DOI: 10.5061/dryad.bzkh189n1
title: Inbreeding depression in male reproductive traits

description: Inbreeding frequently leads to inbreeding depression, a general reduction
 in trait values and loss of fitness, and it appears that some sexually
 selected traits are especially sensitive to inbreeding, but sperm may be
 an exception. Additionally, because inbreeding depression is always in the
 direction of low fitness, it can reveal the direction of past selection
 acting on trait values. Here, we experimentall manipulate levels of
 inbreeding in a beetle (Tribolium castaneum) by full-sib mating for six
 generations. This breeding design allowed us to track the effects of
 increasing homozygosity on male reproductive traits (sperm and testes
 size), male size and lifespan, and reproductive output within inbred
 families, and on the heritability of these traits. All traits measured
 showed significant inbreeding depression and heritabilities tended to
 increase with inbreeding. Since inbreeding resulted in shorter sperm and
 smaller testes, it suggests that longer sperm and larger testes confer
 higher fitness in this beetle.
description: # Inbreeding depression in male reproductive traits Vasudeva, R.1*, Sales,
 K.2, Gage, M.J.G.†, and Hosken, D.J.3* Summary: This study investigates
 the consequences of inbreeding on male reproductive traits and survival.
 Overall, we initiated small independent populations from an outbred stock
 and from this we carried out full-sib matings for six consecutive
 generations. We tracked many life history traits linked to fitness
 (reproductive success). This work constitutes 29 data files (.csv), image
 files (.jpg) overall that are linked to the findings of this study; ‘.csv’
 format and an Rscript file. RV with help of members of the group initiated
 the small populations and was responsible for data collection, curation
 and KS, MJGG helped maintain the lines for six months due to RV’s absence.
 RV collected much of this data, imaged the traits, measured them and
 carried out the preliminary analysis. Lifespan of the study species is
 long for a small beetle, we tracked individuals until death and thus no
 right-censoring was observed in our dataset. Fodder was replaced
 throughout this two year duration to keep the animals in clean conditions.
 Images collected during the experimental assays for bio-measurements are
 uploaded here in a .zip file (named: “Inbreeding_Reproduction_Images.zip).
 Within the zipped file, • there are four folders (Calibration slide;
 Elytra; Sperm; Testes) • Calibration slide includes graticule images that
 were used to calibrate the morphological aspects of data collection, with
 several .jpg files and a .txt file • The “Measurements.txt” file in the
 above folder describes the specific details on the scope, use of a
 zoom/extender device. • Elytra: has folders with images of elytra (proxy
 for body size) across different generations. • Sperm: has four folders
 with a subset of images taken to quantify this trait. • Testes: a subset
 of folders from the experimental inbreeding and baseline generations,
 these folders include images of the testes through the experiment. • all
 of the above are a subset of the images taken, which have been uploaded,
 and these can be distinguished by the generation it was taken. Calibration
 slides are also included to highlight how these were standardised before
 measurements were made. R Session Info: R version 4.4.2 (2024-10-31)
 Platform: x86_64-apple-darwin20 Running under: macOS Sequoia 15.3.1 Matrix
 products: default BLAS:
