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BI3312: ECOLOGICAL GENOMICS (2024-2025)

Last modified: 23 Jul 2024 11:04


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 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. 

Course Details

Study Type Undergraduate Level 3
Term First Term 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?

  • Either Programme Level 3 or Programme Level 4
  • Any Undergraduate Programme (Studied)
  • Either Programme Level 3 or ZO3011 Animal Evolution and Biodiversity (Passed)
  • 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)

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 familiarize 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: these will be further explored in a series of three practicals that will focus on each one of these aspects.
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.

By the end of the course students should have:

  •  Understanding of what type of questions can be asked in Ecological Genomics;
  • Understanding of how an experiment in Ecological Genomics is performed;
  • Ability to isolate microbial DNA from environmental samples that is suitable for sequencing (this will be the focus of the first practical);
  • Familiarity with a typical bioinformatic pipeline to analyse environmental genomic data (this will be the core of the second practical);
  • Experience with integrating multiple tools for the analysis of typical outputs of “omics” approaches (this will be the subject of the third practical);
  • Ability to critically assess a piece of research in Ecological Genomics.

Taught topics covered include:
Genomics in Microbial Ecology– Population and speciation genomics– Neurogenomics and behavioural plasticity
Ecological epigenomics
Post-genomics and gene function

 

 

Associated Costs

DescriptionValue
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.23.0000

Contact Teaching Time

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

Teaching Breakdown

More Information about Week Numbers


Details, including assessments, may be subject to change until 30 August 2024 for 1st term courses and 20 December 2024 for 2nd term courses.

Summative Assessments

Class Test - Multiple Choice Questions

Assessment Type Summative Weighting 30
Assessment Weeks 17 Feedback Weeks

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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.

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

Critical Essay

Assessment Type Summative Weighting 40
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 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.

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

Oral Presentation: Individual

Assessment Type Summative Weighting 30
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 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.

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
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
ConceptualUnderstandUnderstand what type of questions can be asked in the field of Ecological Genomics and how they can be formulated
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

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