SL40115: Molecular phylogenetics (BB40134)
[Page last updated: 26 October 2023]
| Academic Year: | 2023/24 |
| Owning Department/School: | Department of Life Sciences |
| Credits: | 6 [equivalent to 12 CATS credits] |
| Notional Study Hours: | 120 |
| Level: | Masters UG & PG (FHEQ level 7) |
| Period: |
- Semester 1
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| Assessment Summary: | CW 30%, EX 70% |
| Assessment Detail: |
- BB40134 Coursework (CW 30%)
- BB40134 Examination (EX 70%)
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| Supplementary Assessment: |
- Like-for-like reassessment (where allowed by programme regulations)
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| Requisites: |
Before taking this module you are advised to take BB20023 OR take BB20040 OR take SL20003 OR take SL20006
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| 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.
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| 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.
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| 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.
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| 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.
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| Course availability: |
SL40115 is Optional on the following courses:
Department of Chemistry
- USSC-AFM01 : MSci(Hons) Natural Sciences (Biology with Chemistry stream) (Year 4)
- USSC-AAM01 : MSci(Hons) Natural Sciences (Biology with Chemistry stream) with Study year abroad (Year 5)
- USSC-AKM01 : MSci(Hons) Natural Sciences (Biology with Chemistry stream) with Professional Placement (Year 5)
- USSC-AFM01 : MSci(Hons) Natural Sciences (Biology with Pharmacology stream) (Year 4)
- USSC-AAM01 : MSci(Hons) Natural Sciences (Biology with Pharmacology stream) with Study year abroad (Year 5)
- USSC-AKM01 : MSci(Hons) Natural Sciences (Biology with Pharmacology stream) with Professional Placement (Year 5)
- USSC-AFM01 : MSci(Hons) Natural Sciences (Biology with Physics stream) (Year 4)
- USSC-AAM01 : MSci(Hons) Natural Sciences (Biology with Physics stream) with Study year abroad (Year 5)
- USSC-AKM01 : MSci(Hons) Natural Sciences (Biology with Physics stream) with Professional Placement (Year 5)
- USSC-AFM01 : MSci(Hons) Natural Sciences (Chemistry with Biology stream) (Year 4)
- USSC-AAM01 : MSci(Hons) Natural Sciences (Chemistry with Biology stream) with Study year abroad (Year 5)
- USSC-AKM01 : MSci(Hons) Natural Sciences (Chemistry with Biology stream) with Professional Placement (Year 5)
- USSC-AFM01 : MSci(Hons) Natural Sciences (Physics with Biology stream) (Year 4)
- USSC-AAM01 : MSci(Hons) Natural Sciences (Physics with Biology stream) with Study year abroad (Year 5)
- USSC-AKM01 : MSci(Hons) Natural Sciences (Physics with Biology stream) with Professional Placement (Year 5)
Department of Life Sciences
- USSL-AFB01 : BSc(Hons) Biochemistry (Year 3)
- USSL-AKB01 : BSc(Hons) Biochemistry with Professional Placement (Year 4)
- USSL-AFB02 : BSc(Hons) Biology (Year 3)
- USSL-AKB02 : BSc(Hons) Biology with Professional Placement (Year 4)
- USSL-AFM01 : MBiochem(Hons) Biochemistry (Year 3)
- USSL-AKM01 : MBiochem(Hons) Biochemistry with Professional Placement (Year 4)
- USSL-AFM02 : MBiol(Hons) Biology (Year 3)
- USSL-AKM02 : MBiol(Hons) Biology with Professional Placement (Year 4)
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Notes: - This unit catalogue is applicable for the 2023/24 academic year only. Students continuing their studies into 2024/25 and beyond should not assume that this unit will be available in future years in the format displayed here for 2023/24.
- Courses and units are subject to change 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.
- Find out more about these and other important University terms and conditions here.
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