Last modified: 31 May 2022 13:05
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 showcase the applications of different sequencing approaches and outlining how experimental work in this discipline is designed, executed and analysed. You will fully appreciate the great power of “omics” approaches in the context of a continuously evolving technological landscape.
| Study Type | Undergraduate | Level | 3 |
|---|---|---|---|
| Term | First Term | 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 them 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 – Microbiomes and environmental DNA
theme 2 – Population and speciation genomics
theme 3 – Functional genomics (transcriptomics and epigenetics)
theme 4 – Genome editing and in vivo testing
Finally, in the last week of the course we will discuss how to perform successful research in Ecological Genomics, including writing papers and designing project ideas.
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 explore further 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, a group discussion 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 simple test that you will complete at the end of the three practicals and will represent 30% of your final mark. In the group discussion you will be asked to present as a group the main findings of a paper in Ecological Genomics and you will be asked to assess the contribution of your team-members to the discussion: 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. You will be guided on how to prepare an essay of this kind during two tutorial sessions that will run during the course and on the occasion of the group discussion. Your essay will count 50% of your final grade.
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 two tutorial sessions on the topic and the group discussion. 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 complete a MCQ exam after all three practicals will be 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 exam during 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 work in group and 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 within each group will be asked to assess the contribution of the other team members. Duration: 1 hour |
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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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