Last modified: 25 Oct 2022 14:40
Ecological Genomics is a young and dynamic field where ecology intersects with high-throughput sequencing technologies. This technological revolution has opened exciting potential to address long-standing problems in ecology and evolution from a genome-wide perspective. This course will explore the origins and the meaning of this field of research, and will showcase the applications of different approaches to analyse sequence data, outlining how experimental work in this discipline is designed and executed. You will fully appreciate the great power of “omics” approaches in the context of a continuously evolving technological landscape.
| Study Type | Undergraduate | Level | 3 |
|---|---|---|---|
| Session | First Sub Session | Credit Points | 15 credits (7.5 ECTS credits) |
| Campus | Aberdeen | Sustained Study | No |
| Co-ordinators |
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The course is structured so that you will be initially introduced to the field of Ecological Genomics during the first week of the course. In this general introduction you will familiarized with the discipline. We will discuss how we define it and how it quickly changed (and still changes) over time. We will also explore the common steps of an experimental approach in Ecological Genomics, starting from asking the right questions and correctly designing an experiment, and then moving to performing sampling in the field, processing samples in the lab, analysing high-throughput datasets and making sense of the output in preparation of a publication. Thereafter, you will be exposed to a range of different “omics” approaches across different themes, each of them running in a separate week for four weeks. Each theme will follow the same structure as in the general introduction for the specific approach considered, and will be presented by a member of the School of Biological Sciences who actively perform research in the field. The topics covered in each theme will be as follows:
theme 1 – Genomics in Microbial Ecology
theme 2 – Population and speciation genomics
theme 3 – Functional genomics (transcriptomics and epigenetics)
theme 4 – Post-genomics and gene function
There will be three practicals associated with the course, organized as follows:
1) the first practical will be executed in a science lab and you will learn how to isolate microbial DNA that is suitable for sequencing from environmental samples such as decaying leaf matter;
2) for the second practical you will be based in a computer lab and you will go through a typical bioinformatic pipeline to analyse environmental genomic data – similar to what you would obtain by sequencing the DNA extracted during the first practical;
3) the third practical will also be based in a computer lab and will give you a chance to further explore the typical output of one “omics” approach of your choice, among those covered in the course themes. You will work under the supervision of the instructor who coordinates the theme, and you will familiarize with the software and analytical approaches that are normally used to process that specific “omics” output.
Assessments comprise continuous assessments during each practical, an oral presentation and a final reflective report on a recent paper in Ecological Genomics that you will read and critically analyse. Your engagement with the practicals will be assessed with a MCQ test that you will complete at the end of the three practicals and will represent 30% of your final mark. In the oral presentation you will be asked to present the main findings of a paper in Ecological Genomics: this will represent 20% of your final mark. For the final assessment you will be asked to read a recent paper in Ecological Genomics and prepare an essay that critically analyses it. Your essay will count 50% of your final grade. You will be guided on how to prepare the oral presentation and the written essay during two tutorial sessions that will run during the course.
| Description | Value |
|---|---|
| Students should possess a Howie laboratory coat and safety glasses. Further details of requirements can be found on the course's MyAberdeen page. The cost listed here is approximate. | GBP 23.00 |
Information on contact teaching time is available from the course guide.
| Assessment Type | Summative | Weighting | 50 | |
|---|---|---|---|---|
| Assessment Weeks | 18 | Feedback Weeks | ||
| Feedback |
Students will be asked to read a paper in Ecological Genomics and to write a report that contains the following components: 1) a graphical abstract of the main results and the methods used in the study; 2) an assessment of the experimental pipeline adopted in the study with suggestions of possible alternatives; 3) a conclusion section indicating possible ways to move forward in the research described in the paper. They will be asked to use the knowledge acquired during the tutorial and the oral presentation. A range of 10 papers suggested by the course contributors at the beginning of the course will be available for the student to choose. |
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| Knowledge Level | Thinking Skill | Outcome |
|---|---|---|
| Procedural | Analyse | Integrate multiple tools for bioinformatic analyses to process a typical dataset obtained with an “omic” approach |
| Procedural | Understand | Understand how an experiment in Ecological Genomics is performed, from experimental design, to sample collection, molecular work, and analysis of the output |
| Reflection | Create | Critically assess a piece of research in Ecological Genomics, identify weaknesses and propose ideas to expand the research |
| Assessment Type | Summative | Weighting | 30 | |
|---|---|---|---|---|
| Assessment Weeks | 17 | Feedback Weeks | ||
| Feedback |
Students will be asked to engage with an MCQ exam after all three practicals have been completed. They will be tested on their understanding of the pipelines and tools used for each practical. They will be given a chance to practice the types of question asked in the MCQ after each practical. |
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| Knowledge Level | Thinking Skill | Outcome |
|---|---|---|
| Procedural | Analyse | Integrate multiple tools for bioinformatic analyses to process a typical dataset obtained with an “omic” approach |
| Procedural | Apply | Carry out the isolation of microbial DNA from soil samples |
| Procedural | Understand | Understand how an experiment in Ecological Genomics is performed, from experimental design, to sample collection, molecular work, and analysis of the output |
| Assessment Type | Summative | Weighting | 20 | |
|---|---|---|---|---|
| Assessment Weeks | 16 | Feedback Weeks | ||
| Feedback |
Students will critically analyse a paper in Ecological Genomics and associated datasets. They will be asked to present the main finding of the paper, the methods used and also ideas to trigger discussion about how the study could be improved/continued in the future. Students will engage in a tutorial showing how to present a paper and they will have a chance to practice their presentation in front of the class. |
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| Knowledge Level | Thinking Skill | Outcome |
|---|---|---|
| Conceptual | Understand | Understand what type of questions can be asked in the field of Ecological Genomics and how they can be formulated |
| Procedural | Understand | Understand how an experiment in Ecological Genomics is performed, from experimental design, to sample collection, molecular work, and analysis of the output |
| Reflection | Create | Critically assess a piece of research in Ecological Genomics, identify weaknesses and propose ideas to expand the research |
There are no assessments for this course.
| Assessment Type | Summative | Weighting | ||
|---|---|---|---|---|
| Assessment Weeks | Feedback Weeks | |||
| Feedback |
Resit the component of the coursework that was failed; pass grades from other components carried forward |
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| Knowledge Level | Thinking Skill | Outcome |
|---|---|---|
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| Knowledge Level | Thinking Skill | Outcome |
|---|---|---|
| Procedural | Apply | Carry out the isolation of microbial DNA from soil samples |
| Procedural | Analyse | Integrate multiple tools for bioinformatic analyses to process a typical dataset obtained with an “omic” approach |
| Conceptual | Understand | Understand what type of questions can be asked in the field of Ecological Genomics and how they can be formulated |
| Reflection | Create | Critically assess a piece of research in Ecological Genomics, identify weaknesses and propose ideas to expand the research |
| Procedural | Understand | Understand how an experiment in Ecological Genomics is performed, from experimental design, to sample collection, molecular work, and analysis of the output |
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