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BB40134: Molecular phylogenetics

Follow this link for further information on academic years Academic Year: 2014/5
Further information on owning departmentsOwning Department/School: Department of Biology & Biochemistry
Further information on credits Credits: 6
Further information on unit levels Level: Masters UG & PG (FHEQ level 7)
Further information on teaching periods Period: Semester 1
Further information on unit assessment Assessment Summary: EX 60%, MC 20%, OT 20%
Further information on unit assessment Assessment Detail:
  • Computer assignment 1 (MC 20%)
  • Computer assignment 2 (OT 20%)
  • Examination (EX 60%)
Further information on supplementary assessment Supplementary Assessment: Like-for-like reassessment (where allowed by programme regulations)
Further information on requisites Requisites: Before taking this unit you must (take BB20023 or take BB20110) and take BB20040
Further information on descriptions Description: Aims:
To outline how scientists can infer and interpret evolutionary relationships using molecular data and how this process is both informed by and informs our understanding of molecular evolution. To provide practical skills in molecular phylogenetic inference.

Learning Outcomes:
After taking this course the student should be able to:
* explain what phylogenetic inference is, how molecular sequence data can be used for this, and how to critically interpret phylogenetic trees.
* give a detailed explanation of what rates of genetic variation are, why there are different rates, and what effects this can have on molecular evolution and phylogenetic inference.
* describe the theories and methodologies of multiple sequence alignment.
* describe the theories, methodologies, and practical applications of the most common methods of phylogenetic inference (distance, parsimony, maximum likelihood, quartet puzzling).
* expound on what the major methodological and biological considerations/limitations are in phylogenetic inference and some of the approaches to accommodate/correct for these.
* explain the most common methods to assess confidence in phylogenetic inferences.
* practically carry out sequence data collection from databases, multiple sequence alignments, phylogenetic inferences using a number of different methods and with assessments of confidence, and critically interpret and evaluate the resultant phylogenetic trees.

Learning and studying T/F/A, Written communication T/F/A, Information technology T/F/A, Information handling & retrieval T/F/A, Working independently T/F.

Selectionist and neutralist theories of evolution. Genetic mutation. Molecular clock theory. Molecular phylogenetics in perspective. Phylogenetic trees and their interpretation. Obtaining and assessing phylogenetically informative characters. Sequence alignment. Models of evolution. Common methods of inference. Assessing confidence for inferences. Methodological considerations/limitations. Considerations/limitations due to the nature of molecular evolution. Examples. Practical alignment and inference exercises.
Further information on programme availabilityProgramme availability:

BB40134 is Optional on the following programmes:

Department of Biology & Biochemistry Programmes in Natural Sciences
  • UXXX-AFB01 : BSc(Hons) Natural Sciences (Year 3)
  • UXXX-AAB02 : BSc(Hons) Natural Sciences with Study year abroad (Year 4)
  • UXXX-AKB02 : BSc(Hons) Natural Sciences with Year long work placement (Year 4)
  • UXXX-AFM01 : MSci(Hons) Natural Sciences (Year 4)
  • UXXX-AKM02 : MSci(Hons) Natural Sciences with Professional Placement (Year 5)
  • UXXX-AAM02 : MSci(Hons) Natural Sciences with Study year abroad (Year 5)

* This unit catalogue is applicable for the 2014/15 academic year only. Students continuing their studies into 2015/16 and beyond should not assume that this unit will be available in future years in the format displayed here for 2014/15.
* Programmes and units are subject to change at any time, in accordance with normal University procedures.
* Availability of units will be subject to constraints such as staff availability, minimum and maximum group sizes, and timetabling factors as well as a student's ability to meet any pre-requisite rules.