No evidence for paternal age effects on sons or daughters, when accounting for paternal sperm storage
Data files
Mar 19, 2025 version files 5.43 MB
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f0_survivalData.csv
19.29 KB
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F0ReproductionData.csv
17.11 KB
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F1Reproduction.csv
218.07 KB
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F1SurvivalData.csv
60.56 KB
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README.md
5.70 KB
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sperm_storage_simple.Rmd
33.25 KB
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sperm-storage-simple.html
5.04 MB
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stripping_F1.csv
35.26 KB
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stripping_fertility.csv
3.05 KB
Abstract
A father’s age at conception is predicted to affect not only his own fertility but also his offspring’s fitness. Offspring born to old fathers are assumed to be less fit than those of young fathers. However, under low mating rates, paternal age might be confounded with the duration for which mature sperm are stored in fathers prior to ejaculation. Studies that disentangle the confounding paternal effects of sperm storage duration from those of age, on offspring, are lacking. We use Drosophila melanogaster to test the separate and interactive effects of paternal age and sexual rest on offspring fitness. As expected, old fathers produce fewer offspring than young fathers, however, paternal age does not influence the survival or age-dependent reproductive success of sons or daughters. Instead, a long duration of paternal sexual rest negatively impacts the reproductive success of the conceived sons. Furthermore, daughters of low reproductive quality selectively disappear with age, but sons do not, highlighting that demographic processes can further modulate paternal age effects. Overall, we highlight that paternal age effects might not be as pervasive as previously assumed, and suggest that paternal sexual rest might be more important in influencing offspring phenotypes.
https://doi.org/10.5061/dryad.cnp5hqcgg
Description of the data and file structure
Data analysis and data files
Software: R v4.3.1
Packages: pacman, tidyverse, dplyr, kableExtra, emmeans, bookdown, performance, remotes, patchwork, ggplot2, gamm4, MCMCglmm, knitr, rmarkdown, lme4, lmerTest, mgcv, DHARMa, coxme, survminer, Rmisc, survival, sjstats, ggpmisc, sjPlot, glmmTMB, MASS, tidymv, plot3D, graphics, reshape, reshape2, AICcmodavg, psych, effectsize, TMB, CoxR2
Note: The readme file contains the names of each datafile used in our paper, containing all the data relevant to our study. The metadata for each file is provided below, and includes the column names and their descriptions.
FILES
Data and code file overview
This data repository consist of two code files and six data files.
Code files:
1. sperm storage simple.RMD: code used to analyse data for this experiment/project. The script is run in the same order as is written.
2. Sperm-storage-simple.html: provides the complete run of our entire code along with results generated in-code. The code is exactly like the file above but in a different format
Data files:
3. f0_survivalData.csv: Data used for constructing population-level survival curves of fathers in Rep 1 and 2.
a. Rep: replicate/block
b. ID: Male ID
c. Born: date of emergence
d. Died: date of death
e. LS: lifespan
f. Censor: 1- if death was observed, 0- if death was not observed.
4. F0ReproductionData.csv: datasheet for paternal reproductive output. Note: missing cell values for the columns: “F1_assays”, “Stripping_offspring”, “Stripping_TotalMatings” means that data on those individuals was not collected and assay on those individuals not conducted. Missing cell values for F1_counts means that those individuals did not have their offspring counted, due to either escaping/dying/or not mating.
a. Row_num: Row number
b. Rep: Replicate number
c. Paternal_ID: ID of the father used for the assay
d. Treatment: overall male age and sperm storage duration treatment
e. Male_age: age of the male used- O is old, Y is young
f. Sperm_age: duration of sexual rest of the father/male- O is long, Y is short
g. Mated: whether or not the male mated in the F0 mating assay
h. Mating_duration: duration of copulation
i. F1_assays: Whether offspring from this male were used for the F1 paternal effects assay
j. F1_counts: number of offspring produced by the male
k. Stripping_offspring: Number of total offspring produced by the male if used in the stripping assay, with 10 females
l. Stripping_TotalMatings: number of females the male mated with and fertilised, in the stripping assay
5. F1Reproduction.csv: datasheet with age-dependent reproductive output for sons and daughters used in the offspring assays
a. Obs_num: row number
b. Rep: Replicate number
c. F1_ID: ID of the individual offspring
d. F0_ID: ID of the father who conceived that offspring
e. Paternal_age: age of the father who conceived that offspring (old or young)
f. Paternal_sperm_age: sexual rest duration of the father who conceived that offspring
g. Sex: Sex of the offspring
h. F1_Age: Age of the offspring when its reproductive output was assayed
i. F2_count: number of offspring conceived by the sons and daughters used in the offspring assays
6. F1SurvivalData.csv: Lifespan data associated with the F1 generation.
a. F1_ID: ID of the son/daughter
b. Rep: replicate/block number
c. Paternal_ID: ID of the father who conceived the offspring
d. Paternal_age: age of the father who conceived that offspring (old or young)
e. Paternal_sperm_age: sexual rest duration of the father who conceived that offspring
f. Paternal_treatment: overall treatment (age and sexual rest) of the father
g. Sex: sex of the offspring
h. LS: Lifespan of the offspring when recorded
i. Censored: 1- if death was observed, 0- if death was not observed.
7. stripping_F1.csv: Datasheet for F0 stripping assay, for offspring count/fecundity data
a. Male_ID: ID of the male used in the stripping assay
b. Treatment: overall treatment (age and sexual rest) of the F0 male
c. Female_ID: ID of the female used in the stripping assay
d. Fecundity: number of offspring produced by the male with the specific female in the stripping assay
e. Rank: assumed rank of the female in the male’s mating order
f. Age: Age of the male
8. stripping_fertility.csv: Datasheet for F0 stripping assay, for male fertility data
a. Male_ID: ID of the male used in the stripping assay
b. Treatment: overall treatment (age and sexual rest) of the F0 male
c. Age: Age of the male
d. Fecundity: total fecundity of the male in the stripping assay with 10 females
e. N_vials: number of vials used to assay male fecundity with each female in the stripping assay
f. Fecundity_perFemales: average number of offspring produced by the male with the fertilised females, in the stripping assay
g. N_fertility: Number of females out of 10, that the male fertilised successfully in the stripping assay.
Code/software
Software: R v4.3.1
Packages: pacman, tidyverse, dplyr, kableExtra, emmeans, bookdown, performance, remotes, patchwork, ggplot2, gamm4, MCMCglmm, knitr, rmarkdown, lme4, lmerTest, mgcv, DHARMa, coxme, survminer, Rmisc, survival, sjstats, ggpmisc, sjPlot, glmmTMB, MASS, tidymv, plot3D, graphics, reshape, reshape2, AICcmodavg, psych, effectsize, TMB, CoxR2
Access information
Other publicly accessible locations of the data:
- 10.17605/OSF.IO/GQ9J2
Data was collected via experiments conducted in 2022 and 2023. Data were processed on R studio and MS excel.