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Module

BIO2036 : Molecular Evolution and Systematics

  • Offered for Year: 2021/22
  • Module Leader(s): Professor John Bythell
  • Lecturer: Dr Maria Del Carmen Montero-Calasanz, Dr Maxim Kapralov
  • Owning School: Natural and Environmental Sciences
  • Teaching Location: Newcastle City Campus
Semesters
Semester 2 Credit Value: 20
ECTS Credits: 10.0

Aims

This module provides a theoretical basis and practical understanding of molecular evolution, enabling students to ‘speak the language’ of modern genomic biology and undertake basic research to generate, access, manipulate and analyse molecular genetic data to address the systematics and phylogenetic relationships of organisms across the tree of life. Practical emphasis will be on molecular identification, classification and barcoding applications, including the Barcode Of Life Data (BOLD) programme. These techniques are also applicable to forensics and environmental DNA (eDNA) studies, where the presence of species are detected from environmental samples or unrecognisable remains. The concept of barcoding will also be expanded on, introducing the use of high-throughput next-generation sequencing (NGS) to characterise population or whole-community structure (metabarcoding or metagenomics).

Outline Of Syllabus

Lectures

Lectures will cover a range of subjects underlying molecular evolution, focussing particularly on the methods and interpretation of molecular data for characterisation, identification, systematics and phylogenetics. This will include:

- The molecular basis of biology and evolution
- Allele dynamics and populations
- DNA and amino acid sequence evolution
- DNA and protein sequencing technologies, applications and experimental design considerations
- Rates and patterns of molecular evolution

Lectures are supported by the recommended text (Graur 2016), which also provides a broader context.

Computer Lab Practicals and self-study exercises

Computer practicals are based on MEGA sequence analysis software and other freeware commonly used to analyse and manipulate DNA and protein sequences and build robust phylogenetic trees to support assessment of evolutionary relationships.

Laboratory Practicals

Cover all aspects of sample collection, DNA extraction, PCR amplification of barcoding markers and preparation of samples for sequencing.

Teaching Methods

Teaching Activities
Category Activity Number Length Student Hours Comment
Guided Independent StudyAssessment preparation and completion112:0012:00Computer practical assessment (4 x exercises x 3hr each)
Guided Independent StudyAssessment preparation and completion146:0046:00Revision plus exam (2hr)
Scheduled Learning And Teaching ActivitiesLecture171:0017:00N/A
Guided Independent StudyDirected research and reading41:004:00Preparation for computer practicals - Reading self-study guides
Guided Independent StudyDirected research and reading172:0034:00Directed further reading (references provided in lectures)
Scheduled Learning And Teaching ActivitiesPractical43:0012:00Computer cluster
Scheduled Learning And Teaching ActivitiesPractical33:009:00Laboratory practical - Ridley Labs A+B
Guided Independent StudyDirected research and reading31:003:00Prep for lab practicals - Reading lab protocols, H&S documents, further directed reading
Guided Independent StudySkills practice33:009:00Follow up to lab practicals - Figure and table preparation, upload of materials to fileshare
Guided Independent StudyReflective learning activity46:0024:00Follow-up pylogenetics exercises - further computer exercises with model answers (formative)
Scheduled Learning And Teaching ActivitiesDrop-in/surgery11:001:00Revision Q+A session
Guided Independent StudyIndependent study171:0017:00Lecture follow up and consolidation
Guided Independent StudyIndependent study112:0012:00Independent study (research papers)
Total200:00
Teaching Rationale And Relationship

Lectures provide fundamental knowledge and understanding of the molecular basis of evolution and a broad awareness of the applications of modern analysis methods including next-generation sequencing. The skills to acquire, manipulate, analyse and present molecular sequence data are developed via computer-based practicals and associated follow-on exercises, providing formative assessment for subject-specific and generic skills development. Practical laboratory sessions develop laboratory skills in DNA extraction and PCR for phylogenetics analysis, using samples collected and identified from the field using morphological characteristics. Sequence data obtained in the laboratory are subject to phylogenetics analysis in an assessed computer practical. In combination, this provides a logical and coherent analysis from sample collection to phylogenetics analysis, with a real example to stimulate deep learning.

Assessment Methods

The format of resits will be determined by the Board of Examiners

Exams
Description Length Semester When Set Percentage Comment
Written Examination1201A70N/A
Other Assessment
Description Semester When Set Percentage Comment
Practical/lab report2M30Computer practical assignment based on sequences obtained in the lab practical
Formative Assessments
Description Semester When Set Comment
Practical/lab report2MFollow-up additional exercises with model answers for each computer practical
Assessment Rationale And Relationship

The written examination tests knowledge of the principles and practices of molecular evolution, molecular genetics and genomics technologies, as well as the ability to interpret the literature in this field. The exam consists of compulsory short-answer questions to test understanding across the subject, as well as a choice (1/3) of essay question to assess deeper understanding in a selected area and the ability to integrate material from wider reading. The skills to acquire, manipulate, analyse and present molecular sequence data are tested by means of an assessed computer laboratory report, undertaking a phylogenetics analysis on the organisms sequenced as part of the laboratory practical. The practical assessment includes elements of data acquisition from online databases, sequence alignment and phylogenetic tree construction, as well as assessment of the interpretation and presentation of information, including practical molecular lab results.

Reading Lists

Timetable