Unit information: Phylogenetic Methods in Palaeobiology in 2021/22

Unit name	Phylogenetic Methods in Palaeobiology
Unit code	EASCM0035
Credit points	10
Level of study	M/7
Teaching block(s)	Teaching Block 1A (weeks 1 - 6)
Unit director	Professor. Pisani
Open unit status	Not open
Pre-requisites	None
Co-requisites	None
School/department	School of Earth Sciences
Faculty	Faculty of Science

Description including Unit Aims

The unit aims to introduce students to:

• Phylogenetics using parsimony as an easy to understand, exemplar, method
• Modern phylogenetic methods: (A) Maximum Likelihood; (B) Bayesian Analysis
• Modern dating methods to derive evolutionary timescales integrating fossils and genomic data (Molecular clocks)
• Supercomputing and the UNIX environment

In this unit students will gain a general understanding of modern methods in macroevolutionary analysis through a series of lectures covering Phylogenetic reconstruction, Inference of divergence time and the Comparative method. Practicals will include how to use supercomputers (using a UNIX/LINUX shell interface) and how to use an array of standard software for data analysis (e.g. PAUP MrBayes Phylobayes).

Practicals 1 to 3 are formative: students complete a series of exercises to learn how to use a diversity of phylogenetic software. Feedback will be provided.

Practical 4 is a Graded Practical: students are given a problem to complete that will be marked. The mark for this work gives the overall unit mark.

Practical 5 is formative: students use this practical class to review the work undertaken in practicals 1 – 3 and continue to work on the assessed assignment set in practical 4. Students can request feedback on specific topics

Intended Learning Outcomes

Students will:

• have transferable skills that are of use outside palaeontology (A) working with supercomputers in a Unix environment (B) basics of computer scripting
• be able to analyse morphological and molecular data to determine the evolutionary relationships of living and extinct organisms
• be able to use appropriate software (e.g. Paup, MrBayes), to test the veracity of phylogenetic hypotheses
• understand morphological character coding and how to use it to discover phylogenetic patterns in the tree of life
• understand the Molecular clock and molecular phylogenetics/phylogenomics
• be able to use a range of phylogenetic tree-finding methods - parsimony, maximum likelihood, and Bayesian analysis
• understand and be able to implement combined (total evidence) analyses of molecular and morphological data – including fossils

Teaching Information

The unit will be taught through a combination of

• asynchronous online materials and, if subsequently possible, synchronous face-to-face lectures
• synchronous office hours
• asynchronous directed individual formative activities and exercises
• guided, structured reading
• practical work in the laboratory

Students who either begin or continue their studies in an online mode may be required to complete laboratory work, or alternative activities, in person, either during the academic year 2020/21 or subsequently, in order to meet the intended learning outcomes for the unit, prepare them for subsequent units or to satisfy accreditation requirements.

Assessment Information

Coursework (100%)

In Practical 4 students are assigned one assessed exercise. This consists of a paper to read and a dataset to analyse. During the practical students will complete phylogenetic analyses of the given dataset and compare their results with those of the published paper.

Students' results are written up as a short Research Paper (500 words minimum - 1200 words maximum & one figure, if necessary with panels) + References.

Resources

If this unit has a Resource List, you will normally find a link to it in the Blackboard area for the unit. Sometimes there will be a separate link for each weekly topic.

If you are unable to access a list through Blackboard, you can also find it via the Resource Lists homepage. Search for the list by the unit name or code (e.g. EASCM0035).

How much time the unit requires
Each credit equates to 10 hours of total student input. For example a 20 credit unit will take you 200 hours of study to complete. Your total learning time is made up of contact time, directed learning tasks, independent learning and assessment activity.

See the Faculty workload statement relating to this unit for more information.

Assessment
The Board of Examiners will consider all cases where students have failed or not completed the assessments required for credit. The Board considers each student's outcomes across all the units which contribute to each year's programme of study. If you have self-certificated your absence from an assessment, you will normally be required to complete it the next time it runs (this is usually in the next assessment period).
The Board of Examiners will take into account any extenuating circumstances and operates within the Regulations and Code of Practice for Taught Programmes.