NBIK21000U Phylogenomic Applications in Biodiversity Research

Volume 2020/2021
Content

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.

 

Module

Period          

Activity

Preparation/Self-study

26-30 July 2021

Reading of literature; exercises; select an independent project (students can analyze their own data or a suggested project)

On-campus module

2-6 August 2021

Lectures; hand-on exercises; discussion of results

Independent project work

9-19 August 2021

Analyze data independently on chosen project; prepare essay and oral presentation

Virtual symposium

20 August 2021

Student presentations on independent projects

Learning Outcome

Knowledge:

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 

 

Skills:

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 

 

Competences:

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.

Academic qualifications equivalent to a BSc degree is recommended. Students should have basic knowledge on ‘omics’ and molecular evolution. Students need basic command-line skills (bash; move between directories, change file names, basic scripting) and of plotting and data wrangling and basic statistics in R (e.g. ggplot, dplyr) or python; specific programming skills needed in phylogenetic or comparative analyses will be introduced in the exercises. The students should bring a laptop to participate in the exercises; all software will be executed on a university server.
The class is taught through lectures and hands-on exercises, scientific literature, group discussions, and an independent project.
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.
  • Category
  • Hours
  • Lectures
  • 10
  • Preparation
  • 37,5
  • Exercises
  • 20
  • Project work
  • 59,5
  • Exam Preparation
  • 10
  • Exam
  • 0,5
  • Total
  • 137,5
Oral
Individual
Continuous feedback during the course of the semester
Feedback by final exam (In addition to the grade)

Instructor feedback on written report
Peer and instructor feedback on oral presentation

Credit
5 ECTS
Type of assessment
Written assignment, 10 days
Oral examination, 20 minutes online symposium
Attendance 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.

Aid
All aids allowed
Marking scale
7-point grading scale
Censorship form
No external censorship
Several internal examiners
Re-exam

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.