NBIK21000U Phylogenomic Applications in Biodiversity Research
MSc Programme in Bioinformatics
With genomic sequencing being routinely applied for non-model
organisms, phylogenetic and comparative genomic analyses have
become standard tools for the study of biodiversity and
conservation. The processing and analysis of such large datasets
requires bioinformatic skills, knowledge of analysis tools, and an
understanding of the fundamentals of molecular sequence evolution.
As genome-wide datasets are being generated at an unprecedented rate, competencies in phylogenetic and comparative genomic analyses are becoming indispensable in many branches of biodiversity research. The purpose of this course is to provide the students with knowledge about the principles of the phylogenetic analyses and comparative analyses with large-scale data. The course will provide participants with the skills to analyze genomic data to study the evolution of biodiversity.
The summer course is composed of three modules: a 1-week preparation/self-study, a 1-week on-campus module with lectures and exercises, and a 2-week module to apply the knowledge in an independent project. The independent project will be presented in a final online symposium.
25-29 July 2022
Reading of literature; exercises; select an independent project (students can analyze their own data or a suggested project)
1-5 August 2022
Lectures; hand-on exercises; discussion of results
Independent project work
8-18 August 2022
Analyze data independently on chosen project; prepare essay and oral presentation
19 August 2022
Student presentations on independent projects
After completing the course, the students will be familiar with:
- The key concepts in phylogeny, evolution and their relatedness to biodiversity
- The genetics of the speciation process, introgression, and incomplete lineage sorting
- The fundamentals of natural selection and the neutral evolution model
- The principle of the diverse computational tools for phylogenetic analyses and comparative analyses
The students will be able to retrieve and analyze genetic sequence data in comparative genomic contexts, to reconstruct phylogenetic trees, and to trace trait evolution on dated phylogenies. Specifically, the students will be able to
- Manage sequence data and perform analyses on a computing cluster
- Extract orthologous sequences from genomic data for various evolutionary analyses
- Use different methods to construct and date phylogenetic trees
- Understand the patterns of speciation and trait evolution based on the phylogenetic trees
- Uncover phylogenetic incongruence and infer introgression and incomplete lineage sorting events
- Detect genomic changes arising under natural selection
The students will be competent in each step of the research cycle - from the question to the dissemination of the work. Specifically, students will be able to
- Formulate relevant research questions to address problems in biodiversity research
- Argue for choice of analytical settings
- Present, interpret and discuss the results of analyses
- Provide constructive feedback on written and oral research presentations
- Reflect critically on the significance of data quality, reproducibility, and analytical framework on conclusions drawn from analysis
A selection of reviews, book chapters and original scientific articles on evolutionary biology, phylogenetic principles and recent studies using genome-wide data in biodiversity research will be made available before the course starts. The literature will be supplied in advance on Absalon.
1) Reading material is sent out before the class, which the students are expected to read in the preparatory week. Questions to guide the reading will accompany some of the material.
2) The on-campus week will consist of lectures to give the theoretical background for the exercises that follow in the hands-on sessions. In the practical sessions, students will be guided to perform their own phylogenetic analyses and comparative sequence analyses. They will discuss their findings with their peers and instructors.
3) The following two weeks, the students are putting their knowledge and skills to use. To answer a specific research question, students will devise an analytical strategy, perform analyses and interpret the results. At the end of this period, the students will prepare a written report and give a short oral presentation of their project and their findings.
- Project work
- Exam Preparation
Instructor feedback on written report
Peer and instructor feedback on oral presentation
- 5 ECTS
- Type of assessment
- Written assignment, 10 daysOral examination, 20 minutes online symposiumAttendance and participation of the on-campus module and the virtual symposium is mandatory.
Written assignment (50% of grade), students turn in a maximum 3-page essay (5-page with images) on the findings of their project at the end of week 4.
Oral presentation (50% of grade), students give a short presentation to report their findings in an online student symposium of 10 minutes and 10 minutes of questions from their peers and instructors.
Both part exams do not need to be passed in the same exam period.
- Exam registration requirements
The student need to take part in the on-campus module.
- All aids allowed
- Marking scale
- 7-point grading scale
- Censorship form
- No external censorship
Several internal examiners
Same as the ordinary examination but will only include instructor questions, not peer feedback.
Previously passed part-exams may be reused in a re-exam.
If the exam requirement is not fulfilled, the student must take the course again the next year.
Criteria for exam assesment
See Learning Outcome. Exam assessment is based on the written and oral presentation of the individual project. The essay is assessed based on the quality of the description of the research question, the chosen analysis strategy and the discussion of the results. The oral presentation is assessed based on the ability to present the different steps of the research cycle and the ability to engage in a scientific discussion regarding the course curriculum.