Inbreeding depression in male reproductive traits
Data files
Mar 06, 2025 version files 154.48 MB
-
Balanced_Corr_Gens_Female_Elytra_Length.csv
8.06 KB
-
Balanced_Corr_Gens_Female_Longevity.csv
4.79 KB
-
Balanced_Corr_Gens_Male_Elytra_Length.csv
8.09 KB
-
Balanced_Corr_Gens_Male_Longevity.csv
4.38 KB
-
Balanced_Corr_Gens_Offspring_Productivity.csv
4.28 KB
-
Balanced_Corr_Gens_Sperm_Length.csv
3.94 KB
-
Balanced_Corr_Gens_Testes_Volume.csv
6.65 KB
-
Balanced_Inbreeding_Elytra.csv
3.55 KB
-
Balanced_Inbreeding_Sperm_length_by_family.csv
6.82 KB
-
Balanced_Offpsring_productivity_March_2018.csv
3.11 KB
-
Balanced_Sperm_Length_Variance_Dec2023.csv
137.24 KB
-
Balanced_Testes_Follicle_Variance.csv
90.60 KB
-
Balanced_Testes_Volume_March_2018.csv
4.46 KB
-
Balanced_Testes_Volume_Variance_Dec2023.csv
142 B
-
Extinctions.csv
75 B
-
G0_G7_Elytra_Male_Female_comparisons.csv
4.30 KB
-
G0_G7_RO_comparisons.csv
985 B
-
G0_G7_SL_comparisons.csv
28.88 KB
-
G0_G7_TV_comparisons.csv
1.54 KB
-
Inbcoeff_Balanced_Inbreeding_Elytra.csv
11.55 KB
-
Inbcoeff_Balanced_Inbreeding_Sperm_length_by_family.csv
7.85 KB
-
Inbcoeff_Balanced_Offpsring_productivity_March_2018.csv
4.24 KB
-
Inbcoeff_Balanced_Testes_Volume_March_2018.csv
5.52 KB
-
Inbcoeff_Extinctions.csv
116 B
-
Inbcoeff_Within_and_between_family_variance_Lifespan.csv
30.88 KB
-
Inbreeding_Elytra.csv
14.83 KB
-
Inbreeding_Reproduction_Images.zip
153.92 MB
-
Inbreeding_RScript_Code.R
69.02 KB
-
README_Inbreeding_depression_in_male_reproductive_traits.docx
39.17 KB
-
README.md
16.38 KB
-
SL_zscores.csv
9.90 KB
-
Within_and_between_family_variance_Lifespan.csv
28.10 KB
-
Within_and_between_family_variance_Reproductive_output.csv
5.94 KB
Abstract
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.
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.