Comparison of pooled semen insemination and single colony insemination as sustainable honeybee breeding strategies

Instrumental insemination of honeybees allows for two opposing breeding strategies. In single colony insemination (SCI), all drones to inseminate a queen are taken from one colony. In pooled semen insemination (PSI), sperm of many genetically diverse drones is mixed and queens are fertilised from the resulting drone pool. While SCI allows for maximum pedigree control, proponents of PSI claim to reduce inbreeding and maintain genetic variance. Using stochastic simulation studies, we compared genetic progress and inbreeding rates in small honeybee populations under SCI and PSI. Four different selection criteria were covered: estimated breeding values (EBV), phenotypes, true breeding values (TBV), and random selection. Under EBV-based truncation selection, SCI yielded 9.0% to 44.4% higher genetic gain than PSI, but had vastly increased inbreeding rates. Under phenotypical or TBV selection, the gap between SCI and PSI in terms of genetic progress narrowed. Throughout, PSI yielded lower inbreeding rates than SCI, but the differences were only substantial under EBV truncation selection. As a result, PSI did not appear as a viable breeding strategy due to its incompatibility with modern methods of genetic evaluation. Instead, SCI is to be preferred but instead of strict truncation selection, strategies to avoid inbreeding need to be installed.

Methods
The zipped folder BeeSim_and_data.zip contains four elements.

The folder "src" witht the source code (written in C) for the version of the Program BeeSim that was used in the article. 
A makefile to compile the code
An R-script named "par_files.r" producing the parameter files that were used for the simulations of the article
A csv-file named "results.csv" containing the simulation results that were used to write the article.

An earlier version of BeeSim has previously been published on Dryad (DOI: 10.5061/dryad.1nh544n) along with extensive documentation on how to use the program. To run the code, the user will further have to install the third-party programs BLUPF90 (Link) and PInCo (Link).

The file "results.csv" contains a table with 11 colums. The first seven colums specify simulation settings while colums 8 to 11 contain simulation results. All simulation results are averaged over the 100 repetitions per setting.

The column "birth.year" refers to the age cohort. As 70 years were simulated, it ranges from 0 to 69. So, results in a row with birth.year value t refer to queens that were born in year t.
The column "fullsibs" takes on the values 5 and 10. Results in a row with fullsibs value n refer to breeding schemes where selected queens produced n offspring queens each.
The column "dpq.in.population" takes on the values 40 and 80. Results in a row with dpq.in.population value n refer to breeding schemes where there were n drone producing queens (DPQ) selected per year.
The column "no.of.iis" takes on the values 1 and 8. Results in a row with no.of.iis value n refer to breeding schemes where there were n instrumental insemination stations per year.
The column "insemination" takes on the values "indiv" and "mixed". Here, "indiv" refers to single colony insemination and "mixed" refers to pooled semen insemination.
The column "correlation" takes on the values "weak" and "strong". It signified how (maternal) queen effects and (direct) worker effects of the selection trait are correlated. Here, "weak" corresponds to the value rQW=-0.18 and "strong" corresponds to the value rQW=-0.53
The column "selection" indicates the selection criterion. It takes on the values "blup", "geno", "pheno", and "rand". "blup" indicates selection for best linear unbiased prediction (BLUP) estimated breeding values, "geno" indicates selection for true breeding values (i.e. for the genotype), "pheno" indicates selection for phenotypes and "rand" indicates random selection.
The column "mean.breeding.value" indicates the average breeding values of queens born in the specified years in the respective breeding programs defined by columns 2 to 7.
The column "mean.inbreeding" indicates the average inbreeding coefficients of queens born in the specified years in the respective breeding programs defined by columns 2 to 7.
The column "genetic.variance.ic" indicates the variance of true breeding values in the inheritance criterion (IC, sum of queen's direct and maternal TBV) of queens born in the specified years in the respective breeding programs defined by columns 2 to 7.
The column "paternal.generation.interval" takes on values between 2 and 3. It indicates how old the DPQ were on average at the time when their drones were used for inseminations. The values are takes as averages over all queens born in the specified years in the respective breeding programs defined by columns 2 to 7.