SIMplyBee

SIMplyBee simulates honeybee populations and breeding programs to model genetics and colony dynamics for conservation and breeding strategy assessment.

Key Features:

• Extension of AlphaSimR: Builds on the stochastic simulator AlphaSimR to provide honeybee-specific simulation capabilities.
• Honeybee-specific classes: Implements SimParamBee, Colony, and MultiColony classes to represent global simulation parameters, individual colonies, and multiple colonies respectively.
• Genomic and quantitative genetics: Simulates individual honeybee genomes and quantitative genetic values, explicitly modeling haplodiploid inheritance and complementary sex determination.
• Social organization and colony events: Models colony-level events and social behaviors including polyandry that influence individual- and colony-level genetics.
• Colony-level aggregation: Supports user-defined functions to aggregate individual genetic values into colony-level metrics for analysis of interactions within colonies.
• Performance and spatial modeling (development focus): Ongoing enhancements target improved genome simulation fidelity, performance optimization, and incorporation of spatial awareness in mating functions and phenotype simulations.

Scientific Applications:

• Breeding strategy evaluation: Assess the effects of different breeding programs on genetic gain and variability in honeybee populations.
• Conservation genetics: Model impacts of management strategies on future genetic diversity and colony resilience.
• Colony dynamics research: Study how social behaviors and colony events alter individual- and colony-level genetic and phenotypic outcomes.
• Method development for haplodiploid systems: Provide a platform for testing and developing genomic and quantitative genetic methods tailored to haplodiploid organisms and complementary sex determination.

Methodology:

SIMplyBee extends AlphaSimR to simulate individual genomes and quantitative genetic values while explicitly modeling haplodiploid inheritance, complementary sex determination, colony events including polyandry, user-defined aggregation of individual-to-colony metrics, and genetic, environmental, and social factors.