🐝 SIMplyBee Explorer

An interactive Shiny application to learn and demonstrate the SIMplyBee R package — a stochastic simulator of honeybee populations and breeding programmes, built on top of AlphaSimR .

Reference paper: Read the SIMplyBee paper by Obšteter J., Strachan. L. K., Bubnič J., Prešern J., Gorjanc G.

The Shiny app was developed by S. Biffani (IBBA-CNR & Dipartimento di Scienze Medico-Veterinarie, UNIPR) & P. Cozzi (IBBA-CNR)

📦 What is SIMplyBee?

SIMplyBee simulates individual bees that form a colony including:

👑 A queen
🐝 Workers (fertilised females)
🐝 Drones (haploid males)
🌸 Virgin queens
💑 Fathers (mating drones stored with the queen)

Multiple colonies can be studied together as an apiary-level simulation.

Teaching tip: with one father, CSD risk may still be 0% under open mating; use the inbred brother-mating option in Colony Setup for a stronger classroom demo.

🔬 Key Features

Haplo-diploid inheritance
Complementary sex determiner (csd) locus
Colony events: swarming, supersedure, collapse
Quantitative genetics & colony values
Genomic information & pedigree-based parentage
Full AlphaSimR compatibility

🗺️ App Navigation

Colony Setup – Found genomes and build a colony
Colony Structure – Visualise castes, CSD, and parentage
Colony Events – Simulate swarm / supersede / collapse
Quant. Genetics – Define traits and simulate colony values
Multi-Colony – Simulate an apiary

⚡ Minimal Working Example

library(SIMplyBee) library(AlphaSimR) # 1. Create founder genomes founderGenomes <- quickHaplo(nInd = 6, nChr = 1, segSites = 100) # 2. Set up global simulation parameters SP <- SimParamBee$new(founderGenomes) # 3. Create virgin queens from founder genomes basePop <- createVirginQueens(founderGenomes, simParamBee = SP) # 4. Create a drone congregation area (DCA) DCA <- createDrones(basePop[2:6], nInd = 100, simParamBee = SP) droneGroup <- pullDroneGroupsFromDCA(DCA, n = 1, nDrones = 15, simParamBee = SP) # 5. Create and mate a colony queen colony <- createColony(x = basePop[1], simParamBee = SP) colony <- cross(colony, drones = droneGroup[[1]], checkCross = 'warning', simParamBee = SP) # 6. Build up the colony colony <- buildUp(colony, nWorkers = 1000, nDrones = 500, exact = TRUE, simParamBee = SP) # 7. Inspect nWorkers(colony) nDrones(colony) pHomBrood(colony, simParamBee = SP)

⚙️ Simulation Parameters

Number of founder genomes:

Number of chromosomes:

Segregating sites per chr:

Possible csd alleles:

Fathers (drones) queen mates with:

Workers at build-up:

Resident drones at build-up:

Mating design:

Open DCA mating (biologically realistic)

Inbred brother mating (classroom CSD demo)

Tip: with one father, open mating often still gives 0% CSD risk because the father may share neither queen csd haplotype. Use the inbred demo to make matching much more likely.

Shared random seed (used in all simulation tabs):

All stochastic tabs derive reproducible, module-specific seeds from this base value.

📋 Colony Setup Log

🧬 Founder Genome Summary

🔑 R Code Used

ℹ️ Note: Run the Colony Setup tab first to create a colony before exploring its structure.

👑 Queens

🐝 Workers

🐝 Drones

💑 Stored fathers

🍩 Live Colony Members

This plot shows castes physically represented in the colony. Fathers are tracked separately as stored mating drones.

🧬 CSD Homozygous Brood

CSD brood risk is computed directly for the current colony with SIMplyBee's CSD functions. The panel below also shows the exact queen and stored-father csd haplotypes used in that calculation.

📊 Worker Relatedness and Parentage

Worker sisterhood is computed from realised worker parentage when available, and falls back to the stored number of fathers otherwise.

ℹ️ Note: Requires a colony created in the Colony Setup tab.

🌪️ Simulate Event

Choose colony event:

Swarm (colony reproduces)

Supersede (queen replaced)

Collapse (colony dies)

Proportion leaving with swarm:

📋 Event Log

📊 Before vs After Event

🍯 Trait Definition

Colony honey yield is modelled as queen contribution + summed worker contribution.

Queen trait : colony-level queen effect
Worker trait : colony-level total worker effect, internally scaled by worker number

Queen trait mean:

Worker trait mean (colony total):

Heritability (h²):

Genetic correlation Q–W:

Additional colony environmental SD:

Number of colonies:

Workers per colony:

📊 Colony Honey Yield Distribution

🔬 Genetic Signal and Selection Response

These plots are meant to respond to heritability: higher h² makes colony phenotype track genetic value more closely, so selection on phenotype captures more genetic merit.

📋 Summary Statistics

🏠 Apiary Setup

Number of colonies in apiary:

Founder genomes:

Workers per colony:

Possible csd alleles:

Simulate swarming in some colonies?

Proportion of colonies that swarm: