DOI: 10.5061/dryad.stqjq2c8t
title: Data from: Comparison of pooled semen insemination and single colony insemination as sustainable honeybee breeding strategies

description: 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.
description: 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 r<sub>QW</sub>=-0.18 and "strong" corresponds to the value r<sub>QW</sub>=-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.
description: # Comparison of pooled semen insemination and single colony insemination
 as sustainable honeybee 
 The dataset comprises the source code of the stochastic simulation program
 BeeSim that was used in the article. Along with the program comes an
 R-script that produces the necessary parameter files and a results file
 that contains the concrete simulation results presented in the article. ##
 Description of the data and file structure The zipped folder
 **BeeSim_and_data.zip** contains four elements. 1. The folder **src** with
 the source code for the version of the Program BeeSim that was used in the
 article. 2. A **makefile** to compile the code 3. An R-script named
 **par_files.r** producing the parameter files that were used for the
 simulations of the article 4. A csv-file named **results.csv** containing
 the simulation results that were used to write the article. ###
 Description of the source code The source code of the program is
 distributed over nine files that are contained in the folder **src**. It
 is written in the programming language C. * **src/CBeeSim_main_mt.c**
 contains the `main` function. The functions specified in this file
 orchestrate the broad sequence of events. I.e., reading of option
 settings, reading of parameter files, simulation of the breeding setup,
 freeing of the alloc'd space. * **src/CBeeSim_mt.c** specifies the
 functions that are used for the actual simulation of individual breeding
 years. For the specified number of years, new queens are born, get mated,
 undergo a performance test, and are selected to reproduce. *
 **src/CBeeSim_mt.h** is the common header file for all functions defined
 in files of the folder **src**. * **src/gauss.c** is a small file
 containing a few general functions that help in the generation of random
 variavles of the right type. For example, it contains a function that
 returns a random value following a Gaussian distribution. Hence the name.
 * **src/initializations_mt.c** contains functions that initialize
 important large abstract objects whose specifications are not known at
 compile time. For example a relationship matrix of the right size has to
 be created. * **src/lazy.c** contains small helper functions that reduce
 writing effort. For example the function `xmalloc` allocates space with
 `malloc` and aborts the program if the allocation failed. *
 **nullstructs_mt.c** defines for the smaller structs used in the program,
 what their null setting should be. * **src/read_from_parameter_file.c**
 specifies the functions that are used to read the simulation parameters
 from the parameter files prior to the actual simulation of the breeding
 process. * **src/write_to_files.c** defines the functions that are used to
 write the output files. ### Compilation The **makefile** allows to compile
 the source code. Writing the command "make" in the command line
 will trigger the creation of a folder **bin** containing the executable
 file **bin/BeeSim**. This has only been tested under Ubuntu. ### Use of
 the program Generally, the program is called with a command of the form
 ``` bin/BeeSim [OPTIONS] [PARAMETER FILE] ``` The `[OPTIONS]` are declared
 by a minus sign (-) followed by a letter. Relevant examples for such
 options are * `-a` invokes printing of all relevant simulation results to
 files * `-F` triggers the use of a Finite Locus Model for the
 honeybees' genetics (instead of the default Infinitesimal Model) *
 `-p` triggers phenotypical selection instead of the default selection for
 BLUP breeding values. If the program is called with option `-h`, a full
 list of possible options is shown. The simulations of the article used the
 options `-a` and `-F`. The parameter file is used to relay numerical
 parameters to the simulations. For example, under the heading
 `YEARS_TO_BE_SIMULATED` it is to be specified, over how many years the
 simulated breeding experiment should expand. `REPETITIONS` specifies, how
 often it is to be repeated, etc. Some parameter settings are outsourced to
 more specialized parameter files. For example, the heading
 `MATING_CONTROL` expects a path to another file which then specifies the
 parameters relating to mating control (such as
 `PERCENTAGE_OF_CONTROLLED_MATING_BREEDING_PER_YEAR`, specifying which
 percentage of breeding queens is mating in a controlled fashion each
 year). The file **par_files.r** contains R code that was used to create
 the parameter files used in the article. Calling ``` Rscript --vanilla
 par_files.r ``` triggers the creation of 128 folders containing the
 parameter files used for simulating the different breeding schemes of the
 article. Own parameter sets can be created by using one of these 128 sets
 of parameters and changing them according to one's needs. The
 headings used in the parameter files are generally self-explaining. An
 earlier version of BeeSim has previously been published on Dryad (DOI:
 [10.5061/dryad.1nh544n](https://doi.org/10.5061/dryad.1nh544n)) along with
 extensive documentation on how to use the program. There also all the
 individual headings are explained in detail. To run the code, the user
 will further have to install the third-party programs BLUPF90
 ([Link](http://nce.ads.uga.edu/wiki/doku.php)) and PInCo
 ([Link](https://doi.org/10.1111/jbg.12347)) (and specify their locations
 in the parameter files under the respective headings `BLUPF90` and
 `INVERSE_RELATIONSHIPS`). ### Results of the study The file
 **results.csv** contains the results of the simulations used for the
 article. It consists of a table with 11 columns. The first seven columns
 specify simulation settings while columns 8 to 11 contain simulation
 results. All simulation results are averaged over the 100 repetitions per
 setting. 1. 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. 2. 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. 3. 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. 4. 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. 5. The
 column "insemination" takes on the values "indiv" and
 "mixed". Here, "indiv" refers to single colony
 insemination and "mixed" refers to pooled semen insemination. 6.
 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 r<sub>QW</sub>=-0.18
 and "strong" corresponds to the value
 r<sub>QW</sub>=-0.53 7. 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. 8. 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. 9.
 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. 10. 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. 11. 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. Queens that were born in years 0 and 1 form the
 base population. They are simulated without parents. Thus, for them no
 paternal.generation.interval could be calculated and they received the
 value "NA".