PhD course: Population Genomics BIO9001 - 2022

The Faculty of Biosciences and Aquaculture at Nord University takes great pleasure in inviting you to the biannual PhD course "Population Genomics" (BIO9001), 28 February - 4 March 2022

Start date:

28 February 2022 09:00

End date:

06 March 2022 17:00

Location:

Bodø

​​​​​​​​​​​​​​​​​​​​​​​​​​​​​​​​This is an intensive one-week course with lectures and hands-on exercises, Monday to Friday, 9h-17h, with 1 hour lunch break. About half the time will be devoted to lectures, and the other half to exercises. Lectures and exercises are 35 hours in total, and self-study is estimated to 30 hours. Preparation time for written report (home exam) is estimated to 35 hours. The total workload is thus about 100 hours.

The plan of the five days, with two sessions per day, is as follows:

Session 1: welcome, practicalities, course introduction (JR)
Session 2: introduction to command line (unix), data formats, data conversion (MJ/AJ)
Session 3: introduction to R (AJ/MJ)
Session 4: population genetic theory (OG/ET)
Session 5: analysis of population structure (OG/IS)
Session 6: population history, demographic inference, coalescence (ET/MR)
Session 7: genomic basis of adaptive evolution & inference of selection (ET/MR/OG/IS)
Session 8: admixture and introgression/hybridization (MR/IS)
Session 9: landscape genomics, gene-environment correlations (KS/BP)
Session 10: Open lab and introduction to the home exam (JR)​

Students bring their own laptops with the latest version of R and RStudio installed. Some R packages will also be needed. The students will receive a reading list and software installation instructions before the start of the course and are expected to prepare well.​

Course timetable
Below you can find the timetable for the various lectures (L) and practicals (P). On Monday we start exceptionally at 09:45.
timetable population genomics.png
Learning outcomes and competencies

After having completed the course, the students should:
 
Knowledge - have acquired in-depth understanding of topics, theories, processes, tools and methods used in population genomics.
 
Skills - have acquired the tools and abilities to conduct population genomic analyses, including data quality control, analyses, and interpretation of results.
 
General competencies -
1) be able to exchange views and experiences with evolutionary and molecular biologists and contribute to the development of good practice;
2) develop an understanding of modern scientific research in population genomics.

 
Prerequisites
Basic knowledge of genetics and statistics. Prior experience with command-line programs (in particular R/Rstudio) or Unix will be an advantage.
 
Assessment
The assessment will be report-based. The students will analyse a population genomic dataset (preferably their own data or data related to their own research topic), interpret and write a report. The students deliver the report within a month after the end of the course (deadline: 11th of April 14:00).

Course excursion (5 - 6 March)
Bodø’s beautiful surroundings offer many opportunities for outdoor activities. On March 5, we are planning to take a Sea safari (with a zodiac boat) to Saltstraumen, one of the world’s strongest tidal currents, followed by an authentic stone age dinner in Tuvsjyen, Saltstraumen. The total price for this day is about Nok 1600. On 6th of March, we watch the weather forecast, check the snow quality and count the number of outdoor enthusiasts. Based on this we decide for cross country skiing, a beach hike or a small mountain hike.

Course preparation
Literature
Please read the following articles prior to the start of the course:

  • Gaggiotti & Foll. 2010. Mol. Ecol. Res. 10:821-830
  • Jost et al. 2018. Evol. Apps. 11:1139-1148
  • Francois O & E Durand. 2010. Mol. Ecol. Res. 10:773-784.

These articles as well as more background articles about population genetics can be found here (check again later if the link does not work).

Software installation
Please bring a laptop with the following software installed:

  • R version 4.1.0 or higher
  • RStudio (only to be installed after you have installed R)
  • For Windows laptops: a ssh client such as MobaXterm or PuTTY

If you have no prior experience with these applications, you can take a look to these great tutorials by Evolution and Genomics :

​Practical information

Accomodation 
The most affordable accommodation in Bodø is offered by Studentinord in Nordavind, which is located on campus (www.studentinord.no/shortterm/korttidsleie-Nordavind). Please register as soon as possible, since they are usually booked. Alternatives include airbnb, or ho(s)tels such as Scandic, Radisson Blu, Thon, Clarion, Bodø Hotell, City Hotel Bodø or Bodø Hostel.

Public transport and directions 
Nord University campus Bodø is located 10 km from the city center, but can be reached in 20 minutes with bus 1, or in 30 minutes with bus 2. The apps (“Billett Nordland” for tickets and “Reis Nordland” for time tables) make it easy and cheaper to take the bus. To find your way on campus, check Mazemap. On Monday, we meet at Alexandria at 9h30.

Azure Lab Services 
​For the practical sessions, we will be using virtual machines via Microsoft Azure Lab Services. Shortly before the course, you will receive a link to register to the Azure platform. Access via ssh will be demonstrated during the first session.​

Start date:

28 February 2022 09:00

End date:

06 March 2022 17:00

Location:

Bodø
Population genomics 2022.jpg










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Number of ECTS

When
Classes: 28 Feb. - 6 March 2022
Excursion: 5 - 6 March 2022 (optional; info follows)
 
Faculty 
Course coordination:
Joost Raeymaekers (JR)

Invited lecturers:
Britta Meyer (BM)
Mark Ravinet (MR)
Emiliano Trucchi (ET)
Oscar Gaggiotti (OG)
Bart Peeters (BP)
Kostas Sagonas (KS)
Anja Westram (AW)
Lars Martin Jakt (MJ)
Irina Smolina (IS)
Alexander Jüterbock (AJ)
​​​
 
Registration is on a first-come, ​first-serve basis​