Genetic relatedness of individual honeybees using SIMplyBee

Introduction

This repository contain R scripts that demonstrates the principles of expected and realised genetic relatedness among individual honeybees using SIMplyBee.

If you have no experience with SIMplyBee, we suggest you go to the software's website simplybee.info and study the tutorials. This repository uses SIMplyBee to simulate honeybee populations as described in the below manuscript and to calculate and summarise relatedness between individual honeybees.

As of the 20.05.24, we have a paper associated with these scripts in the final stages of writing. In the coming weeks, a link to the pre-print manuscript will be available here.

Respository contents

The YearCycleSimulation folder contains Scripts and Plotting Data

Scripts contains:

• SimulateFounderPop.R uses SIMplyBee to create founder population genomes.
• YearCycle_Relatedness.R runs a yearly cycle of honeybee population for 10 years and calculates and summarizes genetic relatedness for three different honeybee populations.
• Plot_YearCycle_output.R processes the output data of the YearlyCycle_Relatedness.R and create plots to visualise the data.

Plotting Data contains:

• FounderGenomes_ThreePop_16chr.RData is the output file of the script SimulateFounderPop.R that can be downloaded and used to by-pass this part of the simulation, as it can be time-consuming.