SIMplyBee: an R package to simulate honeybee populations and breeding programs

Area of Science:

• * Population Genetics
• * Animal Breeding
• * Apiculture

Background:

• * Western honeybees are vital globally but face population decline, impacting economics and genetic diversity.
• * Breeding and conservation programs are crucial, necessitating efficient simulation tools.
• * Existing simulators lack detailed honeybee population modeling capabilities.

Purpose of the Study:

• * To introduce SIMplyBee, a holistic R package for simulating honeybee populations and breeding programs.
• * To provide a flexible platform for testing diverse breeding and conservation strategies.
• * To enhance research in honeybee genetics and quantitative genetics.

Main Methods:

• * SIMplyBee extends the AlphaSimR package with honeybee-specific classes (SimParamBee, Colony, MultiColony).
• * Incorporates key honeybee reproductive and social characteristics: haplodiploidy, complementary sex determination, and polyandry.
• * Simulates individual genomes, colony events, and quantitative genetics at individual and colony levels.

Main Results:

• * Successfully implemented simulation of honeybee genomes, colonies, and haplodiploid inheritance.
• * Demonstrated capabilities in managing multiple colonies and simulating colony events.
• * Provides tools for obtaining genomic data and quantitative genetics metrics.

Conclusions:

• * SIMplyBee offers a comprehensive platform for simulating honeybee populations and evaluating breeding strategies.
• * Enables modeling of intra-colony interactions for genetic gain and variability assessment.
• * Future work will focus on genome simulation, performance optimization, and spatial awareness.