Population genetics of polyploids, from theory to practice

• Tutorial with questions only for Days 1-4 and the same Tutorial with answers (pre-final version)

• Schedule of the week

Day 0 

Introduction to scripting and simulations in R

Getting to grips with using R to simulate diploid and polyploid populations

Day 1 

Introduction to autopolyploid population genetics theory, population diversity and differentiation

Genetic diversity, HWE, analogues of F-statistics, missing dosage problem (theory & simulations)

Software

R Scripts for days 1 & 2

• Slides on STRUCTURE interpretation 

Day 2

Impact of mixed-mating on autopolyploid populations & Clustering methods

Inbreeding - Double reduction - Estimating selfing rates with mixed ploidy - clustering mixed ploidy populations (simulations &empirical analyses)

Software

Sample data

Day 3 

Evolutionary history reconstruction in polyploid species and populations

Genetic structure, diversity and differentiation of mixed-ploidy systems using genome-wide SNP data (empirical analyses)

Software

Day 4 

Selection in diploids vs polyploids

Detecting footprints of selection in mixed-ploidy systems using genome-wide SNP data (empirical analyses)

• Introductory slides and a theory paper

• General overview of topics for Day 3 & 4 in Majda's manuscript and associated GitHub