 /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libRlapack.dylib; LAPACK version 3.12.0 locale: \[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 time zone: Europe/London tzcode source: internal attached base packages: \[1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): \[1] vctrs_0.6.5 cli_3.6.3 TH.data_1.1-3 rlang_1.1.5 estimability_1.5.1 Formula_1.2-5\ \[7] car_3.1-3 generics_0.1.3 xtable_1.8-4 zoo_1.8-12 glue_1.8.0 performance_0.13.0 \[13] grid_4.4.2 carData_3.0-5 tibble_3.2.1 abind_1.4-8 MASS_7.3-61 mvtnorm_1.3-3\ \[19] lifecycle_1.0.4 multcomp_1.4-28 insight_1.0.2 compiler_4.4.2 codetools_0.2-20 dplyr_1.1.4\ \[25] sandwich_3.1-1 emmeans_1.10.7 coda_0.19-4.1 pkgconfig_2.0.3 rstudioapi_0.17.1 lattice_0.22-6\ \[31] R6_2.6.0 tidyselect_1.2.1 splines_4.4.2 pillar_1.10.1 magrittr_2.0.3 Matrix_1.7-1\ \[37] tools_4.4.2 survival_3.7-0 remotes_2.5.0 ### Filename: Balanced\_Corr\_Gens\_Female Elytra Length.csv Dataset describing father-daughter elytra length (proxy for body size) measurements (in m) between generation through inbreeding to calculate heritability. Column A: Corr_Gen Correlations between generations Column B: Fam.ID Replicate family identification Column C: EL1_mm Elytra length of the parental generation in ‘mm’ Column D: EL2_mm Elytra length of the daughter generation in ‘mm’ Column E: EL1 Elytra length of the parental generation in ‘m’ Column F: EL2 Elytra length of the daughter generation in ‘m’ Column G: ID sex of the individual; female ### Filename: Balanced\_Corr\_Gens\_Female Longevity.csv Dataset describing father-daughter lifespan (in weeks) between generation through inbreeding to calculate heritability. Column A: Corr_Gen Correlations between generations Column B: Fam.ID Replicate family identification Column C: Age1_weeks Lifespan in (weeks) female 1 (mother) Column D: Age2_weeks Lifespan in (weeks) female 2 (daughter) Both female 1 and 2 are related Column E: ID sex of the individual; female   ### Filename: Balanced\_Corr\_Gens\_Male Elytra Length.csv Dataset describing father-son elytra length (proxy for body size) measurements (in m) between generation through inbreeding to calculate heritability. Column A: Corr_Gen Correlations between generations Column B: Fam.ID Replicate family identification Column C: EL1_mm Elytra length of the parental generation in ‘mm’ Column D: EL2_mm Elytra length of the son generation in ‘mm’ Column E: EL1 Elytra length of the parental generation in ‘m’ Column F: EL2 Elytra length of the son generation in ‘m’ Column G: ID sex of the individual; male   ### Filename: Balanced\_Corr\_Gens\_Male Longevity.csv Dataset describing father-son lifespan (in weeks) between generation through inbreeding to calculate heritability. Column A: Corr_Gen Correlations between generations Column B: Fam.ID Replicate family identification Column C: Age1_weeks Lifespan in (weeks) male 1 (father) Column D: Age2_weeks Lifespan in (weeks) male 2 (son) Both male 1 and 2 are related Column E: ID sex of the individual; male ### Filename: Balanced\_Corr\_Gens\_Offspring Productivity.csv Dataset describing reproductive output (offspring counts, over 7 days of oviposition) of parental generation against the offspring generation through inbreeding to calculate heritability. Column A: Corr_Gen Correlations between generations Column B: Fam.ID Replicate family identification Column C: Ofs1 (counts) Offspring produced by a pair in the parental generation Column D: Ofs1 (counts) Offspring produced by a pair in the offspring generation ### Filename: Balanced\_Corr\_Gens\_Sperm Length.csv Dataset describing total sperm length (m) of parental generation against the offspring generation through inbreeding to calculate heritability. Column A: Corr_Gen Correlations between generations Column B: Fam.ID Replicate family identification Column C: SL1 (m) Sperm length measured in the parental generation Column D: SL2 (m) Sperm length measured in the offspring generation   ### Filename: Balanced\_Corr\_Gens\_Testes Volume.csv Dataset describing testes volume (mm3 and m3) of parental generation against the offspring generation through inbreeding to calculate heritability. Column A: Corr_Gen Correlations between generations Column B: Fam.ID Replicate family identification Column C: TV1_mm Testes volume measured (mm3) in the parental generation Column D: TV2_mm Testes volume measured (mm3) in the offspring generation Column E: TV1 (m3) Testes volume measured (m3) in the parental generation Column F: TV2 (m3) Testes volume measured (m3) in the offspring generation   ### Filename: Balanced\_Inbreeding\_Elytra.csv Dataset describing Male elytra length (mm) through inbreeding. Column A: Family Replicate, independent families that were randomly numbered at the start Column