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DEGREE REGULATIONS & PROGRAMMES OF STUDY 2020/2021

Information in the Degree Programme Tables may still be subject to change in response to Covid-19

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DRPS : Course Catalogue : School of Biological Sciences : Evolutionary Biology

Undergraduate Course: Trees of Life (EVBI10009)

Course Outline
SchoolSchool of Biological Sciences CollegeCollege of Science and Engineering
Credit level (Normal year taken)SCQF Level 10 (Year 4 Undergraduate) AvailabilityNot available to visiting students
SCQF Credits10 ECTS Credits5
SummaryThe overarching theme would be to examine how tree-based approaches (phylogenetic and coalescent) provide a framework for understanding pattern and process in evolutionary biology. The course would consolidate the students┐ previous understanding of phylogenetic inference methods, and extend them to a conceptual understanding of state-of-the-art approaches. At each stage it would focus on the biological context or motivation for tree-inference, and on the value of a phylogenetic and/or coalescent perspective.

Topics to be covered: Tree interpretation; Tree inference; Support; Alignment; Rooting; Molecular clocks and calibration; Patterns of sequence evolution on trees, Coalescent Trees; Gene-trees versus species-trees; Reticulation and horizontal transfer; Macro-evolutionary inferences; Trait evolution / comparative method; Rapid radiations.
Course description Topics to be covered: Tree interpretation; Tree inference; Support; Alignment; Rooting; Molecular clocks and calibration; Patterns of sequence evolution on trees, Coalescent Trees; Gene-trees versus species-trees; Reticulation and horizontal transfer; Macro-evolutionary inferences; Trait evolution / comparative method; Rapid radiations.

The overarching theme is the use of tree-based approaches (phylogenetic and coalescent) to provide a framework for understanding pattern and process in evolutionary biology. The course consolidate the students' previous understanding of phylogenetic inference methods, and extends them to a conceptual understanding of state-of-the-art approaches.

In week one Students will review their understanding of phylogenetic trees and how they are inferred. In week two they will be introduced to state-of-the-art phylogenetic inference and get a refresher on sequence databases and handling sequence data. Week three will focus on alignment methods (i.e. homology inference) and its impact on phylogenetic analyses, and week four on rooting trees and the impact of rooting methods. Week five will focus on current methods for inferring the timescale of phylogenies, and week six will introduce the use of phylogenies for inferring patterns of genome evolution. Weeks seven and eight will consider trees of individuals as well as trees of species, and the ways in which gene trees relate to species trees. Weeks nine and ten will show how 'tree thinking' can be used to address big questions in evolutionary and comparative biology.

The course will be partnered with a series of short computer practicals that will allow students to put the methods from the lectures into practice, and the class data generated will be used to write a report that will form the basis of the in-course assessment.

At each stage the coruse focuses on the biological context or motivation for tree-inference, and on the value of a 'tree thinking' perspective.

Entry Requirements (not applicable to Visiting Students)
Pre-requisites Co-requisites
Prohibited Combinations Other requirements None
Additional Costs 0
Course Delivery Information
Academic year 2020/21, Not available to visiting students (SS1) Quota:  20
Course Start Semester 1
Course Start Date 21/09/2020
Timetable Timetable
Learning and Teaching activities (Further Info) Total Hours: 100 ( Lecture Hours 14, Seminar/Tutorial Hours 2, Supervised Practical/Workshop/Studio Hours 9, Formative Assessment Hours 1, Summative Assessment Hours 2, Revision Session Hours 1, Programme Level Learning and Teaching Hours 2, Directed Learning and Independent Learning Hours 69 )
Assessment (Further Info) Written Exam 0 %, Coursework 100 %, Practical Exam 0 %
Additional Information (Assessment) 100% In-Course Assesment
Feedback Not entered
No Exam Information
Learning Outcomes
On completion of this course, the student will be able to:
  1. Understand how evolution gives rise to tree-like (branching) patterns of relatedness, how these patterns can be inferred from genetic data, and how inferring these patterns is useful to biologists
  2. Be able to use available software and databases to identify and prepare data for phylogenetic analysis, and to perform phylogenetic analyses on those data
  3. Be able to interpret the relationships and patterns implied by phylogenetic trees, and to critically assess phylogenetic trees in light of the data and methods used to construct them
  4. Be able to depict phylogenetic relationships using available software, and to present the associated results and inference methods to an informed audience
  5. Be able to work independently on an analytical project, and be able to integrate your findings with those of others
Reading List
None
Additional Information
Graduate Attributes and Skills Not entered
KeywordsPhylogeny,Molecular Clock,Gene-tree,Alignment,Evolution,Coalescent,Macroevolution
Contacts
Course organiserDr Darren Obbard
Tel: (0131 6)51 7781
Email: darren.obbard@ed.ac.uk
Course secretaryMiss Rachel Law
Tel: (0131 6)51 3689
Email: Rachel.Law@ed.ac.uk
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