Genomics & Evolution of Complex Traits (BIOL3350)

Course overview

This course will provide students with a foundation for understanding the genetic basis and evolution of traits that are influenced by both genetics and the environment. In many cases, these ‘complex’ traits are controlled by large numbers of genes and their genetic study requires a specialised approach. This course covers theory, methods, and applications of quantitative genetics. With a strong emphasis on phenotypic microevolution, the course will cover the evolution of complex traits, such as life histories, morphology, complex behaviours, and disease. The course centres around the study of two fundamental relationships; the genotype-phenotype map and the phenotype-fitness map. We cover the predictive theories for evolution by natural selection and the measurement of evolvability and constraints. Approaches for genetic dissection of complex traits including Quantitative Trait Locus (QTL) and Genome-wide Association Studies (GWAS) will be covered as well as specialised approaches for inferring causal relationships such as Mendelian Randomisation. Example topics include the evolution of life histories (e.g. ageing) and trade-offs, adaptive radiations, pleiotropy and its consequences, mutation and the maintenance of genetic variation. Case studies span natural variation in wild populations through to human disease. The human genetics module is delivered by leading human geneticists from UQ's Institute for Molecular Bioscience.

Only a very small fraction of traits are controlled by a single gene. Rather, the vast majority of traits are influenced by many different mutations in the genome residing within or around literally hundreds of genes. In many cases these so called ‘complex traits’ are the exact ones we need to understand for improving human health, developing productive crops and livestock, and understanding how species can mount evolutionary responses to environmental change.ﾠ This course introduces the field of complex trait genetics and genomics from both applied and evolutionary perspectives. We will help you to develop a deep understanding and practical skills in quantitative genetic analysis.ﾠ Thanks to an explosion of DNA sequence data, facilitated through the DNA sequencing revolution, many of the significant advances currently being made in human and evolutionary genetics are in this field and it is becoming increasingly important for geneticists to have training in this area. This course will build on and extend your genetic knowledge gained in Genetics (BIOL2202). As the field of complex trait genetics is of a statistical nature, we recommend students take at least second level statistics (BIOL2006). We have a very hands-on course structure, with only one formal lecture per week and the reminder of class time spent in interactive small group tutorial and lab sessions.

Course requirements

Assumed background

Students should have completed BIOL2006 and BIOL2202 before enrolling in this course.

Prerequisites

You'll need to complete the following courses before enrolling in this one:

BIOL2202 or BIOL2902

Recommended prerequisites

We recommend completing the following courses before enrolling in this one:

BIOL2006 or BIOL2106, BIOL2201

Recommended companion or co-requisite courses

We recommend completing the following courses at the same time:

BIOL3380

Course staff

Timetable

The timetable for this course is available on the UQ Public Timetable.

Aims and outcomes

This course aims to provide a foundation for understanding the genetics and evolution of traits affected by multiple genes and the environment. The emphasis will be on the genetics and evolution of complex phenotypes such as life histories, performances including behaviour, and human diseases. We cover genetic analysis from basic variance components through to the genetic dissection of complex traits using Quantitative Trait Locus (QTL) and Genome-wide association studies (GWAS). Via a strong practical component, students will also acquire hands on skills with current techniques for the genetic analysis of complex traits.

Learning outcomes

After successfully completing this course you should be able to:

Assessment

Assessment summary

Assessment details

Mid Semester exam

• Identity Verified
• In-person

Mode

Written

Category

Examination

Weight

30%

Due date

28/08/2024

This exam will take place during the scheduled Workshop in Week 6

Other conditions

Student specific, Time limited.

See the conditions definitions

Task description

Exam details

Submission guidelines

Deferral or extension

You may be able to defer this exam.

Please refer to UQ guide for deferring exams

Major assignment

Mode

Written

Category

Paper/ Report/ Annotation

Weight

30%

Due date

10/10/2024 2:00 pm

Other conditions

Student specific.

See the conditions definitions

Task description

Submission guidelines

Report must be submitted via Turnitin

1. Access the Assessment folder on the course Blackboard site

2. Check that you have the correct file - the final version of your report.

3. Upload an electronic version through the assessment Turnitin site

Deferral or extension

You may be able to apply for an extension.

The maximum extension allowed is 7 days. Extensions are given in multiples of 24 hours.

Late submission

A penalty of 10% of the maximum possible mark will be deducted per 24 hours from time submission is due for up to 7 days. After 7 days, you will receive a mark of 0.

If you fail to meet the submission deadline for any assessment item, then 10% of the available marks (assessment marked from value) will be deducted as a late penalty for every day (or part day) late after the due date. For example, if you submit your assignment 1 hour late you will be penalised 10%; if your assignment is 24.5 hours late you will be penalised 20% (because it is late by one 24-hour period plus part of another 24-hour period). 10% will be deducted per day for up to 7 calendar days, at which point your submission will receive a mark of zero (0) unless an extension has been approved. 

