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Module

BIO2036 : Molecular Evolution and Systematics

  • Offered for Year: 2020/21
  • Module Leader(s): Professor John Bythell
  • Lecturer: Dr Maxim Kapralov, Dr Maria Del Carmen Montero-Calasanz
  • 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
Structured Guided LearningLecture materials171:0017:00Asynchronous online recorded lectures
Guided Independent StudyAssessment preparation and completion112:0012:00Computer practical assessments (including formative exercises)
Guided Independent StudyAssessment preparation and completion33:009:00Lab follow up - Figure and table preparation, upload of materials to fileshare)
Guided Independent StudyAssessment preparation and completion148:0048:00Revision plus exam (2 h)
Guided Independent StudyDirected research and reading172:0034:00Directed further reading (references provided in lectures)
Scheduled Learning And Teaching ActivitiesPractical42:008:00Synchronous online workshops on computer practical exercises
Guided Independent StudyDirected research and reading31:003:00Reading lab protocols, H+S documents, further directed reading
Scheduled Learning And Teaching ActivitiesPractical23:006:00Initial collection and ID practical. Practicals replaced with video recorded sessions
Scheduled Learning And Teaching ActivitiesPractical44:0016:00Computer practical Self study guides (4 x 4 h)
Scheduled Learning And Teaching ActivitiesDrop-in/surgery51:005:00Synchronous online Q/A drop in to support lectures lectures
Guided Independent StudyIndependent study112:0012:00Independent study (research papers)
Guided Independent StudyIndependent study171:0017:00Lecture follow-up + consolidation
Guided Independent StudyIndependent study43:0012:00Further computer exercises with model answers (formative assessment)
Scheduled Learning And Teaching ActivitiesModule talk11:001:00Revision Q/A Session - synchronous online
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

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 report2M30Computer practical assignment
Written exercise2M70Take home written assessment
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 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