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BB40134: Molecular phylogenetics

[Page last updated: 15 October 2020]

Follow this link for further information on academic years Academic Year: 2020/1
Further information on owning departmentsOwning Department/School: Department of Biology & Biochemistry
Further information on credits Credits: 6      [equivalent to 12 CATS credits]
Further information on notional study hours Notional Study Hours: 120
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: CW 30%, EX 60%, MC 10%
Further information on unit assessment Assessment Detail:
  • MCQ Test (MC 10%)
  • Coursework (CW 30%)
  • 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 module you are advised to take BB20023 OR take BB20040
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.

Skills:
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.

Content:
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
  • USBB-AFB02 : BSc(Hons) Biochemistry (Year 3)
  • USBB-AKB06 : BSc(Hons) Biochemistry with Professional Placement (Year 4)
  • USBB-AFB03 : BSc(Hons) Biology (Year 3)
  • USBB-AKB07 : BSc(Hons) Biology with Professional Placement (Year 4)
  • USBB-AKB08 : BSc(Hons) Molecular and Cellular Biology with Professional Placement (Year 4)
Programmes in Natural Sciences
  • UXXX-AFM01 : MSci(Hons) Natural Sciences (Biology with Chemistry stream) (Year 4)
  • UXXX-AAM02 : MSci(Hons) Natural Sciences (Biology with Chemistry stream) with Study year abroad (Year 5)
  • UXXX-AKM02 : MSci(Hons) Natural Sciences (Biology with Chemistry stream) with Professional Placement (Year 5)
  • UXXX-AFM01 : MSci(Hons) Natural Sciences (Biology with Pharmacology stream) (Year 4)
  • UXXX-AAM02 : MSci(Hons) Natural Sciences (Biology with Pharmacology stream) with Study year abroad (Year 5)
  • UXXX-AKM02 : MSci(Hons) Natural Sciences (Biology with Pharmacology stream) with Professional Placement (Year 5)
  • UXXX-AFM01 : MSci(Hons) Natural Sciences (Biology with Physics stream) (Year 4)
  • UXXX-AAM02 : MSci(Hons) Natural Sciences (Biology with Physics stream) with Study year abroad (Year 5)
  • UXXX-AKM02 : MSci(Hons) Natural Sciences (Biology with Physics stream) with Professional Placement (Year 5)
  • UXXX-AFM01 : MSci(Hons) Natural Sciences (Chemistry with Biology stream) (Year 4)
  • UXXX-AAM02 : MSci(Hons) Natural Sciences (Chemistry with Biology stream) with Study year abroad (Year 5)
  • UXXX-AKM02 : MSci(Hons) Natural Sciences (Chemistry with Biology stream) with Professional Placement (Year 5)
  • UXXX-AFM01 : MSci(Hons) Natural Sciences (Physics with Biology stream) (Year 4)
  • UXXX-AAM02 : MSci(Hons) Natural Sciences (Physics with Biology stream) with Study year abroad (Year 5)
  • UXXX-AKM02 : MSci(Hons) Natural Sciences (Physics with Biology stream) with Professional Placement (Year 5)

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