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DRPS : Course Catalogue : School of Biological Sciences : Plant Science

Postgraduate Course: Phylogenetics and Population Genetics (PLSC11001)

Course Outline
SchoolSchool of Biological Sciences CollegeCollege of Science and Engineering
Credit level (Normal year taken)SCQF Level 11 (Postgraduate) AvailabilityNot available to visiting students
SCQF Credits10 ECTS Credits5
SummarySince the acceptance of the theory of evolution, biologists have sought to investigate the relationships of organisms, to uncover the 'tree of life', and to understand the population genetic bases of evolutionary processes.
Phylogenetics is a discipline with wide application that attempts to establish evolutionary relationships by making inferences from the inherent similarities and differences of organisms. It is generally accepted that classification should be based upon knowledge of relationships, which are also needed for testing biogeographic and evolutionary hypotheses. Increasingly, molecular data are used to reconstruct phylogenies as this provides an extensive suite of characters that can be compared across a wide range of organisms.

Population genetics focuses on examining the amounts and partitioning of genetic variation and establishing the evolutionary processes underlying population differentiation and diversification. This provides insights into how some groups of populations remain on a common evolutionary trajectory and others diversify into different ecotypes or species. Population genetic approaches also are widely used in modern conservation programmes in which the conservation of genetic biodiversity is an explicit goal.

At the interface of population genetics (diversity and differentiation within species) and phylogenetics (relationships and differentiation between species) is the nature of the species themselves. The course ends with a discussion of the definition of plant species, and how the disciplines of population genetics and phylogenetics can contribute towards enhanced understanding of the most appropriate concept(s) of what constitutes a species.
Course description The course includes the following sessions: Introduction to phylogenetics; Taxon sampling; Introduction to morphological characters and character coding; Matrix building and sequence alignment; Introduction to molecular characters, genomes and gene regions; Introduction to parsimony; Rooting phylogenetic trees; Support and confidence measures; Advanced parsimony analysis; Introduction to likelihood and Bayesian analysis; Combining characters; Character mapping and optimisation; Species concepts. There will be sessions taken by visiting scientists.

The course includes the following sessions: Introduction to population genetic theory; Introduction to molecular biology; Molecular approaches to population genetics; GM gene flow, adaptation and phylogeography; Conservation genetics.
Entry Requirements (not applicable to Visiting Students)
Pre-requisites Co-requisites It is RECOMMENDED that students also take Angiosperm Evolution and Biodiversity (PGBI11016) AND Angiosperm Biodiversity Practicals (PGBI11017)
Prohibited Combinations Other requirements None
Additional Costs none
Course Delivery Information
Academic year 2015/16, Not available to visiting students (SS1) Quota:  None
Course Start Block 5 (Sem 2) and beyond
Timetable Timetable
Learning and Teaching activities (Further Info) Total Hours: 100 ( Supervised Practical/Workshop/Studio Hours 40, Programme Level Learning and Teaching Hours 2, Directed Learning and Independent Learning Hours 58 )
Assessment (Further Info) Written Exam 100 %, Coursework 0 %, Practical Exam 0 %
Additional Information (Assessment) Two written assignments, an exercise on population genetics and a phylogenetics exercise.
Feedback Not entered
No Exam Information
Learning Outcomes
On completion of this course, the student will be able to:
  1. Background to cladistic parsimony analysis (concepts of homology, character coding, homoplasy, parsimony, tree searches, confidence in resulting phylogenetic hypotheses)
  2. Techniques of molecular phylogenetics (background to DNA and plant genomes, PCR and sequencing (including lab practical), DNA sequence alignment). Other phylogenetic methodologies: maximum likelihood and Bayesian techniques
  3. Background to population genetic analyses (measurements of diversity and partitioning of variation; characteristics of different genomes, influence of species traits on patterns of genetic diversity). Molecular techniques in population genetics (sequencing, RFLPs, AFLPs, RAPDs, isozymes)
  4. Use of genetic data in conservation programmes and the application of population genetics to GMO risk assessments
  5. Adaptive differentiation, phylogeography, and speciation, understanding different species concepts
Reading List
Additional Information
Graduate Attributes and Skills Not entered
Special Arrangements The course takes the form of an intensive two week block. It is based on computer practicals, with discussion sessions also forming an integral element. The required Apple computers are the personal machines of RBGE staff who donate them to the two-week course block. Teaching in a block is therefore the only available option.

The course is also attended by University of Edinburgh PhD students, for whom a short, intensive course is most time-efficient and beneficial. The University offers no alternative course for these students.
Additional Class Delivery Information Class sessions will be timetabled for Monday through Friday for three weeks, Block 1 weeks 1 to 3
Course organiserDr Louis Ronse De Craene
Tel: (0131) 248 2804
Course secretaryMiss Vicky Mactaggart
Tel: (0131 6)51 7052
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