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BI3312: ECOLOGICAL GENOMICS (2021-2022)

Last modified: 16 Sep 2021 12:55


Course Overview

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. 

Course Details

Study Type Undergraduate Level 3
Session First Sub Session Credit Points 15 credits (7.5 ECTS credits)
Campus Aberdeen Sustained Study No
Co-ordinators
  • Dr Fabio Manfredini

What courses & programmes must have been taken before this course?

  • Any Undergraduate Programme (Studied)
  • ()
  • One of BSc Biology or BSc Conservation Biology or BSc Zoology or BSc Marine Biology or Bachelor Of Science In Animal Behaviour And Welfare or BSc Animal Behaviour or BSc Behavioural Biology or MSci Biological Sciences or BSc Biological Sciences (Honours) or BSc Plant and Soil Sciences or BSc Ecology or BSc Environmental Science
  • One of BI2017 Genes and Evolution (Passed) or BI20M3 Molecular Biology of the Gene (Passed) or SM1501 The Cell (Passed)
  • Either Programme Level 3 or Programme Level 4

What other courses must be taken with this course?

None.

What courses cannot be taken with this course?

None.

Are there a limited number of places available?

No

Course Description

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.

 


In light of Covid-19 this information is indicative and may be subject to change.

Contact Teaching Time

Information on contact teaching time is available from the course guide.

Teaching Breakdown

  • 1 Science Laboratory during University week16
  • 1 Practical during University weeks 15, 17, 19
  • 2 Tutorials during University weeks 15, 17 - 20
  • 1 Tutorial during University weeks 16, 16

More Information about Week Numbers


In light of Covid-19 and the move to blended learning delivery the assessment information advertised for second half-session courses may be subject to change. All updates for second-half session courses will be actioned in advance of the second half-session teaching starting. Please check back regularly for updates.

Summative Assessments

Critical Essay

Assessment Type Summative Weighting 50
Assessment Weeks 18 Feedback Weeks

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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.

 

Learning Outcomes
Knowledge LevelThinking SkillOutcome
ProceduralAnalyseIntegrate multiple tools for bioinformatic analyses to process a typical dataset obtained with an “omic” approach
ProceduralUnderstandUnderstand how an experiment in Ecological Genomics is performed, from experimental design, to sample collection, molecular work, and analysis of the output
ReflectionCreateCritically assess a piece of research in Ecological Genomics, identify weaknesses and propose ideas to expand the research

Exam - Multiple Choice Questions

Assessment Type Summative Weighting 30
Assessment Weeks 17 Feedback Weeks

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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.

Learning Outcomes
Knowledge LevelThinking SkillOutcome
ProceduralAnalyseIntegrate multiple tools for bioinformatic analyses to process a typical dataset obtained with an “omic” approach
ProceduralApplyCarry out the isolation of microbial DNA from soil samples
ProceduralUnderstandUnderstand how an experiment in Ecological Genomics is performed, from experimental design, to sample collection, molecular work, and analysis of the output

Oral Presentation: Group

Assessment Type Summative Weighting 20
Assessment Weeks 16 Feedback Weeks

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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

Learning Outcomes
Knowledge LevelThinking SkillOutcome
ConceptualUnderstandUnderstand what type of questions can be asked in the field of Ecological Genomics and how they can be formulated
ProceduralUnderstandUnderstand how an experiment in Ecological Genomics is performed, from experimental design, to sample collection, molecular work, and analysis of the output
ReflectionCreateCritically assess a piece of research in Ecological Genomics, identify weaknesses and propose ideas to expand the research

Formative Assessment

There are no assessments for this course.

Resit Assessments

Resubmission of failed elements

Assessment Type Summative Weighting
Assessment Weeks Feedback Weeks

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Feedback

Resit the component of the coursework that was failed; pass grades from other components carried forward

Learning Outcomes
Knowledge LevelThinking SkillOutcome
Sorry, we don't have this information available just now. Please check the course guide on MyAberdeen or with the Course Coordinator

Course Learning Outcomes

Knowledge LevelThinking SkillOutcome
ProceduralApplyCarry out the isolation of microbial DNA from soil samples
ProceduralAnalyseIntegrate multiple tools for bioinformatic analyses to process a typical dataset obtained with an “omic” approach
ConceptualUnderstandUnderstand what type of questions can be asked in the field of Ecological Genomics and how they can be formulated
ReflectionCreateCritically assess a piece of research in Ecological Genomics, identify weaknesses and propose ideas to expand the research
ProceduralUnderstandUnderstand 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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