Undergraduate Course: Trees of Life (EVBI10009)

Course Outline
School	School of Biological Sciences	College	College of Science and Engineering
Credit level (Normal year taken)	SCQF Level 10 (Year 4 Undergraduate)	Availability	Not available to visiting students
SCQF Credits	10	ECTS Credits	5
Summary	The 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 studentsż 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
Not being delivered

Learning Outcomes
On completion of this course, the student will be able to: The ability to interpret phylogenies and gene trees, and an understanding of their value in biological thinking An understanding of how 'trees' are usually inferred from data, and the ability to infer trees from data using simple methods An awareness of the breadth of evolutionary questions that phylogenies are used to address An awareness and understanding of the common causes of error in tree inference An understanding of the relationship between gene trees and phylogenies