Abstract:

In recent years there has been increased interest in the simulation of honeybee breeding programmes, due to their biological and commercial importance. However, existing simulators do not provide all the functionality to replicate honeybee specificities. We developed an R package, SIMplyBee, which extends the popular AlphaSimR simulator with haplo-diploidy, polyandry, complementary sex determination, caste system, and colony quantitative genetics. We developed two classes representing operational units, Colony and Colonies, and a SimParamBee class holding global honeybee simulation parameters. Next, we assigned four levels of functions; Auxiliary, Population, Colony and Colonies to allow the simulation of both individual and colony events such as swarms or supersedures. To demonstrate the package, we simulated a yearly cycle of an isolated apiary and inspected variability at the csd locus. SIMplyBee represents the first flexible and holistic simulator of honeybee genomes, biology, reproduction, colony events, and quantitative values at individual and colony levels.