B: ID Inbreeding generation Column C: Elytra Elytra length measured (mm)   ### Filename: Balanced\_Inbreeding\_Sperm length by family.csv Dataset describing Total sperm length (m) through inbreeding by family. Column A: Treatment Generation ID Column B: Fam.ID Random family ID Column C: Sperm_length (m) Total sperm length measured (mm) by family, across generations Column D: Trait (nominal tag) Total sperm length measured (Sperm_length) ### Filename: Balanced\_Offpsring productivity March 2018.csv Dataset describing reproductive output over seven days (proxy for offspring produced, counts) through inbreeding by family. Column A: Family Random family ID Column B: ID Generation ID Column C: Offspring Counts- offspring produced over 7 days across generations   ### Filename: Balanced\_Sperm Length Variance\_Dec2023.csv Dataset describing total sperm length through inbreeding and by individual sperm measured per male. Column A: Gen Generation ID Column B: Family.ID Random family ID Column C: Sperm_ID Individual sperm measured Column D: Sperm_length Sperm length measured (m) Column E: Unit Units for measuring the sperm; ‘micrometer’   ### Filename: Balanced\_Testes Follicle Variance.csv Dataset describing testes volumes through inbreeding and by measuring individual follicles per male. Column A: Gen Generation ID Column B: Family Random family ID Column C: follicle.count Number of testes follicles measured per male (maximum of 12 per male) Column D: TV.follicles.mm3 Testes follicles measured to calculate testes volume (mm3) Column E: TV.follicles.microns Testes follicles measured to calculate testes volume (m3)   ### Filename: Balanced\_Testes Volume March 2018.csv Dataset describing testes volumes through inbreeding and by measuring individual male by combining follicle level information. Column A: Family Family ID Column B: ID Generation ID Column C: Testes_vol_mm Testes volume measured per male (mm3) Column D: Testes_vol Testes volume measured per male (m3) ### Filename: Balanced\_Testes Volume Variance\_Dec2023.csv Dataset describing variance in testes volumes through inbreeding combined by families. Column A: Gen Generation ID Column B: TV.var Variance in testes volumes Column C: TV Average testes volume measured per male (m3)   ### Filename: Extinctions.csv Dataset describing small family extinctions through inbreeding. Column A: Gen Generation ID Column B: Extinctions Number of extinctions (counts)   ### Filename: G0\_G7\_Elytra\_Male\_Female comparisons.csv Dataset describing elytra length (mm and m) changes in the extant families that were not inbred at generation 0 and generation 7 in both males and females. Column A: Sex Sex ID (male/female) Column B: Family Family ID Column C: ID Generation ID Column D: Elytra_mm Elytra length (mm) by family across inbreeding generations Column D: Elytra Elytra length (m) by family across inbreeding generations   ### Filename: G0\_G7\_RO comparisons.csv Dataset describing reproductive output (offspring count) changes in the extant families that were not inbred at generation 0 and generation 7. Column A: Family Family ID (independent) Column B: ID Generation ID Column C: Offspring Reproductive output over 7 days   ### Filename: G0\_G7\_SL comparisons.csv Dataset describing total sperm length (m) changes in the extant families that were not inbred at generation 0 and generation 7. Column A: Gen Generation ID Column B: Family.ID Family ID (independent) Column C: Sperm_ID ID of individual sperm measured in m Column D: SL Total sperm length measured in m   ### Filename: G0\_G7\_TV comparisons.csv Dataset describing testes volume (mm3/m3) changes in the extant families that were not inbred at generation 0 and generation 7. Column A: Family Family ID (independent) Column B: ID Generation ID Column C: Testes_vol (mm3) Testes volume per male/family measured in mm3 Column D: Testes_vol_microns (m3) Testes volume per male/family measured in m3   ### Filename: Inbcoeff\_Balanced\_Inbreeding\_Elytra.csv Dataset describing male, female elytra length (m) changes in the extant families by calculating inbreeding coefficients plotted family wise. Column A: Inb.coef Inbreeding coefficient