ForBio course: Population genetics of polyploids, from theory to practice

Objectives: Polyploidy is widespread and frequent in plants (including many crops), but also occurs in animals such as fish and amphibians. However, our understanding of the genetics of polyploid populations and populations of mixed ploidy is still poor. This is mainly because population genetics theory was originally developed for diploids. Moreover, there is often a gap between theory developed for polyploids and its practical implementation. This practically-oriented course will attempt to bridge this gap. Simulation-based exercises (among others using R) will elucidate theoretical foundations of both diploid and polyploid population genetics. Additionally, analyses of real or realistic example datasets (microsatellite and SNP markers) will give participants hands-on training in several available methods for the population genetic analysis of polyploids.

The exact topics will include clustering methods with specific attention to the problem of mixed ploidy, analysis of population genetic/genomic structure in polyploid complexes, effect of mating system variation and analysis of selection in polyploid genomes. Participants will also devote time to a group project focused on application of gathered knowledge in further modelling or on analyses of empirical datasets with discussion of further prospects and methods limitations. Materials from the previous course run can be found here.

Course teachers: Olivier Hardy, Filip Kolář, Patrick Meirmans, Patrick Monnahan, Polina Novikova, Marc Stift

Recommended background: Basic knowledge of R programming language and general knowledge of population genetic foundations of diploid populations (diversity, differentiation). Experience in scripting in R is useful, but for the beginners there will be an extra R-introductory day before the workshop start.

Course level: PhD-level course. Motivated MSc students can be admitted as well. The format of this course requires students to identify the need of using these methods in their research. A 2 ECTS course certificate will be given to students that pass the course by ForBio.

Fee: No course fee.

Travel, food and accommodation: Shared accommodation is free of charge. In addition, ForBio will cover travel for Norwegian ForBio members. Meals are included, and the venue has cooking facilities and participants will prepare food together in shifts.

Course plan: The preliminary course schedule can be downloaded here.

Application. Please submit a ca 200-500 word summary of your research and motivation and the CV, merged in a single PDF file, no later than November 1st 2020. Later applications will be considered until the course is fully booked. In case the participant is willing to provide their own data for the project work (not obligatory), please also attach a short description of the data set (organism, type of markers, analyses done/in progress) and the scientific questions that could be addressed. There is a maximum of 16 participants. If needed, we will select participants based on topical relevance and motivation. Members of ForBio and PhD students will be prioritized (but MSc students and postdocs will also be considered). For non-ForBio members we require registration as ForBio associates (free of charge). Register here.

Contact Hugo de Boer for more information.

Tags: Target capture, Gene capture, Phylogenomics, Target enrichment, Anchored sequencing, Hyb-Seq, Hybrid sequencing
Published July 6, 2020 3:11 PM - Last modified July 6, 2020 3:15 PM