveal evolutionary patterns between genetic lineages.

Learning Outcomes of the Course Unit

1   Understanding evolutionary changes at the molecular level
2   Understanding the basic features of molecular data sets
3   Understanding the logic of phylogenetic inference
4   To create tree topology with phylogenetic analysis methods
5   Recognize gene and species tree analysis
6   To be able to calculate the divergence times of genetic lineages
7   To be able to follow the molecular traces of basic evolutionary patterns

Mode of Delivery

Face -to- Face

Prerequisites and Co-requisites

None

Recomended Optional Programme Components

None

Course Contents

Week Subject Description
1 Definition and scope of molecular phylogenetics
2 Basic concepts of molecular evolution
3 Basic concepts of molecular evolution
4 Sequence databases and creating data sets
5 Multiple sequence alignment and preparation for analysis
6 Selecting models of evolution
7 Detection of genetic distances
8 Overview
9 Phylogenetic approaches: Neighbor-Joining, Maximum Likelihood
10 Phylogenetic approaches: Maximum Parsimony, Bayesian Inference
11 Testing credibility of tree topologies
12 Species delimitation analysis
13 Molecular clock analysis
14 Exploring complex evolutionary relationships with networks

Recomended or Required Reading

Lemey P., Salemi M., and Vandamme A. 2009, The Phylogenetic Handbook, Cambridge University Press.
Felsenstein F. 2004, Inferring Phylogenies, Sinauer Associates, Inc.
Hall B.G., 2011, Phylogenetic Trees Made Easy: A How-To Manual, Sinauer Associates, Inc.
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 VZ Vize
2 FN Final
3 BNS BNS VZ * 0.40 + FN * 0.60
4 BUT Bütünleme Notu
5 BBN Bütünleme Sonu Başarı Notu VZ * 0.40 + BUT * 0.60


Further Notes About Assessment Methods

None

Assessment Criteria

mid-term and final exams

Language of Instruction

Turkish

Course Policies and Rules

Attendance to at least 70% for the lectures is an essential requirement of this course and is the responsibility of the student. It is necessary that attendance to the lecture delivery must be on time. Any unethical behavior that occurs either in presentations or in exams will be dealt with as outlined in school policy. You can find the undergraduate policy at http://web.deu.edu.tr/fen

Contact Details for the Lecturer(s)

cetin.ilgaz@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 4 56
Preparation for midterm exam 1 6 6
Preparation for final exam 1 10 10
Final 1 3 3
Midterm 1 2 2
TOTAL WORKLOAD (hours) 133

Contribution of Learning Outcomes to Programme Outcomes

PO/LOPO.1PO.2PO.3PO.4PO.5PO.6PO.7PO.8PO.9PO.10PO.11PO.12PO.13PO.14
LO.154345
LO.244544
LO.354544
LO.44554454
LO.54554454
LO.64554454
LO.754344454

CONTACT INFORMATION
Dokuz Eylül Üniversitesi Cumhuriyet Bulvarı No: 144 35210 Alsancak / İZMİR
Phone: +90(232) 412 12 12 - Fax: +90 (232) 464 81 35

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