EOS exam

• Identity Verified
• In-person

Mode

Written

Category

Examination

Weight

40%

Due date

End of Semester Exam Period

2/11/2024 - 16/11/2024

Other conditions

Student specific, Time limited.

See the conditions definitions

Task description

Exam details

Submission guidelines

Deferral or extension

You may be able to defer this exam.

Course grading

Full criteria for each grade is available in the Assessment Procedure.

Additional course grading information

Students are required to achieve a score of at least 50% on the final exam, and an overall score of at least 49.5% to pass the course

Students who achieve a mark of less than 35% on the final exam will achieve a grade of 2 for the course (regardless of their total percentage for all assessments in the course).

Supplementary assessment

Supplementary assessment is available for this course.

Should you fail a course with a grade of 3, you may be eligible for supplementary assessment. Refer to my.UQ for information on supplementary assessment and how to apply.

Supplementary assessment provides an additional opportunity to demonstrate you have achieved all the required learning outcomes for a course.

If you apply and are granted supplementary assessment, the type of supplementary assessment set will consider which learning outcome(s) have not been met.

Supplementary assessment can take any form (such as a written report, oral presentation, examination or other appropriate assessment) and may test specific learning outcomes tailored to the individual student, or all learning outcomes.

To receive a passing grade of 3S4, you must obtain a mark of 50% or more on the supplementary assessment.

Additional assessment information

Turnitin submission (if appropriate eg essay, reports, reviews, bibliography etc)

1. Access the Assessment folder on the course Blackboard site
2. Upload an electronic version through the assessment Turnitin site

You are required to submit assessable items on time. If you fail to meet the submission deadline for any assessment item, then 10% of the available marks (assessment marked from value) will be deducted as a late penalty for every day (or part day) late after the due date. For example, if you submit your assignment 1 hour late you will be penalised 10%; if your assignment is 24.5 hours late you will be penalised 20% (because it is late by one 24-hour period plus part of another 24-hour period). 10% will be deducted per day for up to 7 calendar days, at which point your submission will receive a mark of zero (0) unless an extension has been approved. 

Applications for Extensions

Information on applying for an extension can be found here - my.UQ Applying for an extension

Extension applications must be received by the assessment due date and time.

If you are unable to provide documentation to support your application by the due date and time you must still submit your application on time and attach a Word document outlining why you cannot provide the documentation and upload the documentation to the portal within 24 hours.

Please note: While your extension request is being considered, you should work towards completing and submitting your assessment as soon as possible.

If you have been ill or unable to attend class for more than 4 weeks in a semester, we advise you to carefully consider whether you are capable of successfully completing your courses. You might need to consider applying for removal of course. We strongly recommend you seek advice from the Faculty that administers your program.

Extensions with Student Access Plans (SAP)

For extensions up to 7 days, your SAP is all that is required as documentation to support your application. However, extension requests longer than 7 days (for any one assessment item) will require the submission of additional supporting documentation e.g., a medical certificate. A maximum of two applications may be submitted for any one assessment item, unless exceptional circumstances can be demonstrated. All extension requests must be received by the assessment due date and time.

PLAGIARISM will not be tolerated: You should be aware that the University employs purpose built software to detect plagiarism. It is very important that you understand clearly the practical meaning of plagiarism.

Students are encouraged to read the UQ Academic Integrity and Plagiarism policy (http://www.uq.edu.au/hupp/index.html?page=25128) which makes a comprehensive statement about the University's approach to plagiarism, including the approved use of plagiarism detection software, the consequences of plagiarism and the principles associated with preventing plagiarism.

ARTIFICIAL INTELLIGENCE USE (AI)

The assessment tasks in this course evaluate students’ abilities, skills, and knowledge without the aid of Artificial Intelligence (AI).

Students are advised that the use of AI technologies to develop responses is strictly prohibited and may constitute misconduct under the Student Code of Conduct.

Learning resources

You'll need the following resources to successfully complete the course. We've indicated below if you need a personal copy of the reading materials or your own item.

Library resources

Find the required and recommended resources for this course on the UQ Library website.

Learning activities

The learning activities for this course are outlined below. Learn more about the learning outcomes that apply to this course.

Policies and procedures

University policies and procedures apply to all aspects of student life. As a UQ student, you must comply with University-wide and program-specific requirements, including the:

• Student Code of Conduct Policy
• Student Integrity and Misconduct Policy and Procedure
• Assessment Procedure
• Examinations Procedure
• Reasonable Adjustments - Students Policy and Procedure

Learn more about UQ policies on my.UQ and the Policy and Procedure Library.

You'll also need to be aware of the following policies and procedures while completing this course:

• Laboratory Occupational Health and Safety