Postgraduate

Modules

Modules

CSC8307 : Comparative and Evolutionary Genomics

Semesters
Semester 2 Credit Value: 10
ECTS Credits: 5.0

Aims

To provide an outline of the theories and principles which underpin comparative and phylogenetic analyses.
To use computational methods which implement these principles to establish phylogenetic relationships and infer the consequences of genetic change.
To encourage rigorous scientific method through hypothesis testing, and creativity through open-ended exploration of comparative sequence data.
To improve critical assessment skills through the analysis and re-analysis of published work and sequence data.

Whole genomes are being sequenced at an ever increasing rate and comparative analysis of these genomes promises to reveal insights into their evolution and function. The more genome sequences that are available, the more powerful this type of analysis becomes.

This module is designed to introduce students to the methods and concepts in molecular evolution, population genetics and comparative genomics research. The module has a large practical component with a focus on the algorithms and software that are used to measure evolutionary change, infer evolutionary relationships and phylogenies, and carry out comparative genomic analysis.

Outline Of Syllabus

The nature of mutation, and how mutational change is modelled. The relationship between mutation and phenotype.
Representation of phylogegentic networks. Tree and network construction. Distance, parsimony, likelihood and hadamard methods. Testing phylogenetic hypotheses: resampling, likelihood and Bayesian inference.
Molecular change, the molecular clock and neutral evolution.
Comparative genomic analyses: identification of functionally important sequences including genes, control elements, critical amino acids.
Applications of phylogenetic analysis.

Teaching Methods

Teaching Activities
Category Activity Number Length Student Hours Comment
Guided Independent StudyAssessment preparation and completion221:0022:00Lecture follow-up
Scheduled Learning And Teaching ActivitiesLecture221:0022:00Lectures
Scheduled Learning And Teaching ActivitiesPractical161:0016:00Practicals
Guided Independent StudyProject work161:0016:00Coursework
Guided Independent StudyIndependent study241:0024:00Background reading
Total100:00
Teaching Rationale And Relationship

Lectures will be used to introduce the learning material and for demonstrating the key concepts by example. Students are expected to follow-up lectures within a few days by re-reading and annotating lecture notes to aid deep learning.

This is a very practical subject, and it is important that the learning materials are supported by hands-on opportunities provided by practical classes. Students are expected to spend time on coursework outside timetabled practical classes.

Students aiming for 1st class marks are expected to widen their knowledge beyond the content of lecture notes through background reading.

Assessment Methods

The format of resits will be determined by the Board of Examiners

Other Assessment
Description Semester When Set Percentage Comment
Practical/lab report2M100Two pieces of coursework of equal weight. Max 2,000 words each.
Assessment Rationale And Relationship

The assessed practicals will assess the students understanding of how phylogenetic relationships are represented in trees and networks, the different methods used to construct trees and networks, phylogenetic hypotheses testing and the use of comparative analyses to identify functionally important sequences.

Reading Lists

Timetable