Column B: Family Family ID Column C: ID Generation ID Column D: Elytra (m) Elytra length male, female measured in m Column E: Sex Sex (nominal data); male or female   ### Filename: Inbcoeff\_Balanced\_Inbreeding\_Sperm length by family.csv Dataset describing total sperm length (m) changes in the extant families by calculating inbreeding coefficients plotted family wise. Column A: Inb.coef Inbreeding coefficient Column B: Treatment Generation ID Column C: Fam.ID Family ID (independent) Column D: Sperm_length (m) Total sperm length measured in m Column E: Trait Nominal data (Sperm_Length)   ### Filename: Inbcoeff\_Balanced\_Offpsring productivity March 2018.csv Dataset describing reproductive output (proxy for offspring counts) changes in the extant families by calculating inbreeding coefficients plotted family wise. Column A: Inb.coef Inbreeding coefficient Column B: Family Family ID (independent) Column C: ID Generation ID Column D: Offspring (counts) Reproductive output (proxy for offspring counts)   ### Filename: Inbcoeff\_Balanced\_Testes Volume March 2018.csv Dataset describing testes volume (mm3, m3) changes in the extant families by calculating inbreeding coefficients plotted family wise. Column A: Inb.coef Inbreeding coefficient Column B: Family Family ID (independent) Column C: ID Generation ID Column D: Testes_vol_mm (mm3) Testes volume measured in mm3 Column E: Testes_vol (m3) Testes volume measured in m3   ### Filename: Inbcoeff\_Extinctions.csv Dataset describing number of families going extinct through the inbreeding protocol, represented by inbreeding coefficients. Column A: Inb.coef Inbreeding coefficient Column B: Gen Generation ID Column C: Extinctions Number of families going extinct (counts)   ### Filename: Inbcoeff\_Within and between family variance Lifespan.csv Dataset describing lifespan of males, females (in weeks) through the inbreeding protocol, represented by inbreeding coefficients. Column A: Sex Male or female (nominal) Column B: Fam.ID Family ID Column C: Rep.ID Replicate family ID (within a family) Column D: Lifespan (in weeks) Lifespan measured in weeks Column E: Status (1= alive; 0 = dead) Live or dead, binomial code Column F: Gen Generation ID Column G: Inb.coef Inbreeding coefficient (fixed)   ### Filename: Inbreeding\_Elytra.csv Dataset describing male, female (in mm, m) body size through the inbreeding assay by family. Column A: Sex Male or female (nominal) Column B: Family Family ID Column C: ID Generation ID Column D: Elytra_mm (in mm) Elytra length measured in ‘mm’ Column E: Elytra (in m) Elytra length measured in ‘m’   ### Filename: SL\_zscores.csv Dataset describing total sperm length (in m) and z-scores through the inbreeding assay by family Column A: Inb.coef Column B: Treatment Generation ID Column C: Fam.ID Family ID (independent) Column D: Sperm_length (in m) Total sperm length measured in ‘m’ Column E: Trait Sperm_Length Column E: zscore z-scores calculated for sperm length for normalizing the distribution   ### Filename: Within and between family variance Lifespan.csv Dataset describing lifespan (in weeks) variance by sex, family-level through the inbreeding assay. Column A: Sex Male or female (nominal) Column B: Fam.ID Family ID Column C: Rep.ID Replicate nested within each family, two levels A and B Column D: Lifespan (in weeks) Lifespan measured in weeks Column E: Status 1= Alive; 0= Dead (binomial data) Column E: Gen Generation ID   ### Filename: Within and between family variance Reproductive output.csv Dataset describing family level reproductive output (proxy for offspring counts) by family-level through the inbreeding assay. Replicate paired families are present only from the first round of inbreeding prior to that it was the outbred, Gen.0, that was taken directly from the stocks. Column A: Family.ID Family Identification, random ID at the start of the experiment Column B: Rep.Fam Replicate family ID (either A or B), randomly assigned, not independent as they are from the same family Column C: Gen Generation ID Column D: Off.counts (reproductive output, counts proxy for offspring produced) Family-level reproductive output, proxy for offspring count.