DOI: 10.5061/dryad.h18931zx7
title: Data for: Comparative evaluation of phenotypic, pedigree, and family-based selection in insect breeding using stochastic simulation

description: Selective breeding in insects has predominantly relied on phenotypic
 selection without considering relatedness. Selection on estimated breeding
 values could potentially increase genetic gain, but the challenge of
 pedigree tracking complicates this. Family selection can be used as an
 alternative to individual selection, either using combined between- and
 within-family selection, or strict between-family selection with full-sib
 group records as a proxy for individual data. The effectiveness of family
 selection can however be compromised by the presence of unmitigated common
 environment effects. In this study, we employ stochastic simulations to
 explore expected genetic gain and rate of inbreeding in insect populations
 under four single-trait selection schemes: phenotypic selection,
 individual pedigree selection, combined selection using both family and
 individual breeding values for selection, and between-family selection
 using full-sib average phenotypes for breeding value estimation. These
 schemes are compared on genetic gain and rate of inbreeding across five
 trait heritabilities (0.05, 0.1, 0.2, 0.4 and 0.6), two variations in
 number of families in the population (60 or 200), and two offspring group
 structures for the family breeding schemes (1 or 3 sib groups per female)
 with a fixed common environment effect. Selection based on individual
 breeding values results in significantly higher genetic gain than
 phenotypic selection at low heritability (≤0.1), and similar gain at
 heritability &gt;0.1. Phenotypic selection results in a lower rate of
 inbreeding (0.003-0.011) compared to other schemes (0.005-0.055) at low
 heritability (≤0.1), but this difference is reduced as heritability
 increases. Combined selection results in genetic gain between that of the
 phenotypic and individual pedigree schemes, depending on sib group
 structure and heritability. Using between-family selection reduces genetic
 gain (0.23-1.97) compared to other schemes (0.40-4.34). Establishing
 multiple sib-groups mitigates the confounding of genetic and common
 environment effects, and thus the reduction in genetic gain from family
 selection schemes. Increasing the number of families from 60 to 200 in the
 breeding population reduces inbreeding in all scenarios (ΔF at 60 families
 is 0.009-0.055, at 200 families is 0.003-0.031). We conclude that
 selection on individual breeding values yields greater genetic gain
 compared to family breeding values and selection on phenotypes. The
 between-family approach is an alternative when individual pedigrees are
 not feasible to maintain. Phenotypic selection results in both high
 genetic gain and generally low rates of inbreeding, but as heritability
 increases, so does the rate of inbreeding. Therefore, phenotypic selection
 should not be implemented without any inbreeding control in long term
 selection.
description: # Data for: Comparative evaluation of phenotypic, pedigree, and
 family-based selection in insect breeding using stochastic simulation
 [https://doi.org/10.5061/dryad.h18931zx7](https://doi.org/10.5061/dryad.h18931zx7) ## Description of the data and file structure All data is simulated.  ### Files and variables #### Directory and file naming structure 4 directories: **CombSel**: directory for combined selection scenarios **FamSel**: directory for family selection scenarios **IndPedSel:** directory for individual pedigree selection scenarios **PhenSel**: directory for phenotypic selection scenarios Each directory has two folders: **60_families**: scenarios where the population size is 60 families **200_families**: scenarios where the population size is 200 families FamSel and CombSel have two extra directories in each of the 60_families and 200_families folders: 1_group: scenarios where offspring are not split in multiple sib-groups 3_groups: scenarios where offspring are split in three sib-groups Each lowest folder level contains 5 .txt files with the following name structure: scenario+size_groups_replicates_total_data_heritability scenario = CombSel, FamSel, IndPedSel, PhenSel size = small (60 families), large (200 families) groups = either nothing, 1G (1 group), 3G (3 groups) replicates = Number of replicates of the scenario (always 20) heritability = h2005 (0.05), h201 (0.2), h202 (0.2), h204 (0.4), h206 (0.6) #### File structure and variables Each file contains 27 variables and 1.081.800 observations. There are 15 generations of selection replicated 20 times in each data file. Two traits are simulated but only one is part of the selection scheme (trait 1). id: identification of individual sire: identification of father dam: identification of mother sex: male (m) or female (f) generation: generation 1-15 group: id of female + A, B or C at1: additive genetic effect for trait 1 (the selection trait) at2: additive genetic effect for trait 2 (correlated trait, not included in the study. Genetic correlation is -0.3, heritability of trait 2 is 0.4) ct1: common environment effect for trait 1 (only in CombSel and FamSel) ct2: common environment effect for trait 2 (only in CombSel and FamSel) et1: residual effect for trait 1 et2: residual effect for trait 2 TBV_t1: deviation from trait mean for trait 1 (at1 + ct1 + et1) TBV_t2: deviation from trait mean for trait 2 (at2 + ct2 + et2) t1: trait value for trait 1 t2: trait value for trait 2 F: inbreeding coefficient selected: selected as parent of next generation. 0 = no, 1 = yes. indBV: always NA mean_t1: family average value for trait 1 f: number of females in the family m: number of males in the family EBV_t1: estimated breeding value for trait 1 candM: minimum number of males in the family. either 2 (there are 2 or more males in the family after filtering) or NA (there are not 2 or more males in the family after filtering) candF: minimum number of females in the family. either 4 (there are 4 or more females in the family after filtering) or NA (there are not 4 or more females in the family after filtering) candidate: whether family is a candidate family or not, based on filtering criteria. Y = Yes, N = No. rep: replicate (1-20)