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| Course Description |
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| Course Name |
: |
Phylogenetic Analysis |
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| Course Code |
: |
BT-528 |
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| Course Type |
: |
Optional |
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| Level of Course |
: |
Second Cycle |
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| Year of Study |
: |
1 |
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| Course Semester |
: |
Spring (16 Weeks) |
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| ECTS |
: |
6 |
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| Name of Lecturer(s) |
: |
Prof.Dr. HAKAN ÖZKAN
Prof.Dr. SALİH KAFKAS
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| Learning Outcomes of the Course |
: |
Knows DNA markers and how to evaluate them
Knows phylogenetic analysis softwares
Knows parsimony analysis
Knows UPGMA and neighbor joining methods
Knows how to get denrograms and evaluate the data
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| Mode of Delivery |
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Face-to-Face |
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| Prerequisites and Co-Prerequisites |
: |
None |
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| Recommended Optional Programme Components |
: |
None |
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| Aim(s) of Course |
: |
To teach methods in phylogenetic analysis and to evaluate the data |
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| Course Contents |
: |
Morphological markers and scoring, DNA markers and scoring, typing data into computer, using PAUP software, using NTSysPc software, Determination of genetic distance and genetic similarity between plants, Parsimony analysis and Genetic distance method, Analysis of Neighbor joining and UPGMA, Phylogenetic analysis, Evaluating the results and presentation |
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| Language of Instruction |
: |
Turkish |
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| Work Place |
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Classrooms and Molecular Genetic Laboratory of Department of Horticulture, Faculty of Agriculture, University of Cukurova |
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Course Outline /Schedule (Weekly) Planned Learning Activities |
| Week | Subject | Student's Preliminary Work | Learning Activities and Teaching Methods |
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1 |
Morphological markers and scoring |
Reading text notes |
Text notes and related book chapters |
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2 |
DNA markers and scoring |
Reading text notes |
Text notes and related book chapters |
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3 |
DNA markers and scoring |
Reading text notes |
Text notes and related book chapters |
|
4 |
typing data into computer |
Reading text notes |
Text notes and related book chapters |
|
5 |
using PAUP software |
Reading text notes |
Text notes and related book chapters |
|
6 |
using PAUP software |
Reading text notes |
Text notes and related book chapters |
|
7 |
using NTSysPc software |
Reading text notes |
Text notes and related book chapters |
|
8 |
using NTSysPc software |
Reading text notes |
Text notes and related book chapters |
|
9 |
Mid-Term exam |
Reading text notes |
An exam from studied subjects untill the week of exam |
|
10 |
Determination of genetic distance and genetic similarity between plants |
Reading text notes |
Text notes and related book chapters |
|
11 |
Parsimony analysis and Genetic distance method |
Reading text notes |
Text notes and related book chapters |
|
12 |
Analysis of Neighbor joining and UPGMA, |
Reading text notes |
Text notes and related book chapters |
|
13 |
Phylogenetic analysis, Evaluating the results and presentation |
Reading text notes |
Text notes and related book chapters |
|
14 |
Phylogenetic analysis, Evaluating the results and presentation |
Reading text notes |
Text notes and related book chapters |
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15 |
Phylogenetic analysis, Evaluating the results and presentation |
Reading text notes |
Text notes and related book chapters |
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16/17 |
Final Exam |
Reading text notes |
Final exam from all the studied subjects |
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Required Course Resources |
| Resource Type | Resource Name |
| Recommended Course Material(s) |
 Molecular Markers in Plant Genetics and Biotechnology (D. Vienne)
Plant Genotyping: The DNA Fingerprinting of Plants (R.J. Henry)
Molecular Evoılution and Phylogenetics (M. Nei and S. Kumar)
Phylogenetic Trees Made Easy (B.G. Hall)
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| |
| Required Course Material(s) | |
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Assessment Methods and Assessment Criteria |
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Semester/Year Assessments |
Number |
Contribution Percentage |
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Mid-term Exams (Written, Oral, etc.) |
1 |
60 |
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Homeworks/Projects/Others |
3 |
40 |
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Total |
100 |
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Rate of Semester/Year Assessments to Success |
40 |
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Final Assessments
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100 |
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Rate of Final Assessments to Success
|
60 |
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Total |
100 |
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| Contribution of the Course to Key Learning Outcomes |
| # | Key Learning Outcome | Contribution* |
|
1 |
Evaluates and directs his level of learning in the field of knowledge and skills with his expert level critically. |
5 |
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2 |
Transfers current developments in the field of his work, supporting them with quantitative and qualitative data, systematically to the area outside of the field, written, orally and visually. |
5 |
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3 |
Follows national and international publications and attends social interactions and scientific studies in international level, communicates in at least in one foreign language in order to share studies on international base. |
5 |
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4 |
Uses advanced information and communication technologies along with the required level of their computer software. |
5 |
|
5 |
Uses the knowledge in his field for problem solving and / or practical skills in interdisciplinary studies. |
5 |
|
6 |
Improves common knowledge accumulation concerning the Biotechnology in the frame of basic theory and practices. |
5 |
|
7 |
Is aware of scientific, ethical and social values and handles research process with this frame. |
4 |
|
8 |
Handles theories, hypothesis, opinions in the field of Biotechnology with an objective sceptic, logical, analytical manner and evaluates them in critical point of view. |
3 |
|
9 |
Gains comprehensive information about natural and applied sciences and its limits with modern techniques and methods applied. |
4 |
|
10 |
Improves and increases the knowledge to an expert level in the field of biotechnology |
5 |
|
11 |
Understands the interdisciplinary interaction associated with biotechnology. |
5 |
|
12 |
Integrates and interprets the knowledge from different disciplines by his expertrise in biology and generate new information |
5 |
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13 |
Analizes the problems encountered in the field of research methods. |
4 |
|
14 |
Carries out a study requiring expertise in the field independently. |
5 |
|
15 |
Developes new strategic approaches and takes resposibility for analitical solutions for unpredictable complicated problems encountered in applications related to biotechnology. |
4 |
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16 |
Demonstrates leadership in the required environment to solve problems associated with biotechnology. |
4 |
| * Contribution levels are between 0 (not) and 5 (maximum). |
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| Student Workload - ECTS |
| Works | Number | Time (Hour) | Total Workload (Hour) |
| Course Related Works |
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Class Time (Exam weeks are excluded) |
14 |
4 |
56 |
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Out of Class Study (Preliminary Work, Practice) |
13 |
2 |
26 |
| Assesment Related Works |
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Homeworks, Projects, Others |
3 |
10 |
30 |
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Mid-term Exams (Written, Oral, etc.) |
1 |
14 |
14 |
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Final Exam |
1 |
14 |
14 |
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Total Workload: | 140 |
| Total Workload / 25 (h): | 5.6 |
| ECTS Credit: | 6 |
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