BIO2036 : Molecular Evolution and Systematics
- Offered for Year: 2020/21
- 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 is 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
The molecular basis of biology and evolution
Allele dynamics and evolution in populations
DNA and amino acid sequence evolution
DNA and protein sequencing technologies, applications and experimental design considerations
Mitochondrial and chloroplast DNA: evolution and applications in barcoding
Omics technologies, applications and experimental design considerations
Molecular phylogenetics and tree construction
Patterns of molecular evolution: reticulate evolution and phylogenetic networks, domains of life, evolution by ‘molecular tinkering’
Evolution of prokaryotic and eukaryotic genomes
Computer Lab Practicals (3 h) with follow-up self-study exercises
Methods of sequence analysis and phylogenetic tree construction
Laboratory Practicals
Field collection and laboratory analysis of freshwater invertebrate communities using morphological characteristics, identification and relative abundance of OTUs
DNA extraction, PCR amplification, analysis of PCR products and preparation for sequencing
Teaching Methods
Please note that module leaders are reviewing the module teaching and assessment methods for Semester 2 modules, in light of the Covid-19 restrictions. There may also be a few further changes to Semester 1 modules. Final information will be available by the end of August 2020 in for Semester 1 modules and the end of October 2020 for Semester 2 modules.
Teaching Activities
| Category | Activity | Number | Length | Student Hours | Comment |
|---|---|---|---|---|---|
| Guided Independent Study | Assessment preparation and completion | 1 | 12:00 | 12:00 | Computer practical assessments (including formative exercises) |
| Guided Independent Study | Assessment preparation and completion | 1 | 48:00 | 48:00 | Revision plus exam (2 h) |
| Guided Independent Study | Assessment preparation and completion | 3 | 3:00 | 9:00 | Lab follow up - Figure and table preparation, upload of materials to fileshare) |
| Structured Guided Learning | Lecture materials | 17 | 1:00 | 17:00 | Asynchronous online recorded lectures |
| Scheduled Learning And Teaching Activities | Practical | 4 | 4:00 | 16:00 | Computer practical Self study guides (4 x 4 h) |
| Scheduled Learning And Teaching Activities | Practical | 2 | 3:00 | 6:00 | Initial collection and ID practical. Practicals replaced with video recorded sessions |
| Guided Independent Study | Directed research and reading | 3 | 1:00 | 3:00 | Reading lab protocols, H+S documents, further directed reading |
| Scheduled Learning And Teaching Activities | Practical | 4 | 2:00 | 8:00 | Synchronous online workshops on computer practical exercises |
| Guided Independent Study | Directed research and reading | 17 | 2:00 | 34:00 | Directed further reading (references provided in lectures) |
| Scheduled Learning And Teaching Activities | Drop-in/surgery | 5 | 1:00 | 5:00 | Synchronous online Q/A drop in to support lectures lectures |
| Guided Independent Study | Independent study | 4 | 3:00 | 12:00 | Further computer exercises with model answers (formative assessment) |
| Guided Independent Study | Independent study | 17 | 1:00 | 17:00 | Lecture follow-up + consolidation |
| Guided Independent Study | Independent study | 1 | 12:00 | 12:00 | Independent study (research papers) |
| Scheduled Learning And Teaching Activities | Module talk | 1 | 1:00 | 1:00 | Revision Q/A Session - synchronous online |
| Total | 200:00 |
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
Please note that module leaders are reviewing the module teaching and assessment methods for Semester 2 modules, in light of the Covid-19 restrictions. There may also be a few further changes to Semester 1 modules. Final information will be available by the end of August 2020 in for Semester 1 modules and the end of October 2020 for Semester 2 modules.
The format of resits will be determined by the Board of Examiners
Other Assessment
| Description | Semester | When Set | Percentage | Comment |
|---|---|---|---|---|
| Practical/lab report | 2 | M | 30 | Computer practical assignment |
| Written exercise | 2 | M | 70 | Take home written assessment |
Formative Assessments
| Description | Semester | When Set | Comment |
|---|---|---|---|
| Practical/lab report | 2 | M | Follow-up additional exercises with model answers for each computer practical |
Assessment Rationale And Relationship
The written assessment tests knowledge of the principles and practices of molecular evolution, molecular genetics and genomics technologies, as well as the ability to interpret literature in this field. The skills to acquire, manipulate, analyse and present molecular sequence data are tested by means of an assessed computer laboratory report, undertaking a phylogenetic 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. The formative assessments allow students to assess progress of their learning.
Reading Lists
Timetable
- Timetable Website: www.ncl.ac.uk/timetable/
- BIO2036's Timetable