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Information
| Code | BK034 |
| Name | Molecular Phylogenetic Analysis II |
| Term | 2024-2025 Academic Year |
| Term | Spring |
| Duration (T+A) | 2-2 (T-A) (17 Week) |
| ECTS | 6 ECTS |
| National Credit | 3 National Credit |
| Teaching Language | Türkçe |
| Level | Doktora Dersi |
| Type | Normal |
| Mode of study | Yüz Yüze Öğretim |
| Catalog Information Coordinator | Prof. Dr. SERDAR SATAR |
| Course Instructor |
1 |
Course Goal / Objective
he necessary sutructure for obtaining phylogenetic data; sampling sizes, cleaning the sequence, allign the sequences, and their analyze by using different programs (FinchTV, Mega 6.0, DnSp, Arlequin, MrBayes, etc.), methods of creating topologies in their own fields, distances between populations-proximity, analyzing important points in determining gene flow are the aim of the course
Course Content
Molecular phylogenetic analyzes performed by comparing DNA and protein sequences reflect all the information from the first ancestors of which the species began to form, and thus, molecular biology, including evolutionary processes, allows the calculation of molecular evolution rates such as the evolutionary relationships of species and helps us understand these processes better. Phylogenetic studies or inferences have become the routine of many studies at the molecular level. Molecular phylogenitic analyzes, where intense knowledge and statistical complexes and different methods are applied, can lead to the development of erroneous evolutionary hypotheses if not properly applied. For these reasons, it is the content of the course to obtain phylogenetic data in the course of Molecular Phylogenetic Analysis.
Course Precondition
To have taken the basic molecular course.
Resources
Internet resources and applications.
Notes
Nothing.
Course Learning Outcomes
| Order | Course Learning Outcomes |
|---|---|
| LO01 | Allign the DNA and Blast in NCBI |
| LO02 | Learning the programs which are used in molecular genetics |
| LO03 | Rewiev the program results |
| LO04 | Phylogenetic tree drawing |
| LO05 | Analyze of the related taxa which have a position other side of the fork |
Relation with Program Learning Outcome
| Order | Type | Program Learning Outcomes | Level |
|---|---|---|---|
| PLO01 | Bilgi - Kuramsal, Olgusal | Has knowledge on basic topics about general science, general agricultural engineering and plant production | 1 |
| PLO02 | Bilgi - Kuramsal, Olgusal | Knows the biology, ecology, systematics and control strategies of diseases, pests and weeds causing yield losses in plants | |
| PLO03 | Bilgi - Kuramsal, Olgusal | Knows the identification and the biology of the diseases and how to control diseases,pests and weeds causing yield losses in plants in practice. | 2 |
| PLO04 | Bilgi - Kuramsal, Olgusal | Comprehends the plant protection problems, gains the ability to solve the problems via scientific methods | 1 |
| PLO05 | Beceriler - Bilişsel, Uygulamalı | Obtains the skill to use a laboratory, analyzes and evaluates the results and prepares reports. | 4 |
| PLO06 | Bilgi - Kuramsal, Olgusal | Decides to the most useful control strategy to cope with the plant protection problems and gets them to be used correctly. | |
| PLO07 | Bilgi - Kuramsal, Olgusal | Has necessary knowledge to use the essential technologies, synthesizes them to prepare oral presentations. | 3 |
| PLO08 | Yetkinlikler - Alana Özgü Yetkinlik | Gains the ability to identify problems related to the field and to construct and use high-level scientific research methods in solving them. | |
| PLO09 | Yetkinlikler - Alana Özgü Yetkinlik | Being able to independently carry out a work or project that requires expertise in the field, develop new approaches for solving problems encountered in practice and produce solutions by taking responsibility. | |
| PLO10 | Yetkinlikler - Alana Özgü Yetkinlik | Gains the ability to identify problems related to the field and to construct and use high-level scientific research methods in solving them | |
