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Population genomics@Nord

Bijgewerkt: mrt 7

By Joost Raeymaekers.


The 2020 PhD course in Population Genomics at Nord University (course code : BIO9001) is held in Bodø from 9th – 15th of March 2020. The course, sponsored by NORBIS, consists of a series of lectures, demonstrations and computer laboratories that cover theory and practice of population genomics analyses. Topics include population genetic theory, introduction to command line, data formats, coalescence/population demography, analysis of population structure, adaptive evolution and inferring selection, gene-environment interactions, landscape genomics, and the analysis of admixture/hybridisation. Both understanding theory and acquiring the skills to analyse data will be emphasized.


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When?


Classes: 9 - 13 March 2020

Excursion: 14 - 15 March 2020 (optional; info follows)


Faculty


Course coordination:

Joost Raeymaekers (JR)


Invited lecturers:

Britta Meyer (BM)

Mark Ravinet (MR)

EmilianoTrucchi (ET)

Oscar Gaggiotti (OG)

Bart Peeters (BP)


Contributions:

Lars Martin Jakt (MJ)

Irina Smolina (IS)

Alexander Jüterbock (AJ)

Kostas Sagonas (KS)


Programme


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.


Learning outcomes and competence


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.


Evaluation


The evaluation will be report-based. The students will analyze 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: 16th of April 14:00).


Number of ECTS: 5


Registration


You can register here for the course on a first-come, first-serve basis.


Course excursion (14-15 March)


Bodø's beautiful surroundings offer many opportunities for outdoor activities. On 14th of March, 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 15th 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.


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 wit bus 2. Two phone applications ("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.


Time table and rooms - Here are the times and rooms for the various lectures (L) and practicals (P). (*) On Monday we start exceptionally at 09:45.



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.


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


  • R version 3.6.1 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:



Looking forward to see you in Bodø!

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