| PLO11 | Yetkinlikler - Alana Özgü Yetkinlik | Can develop and deepen the knowledge in plant protection in general, in field of expertise in particular, gain the ability to carry out and have studies that will bring innovation to science and reach original results. | |
| PLO12 | Yetkinlikler - İletişim ve Sosyal Yetkinlik | He/she can defend his/her original inventions, opinions, approaches and suggestions in front of experts and discuss them by communicating effectively. | |
| PLO13 | Yetkinlikler - Bağımsız Çalışabilme ve Sorumluluk Alabilme Yetkinliği | Can associate Plant protection-related subjects with other fields of science, and effectively use the knowledge that requires expertise in the evaluation of new and complex ideas, events, and phenomena. | 2 |
| PLO14 | Yetkinlikler - Bağımsız Çalışabilme ve Sorumluluk Alabilme Yetkinliği | Scientific, technological, social and cultural advances in plant protection; can take active roles in creating an information society, solving problems with scientific methods and making decisions. | |
| PLO15 | Beceriler - Bilişsel, Uygulamalı | Can use the knowledge and experience in the field of Plant Protection to solve the problems encountered in the field of production, takes part in public and private organizations or provides consultancy services. | |
| PLO16 | Yetkinlikler - Alana Özgü Yetkinlik | Gains the ability to transform the results of research and projects into reports/thesis and to present and publish them in international meetings and journals. |
Week Plan
| Week | Topic | Preparation | Methods |
|---|---|---|---|
| 1 | Introduction the molecular filogenetics | Read the course notes and books | Öğretim Yöntemleri: Anlatım |
| 2 | Blasting the sequence from NCBI | Read the course notes and books | Öğretim Yöntemleri: Anlatım |
| 3 | Cleaning the sequence and its allign I | Read the course notes and books | Öğretim Yöntemleri: Anlatım |
| 4 | Cleaning the sequence and its allign II | Read the course notes and books | Öğretim Yöntemleri: Anlatım |
| 5 | Cleaning the sequence and its allign III | Read the course notes and books | Öğretim Yöntemleri: Anlatım |
| 6 | Calculation the population genetics values I | Read the course notes and books | Öğretim Yöntemleri: Anlatım |
| 7 | Calculation the population genetics values II | Read the course notes and books | Öğretim Yöntemleri: Anlatım |
| 8 | Mid-Term Exam | Read the course notes and books | Ölçme Yöntemleri: Ödev |
| 9 | Calculation the population genetics values III | Read the course notes and books | Öğretim Yöntemleri: Anlatım |
| 10 | AMOVA Analaysis of the molecular variance Arlequin | Read the course notes and books | Öğretim Yöntemleri: Anlatım |
| 11 | Phylogenetic tree I | Read the course notes and books | Öğretim Yöntemleri: Anlatım |
| 12 | Phylogenetic tree II | Read the course notes and books | Öğretim Yöntemleri: Anlatım |
| 13 | Phylogenetic tree III | Read the course notes and books | Öğretim Yöntemleri: Anlatım |
| 14 | Phylogenetic tree IV | Read the course notes and books | Öğretim Yöntemleri: Anlatım |
| 15 | Discussion about evolutionary relationships of Phylogenetic tree | Read the course notes and books | Öğretim Yöntemleri: Anlatım |
| 16 | Term Exams | Read the course notes and books | Ölçme Yöntemleri: Sözlü Sınav |
| 17 | Term Exams | Read the course notes and books | Ölçme Yöntemleri: Sözlü Sınav |
Student Workload - ECTS
| Works | Number | Time (Hour) | Workload (Hour) |
|---|---|---|---|
| Course Related Works | |||
| Class Time (Exam weeks are excluded) | 14 | 4 | 56 |
| Out of Class Study (Preliminary Work, Practice) | 14 | 4 | 56 |
| Assesment Related Works | |||
| Homeworks, Projects, Others | 1 | 2 | 2 |
| Mid-term Exams (Written, Oral, etc.) | 1 | 12 | 12 |
| Final Exam | 1 | 28 | 28 |
| Total Workload (Hour) | 154 | ||
| Total Workload / 25 (h) | 6,16 | ||
| ECTS | 6 ECTS | ||