DOI: 10.5061/dryad.ngf1vhj6v
title: Data from: Sperm storage causes sperm senescence in human and non-human animals

description: In animals, mature sperm are stored in males before ejaculation, and
 sometimes in females before fertilisation. Sperm storage provides
 evolutionary advantages; however, storage can also cause sperm
 deterioration due to post-meiotic sperm ageing. Yet, the extent of such
 deterioration, the mechanisms driving it, and its consequences remain
 poorly understood. We perform a meta-analysis across humans (115 studies)
 and non-human animals (56 studies, 30 species) to understand the impacts
 of sperm storage. In men, storage via sexual abstinence increases sperm
 oxidative stress and DNA damage, reduces sperm viability and motility. In
 other animals, sperm storage in males and females reduces sperm
 performance and embryo quality. The duration of storage, the method of
 sampling individuals, and the sperm-storing sex also impact observed
 outcomes. The results have implications for fertility clinics, sperm
 selection, captive breeding, and understanding adaptations evolved to
 mitigate stored-sperm deterioration.
description: ## README # Sperm storage causes sperm senescence in human and non-human
 animals Analysis Software: Rv4.3.1 Packages: tidyverse,
 BiocManager,TDbook, ggimage,ggtree, ggsankey, ggalluvial, metafor, meta,
 dplyr, kableExtra, GGally, bookdown, remotes, ggplot2, Matrix, patchwork,
 ggpubr, rotl, ape, Rcpp, treebase, MCMCglmm, orchaRd, LaplacesDemon,
 metaviz, matrixcalc, psychmeta, orchaRd, esc, emmeans, DHARMa, lme4,
 lmerTest, ggpointdensity, viridis, Rmisc, tidytext, ggh4x, hues,
 rphylopic, ggnewscale, ggimage, tidytree, ggtreeExtra, patchwork, ggforce,
 ggsankey Data availability: Code and data associated with this project can
 be found at OSF
 [https://osf.io/jxv7z/files/osfstorage](https://osf.io/jxv7z/files/osfstorage) with the DOI: 10.17605/OSF.IO/JXV7Z. Note: blank cells in all datasets denote NA, and cells for which data is not applicable or not collected. ### Files 1.      **PMSA_animal_papers_list.xlsx:** File containing data related to screening of animal studies. Variables a.       Sheet1 * Source: Whether studies came from personal literature, human dataset, backwards screening of other reviews, or from databases of SCOPUS and web of science (RAYYAN). * Paper ID: ID of study if included in the meta-analysis * Title: Title of study * Year: year of publication of study * Authors: authors of the study * Include_abstract: whether or not study was deemed as appropriate after the abstract screening stage. The main texts of the studies coded as “yes” were then screened. * DOI: DOI of included studies, whenever available * Include_main_text: whether or not study was deemed as appropriate after the main-text screening stage. Studies coded as “Y” were included in our meta-analysis * Reason_specific: reason for excluding the study at the main text screening stage * Analyst: initials of analyst who collected data from the study and screened the study * Comments: specific comments   b.      Sheet2 * Descriptive summary of animal studies, and notes related to animal studies. Tables summarising reasons for excluding studies at the main text screening stage. 2.      **animalsPMSA.csv:** file containing all data collected for animals sperm storage dataset. Variables * Collector: Initials of analyst who collected data * Calculation: Effect size calculation method * Row: Row ID * Paper: Paper/study ID * Cohort: within-paper, cohort ID * Title: Paper/study title * Year: Year of publication of study * DOI: DOI or weblink for accessing the study * Population: whether animals were classified as lab, domestic, wild or captive * Species: species name of studied animal * Max_LS: maximum longevity of the species (usually sex-specific) * Ref_LS: source from which data on maximum longevity was obtained * Class: Taxonomic class * Treatment: Additional treatment that the cohort was subjected to, other than sperm storage, if any * Sex: Sex of individual who stored sperm in the study * Offspring_sex: Sex of offspring when data was on offspring traits and offspring sex was reported * Data_from: where the data in our dataset was taken from within the study * Trait_description; summary of trait as described in the study * Multiplier: Multiplier to multiply the final effect size with, such that negative effect sizes convey deleterious effects of sperm storage and positive effect sizes show beneficial effects * Trait: Trait as classified in our study. These are categorical “words” specifying the trait and are unitless. * Broad_trait: trait binned into three broad categories in our study * Dura_min: minimum duration of sperm storage sampled by the study/effect size * Dura_max: maximum duration of sperm storage sampled by the study * Storage_units: units of time related to Dura_min and Dura_max for sampling of storage duration, and for the Age variables * Age1 to Age8: duration of sperm storage (i.e. sperm age) when study storage treatments were categorical, for each treatment category. The units of the age variable can be found in the “Storage_units” column. * x_1 to x_8: means of traits associated with each sperm storage treatment category. Depending on the trait, they have different units, however, the units themselves do not matter to our analysis. * sd_1 to sd_8: standard deviations of traits associated with each sperm storage treatment category * se_1 to se_8: standard errors of traits associated with each sperm storage treatment category * n_1 to n_8: numbers of (sperm storing) individuals sampled by the study/effect size, associated with each treatment category * N_unique: number of unique individuals sampled in the effect size * N_total: number of total individuals sampled in the effect size, including repeated sampling of the same individuals * Nsamples_1 and Nsamples_2: number of samples (e.g. number of sperm or embryo samples) on which the data was generated in the study for two storage group comparisons. This variable was not used by our study because our level of replication was number of individuals, rather than number of samples. * N_test: numbers of sperm-storing individuals sampled when the study reported a test-statistic * Test_stat: type of test statistic used by the study * Value: value of the test_statistic that tested how sperm storage duration impacted traits * Sampling: whether individuals were sampled cross-sectionally or longitudinally 3.      **Animals_repeatability.csv:** data file containing data collected from two different analysts on the same study, to understand the accuracy of data collection in the animal dataset Variables * Calculation: Effect size calculation method * Analyst: Initials of analyst who collected data * Row_withoutanalyst: Row ID without including analyst ID * Row: row ID including analyst ID * Paper: Paper/study ID * Trait: Trait as classified in our study. These are categorical “words” specifying the trait and are unitless. * Age1 to Age4: duration of sperm storage (i.e. sperm age) when study storage treatments were categorical, for each treatment category * x_1 to x_4: means of traits associated with each sperm storage treatment category. Depending on the trait, they have different units, however, the units themselves do not matter to our analysis. * sd_1 to sd_4: standard deviations of traits associated with each sperm storage treatment category * se_1 to se_4: standard errors of traits associated with each sperm storage treatment category * n_1 to n_4: numbers of (sperm storing) individuals sampled by the study/effect size, associated with each treatment category * N_unique: number of unique individuals sampled in the effect size * N_total: number of total individuals sampled in the effect size, including repeated sampling of the same individuals * Test_stat: type of test statistic used by the study * Value: value of the test_statistic that tested how sperm storage duration impacted traits * Multiplier: Multiplier to multiply the final effect size with, such that negative effect sizes convey deleterious effects of sperm storage and positive effect sizes show beneficial effects 4.      **PMSA-animals.html:** R markdown HTML output for our entire code and analysis related to the animal dataset. Associated data file is “animalsPMSA.csv”. 5.      **animals-repeatability.html:** R markdown HTML output for our entire code and analysis related to the repeatability of data extraction for the animal dataset. Associated data file is “Animals_repeatability.csv”. 6.      **Human_studies_list.xlsx:** File containing data related to screening of human studies. a.       Sheet 1 * PaperID: ID of paper if in the meta-analysis * Row ID: row ID of the paper within this data sheet * Source: Whether studies came from personal literature, backwards and forwards screening of other reviews (RAYYAN), or from databases of SCOPUS and web of science (RAYYAN). * Title: title of study * Year: year of publication of study * Journal: journal of publication of study * Authors: authors of the study * Abstract: study abstract * DOI: doi of study if available * Abstract screen: whether or not study was deemed as appropriate after the abstract screening stage. The main texts of the studies coded as “Included” were then screened. * Full text: whether or not study was deemed as appropriate after the main-text screening stage. Studies coded as “Yes” were deemed as appropriate for our meta-analysis * Authors contacted: whether or not we contacted the authors of the study for extra or missing data * Authors responded: whether or not the authors who were contacted responded * Corresponding author: who the authors were which we contacted * Data from authors: whether authors were able to provide us with missing data for the meta analysis * Comments: additional comments b.      Sheet 2- sheet containing specific reaons for exclusion at the main text screening stage Variable descriptions are identical as the “Sheet 1” sheet, with added variables: * Comments: specific comments for exclusion reason * Reason: summarise reason for exclusion 7.      **Humans_abstinence.csv:** file containing all data collected for the humans sperm storage dataset. Variables * Row: Row ID * Paper: Paper/study ID * Cohort: within-paper, cohort ID * Title: Paper/study title * Year: Year of publication of study * DOI: DOI or weblink for accessing the study * Country: country in which males were sampled * Condition: whether males were healthy, had infertility-related problems, or other health conditions * Male_age: mean age of males sampled in the study, if reported * Data_from: where the data in our dataset was taken from within the study * Trait_description; summary of trait as described in the study * Trait: Trait as classified in our study. These are categorical “words” specifying the trait and are unitless. * Broad_trait: trait binned into three broad categories in our study * Dura_min: minimum duration of sperm storage sampled by the study/effect size (converted to days) * Dura_max: maximum duration of sperm storage sampled by the study (converted to days) * Age1 to Age17: duration of sperm storage (i.e. sperm age) when study storage treatments were categorical, for each treatment category. Units is days. * x_1 to x_17: means of traits associated with each sperm storage treatment category * sd_1 to sd_17: standard deviations of traits associated with each sperm storage treatment category * se_1 to se_17: standard errors of traits associated with each sperm storage treatment category * n_1 to n_17: numbers of (sperm storing) individuals sampled by the study/effect size, associated with each treatment category * N_unique: number of unique individuals sampled in the effect size * N_total: number of total individuals sampled in the effect size, including repeated sampling of the same individuals * N_test: numbers of sperm-storing individuals sampled when the study reported a test-statistic * Test_stat: type of test statistic used by the study * Value: value of the test_statistic that tested how sperm storage duration impacted traits * SE_beta: if the test statistic was a beta coefficient, the standard error of the coefficient * CI_low_OR: if the test statistic was the odds ratio, the lower confidence interval of the odds ratio * CI_high_OR: if the test statistic was the odds ratio, the upper confidence interval of the odds ratio * Calculation: Effect size calculation method * Multiplier: Multiplier to multiply the final effect size with, such that negative effect sizes convey deleterious effects of sperm storage and positive effect sizes show beneficial effects * Sampling: whether individuals were sampled cross-sectionally or longitudinally * Study_type: whether the study was prospective (i.e. males were assigned to sperm storage treatments at the start of the study) or retrospective (i.e. available data on sperm storage was used with males being opportunistically sampled, and sperm storage treatment categories being arbitrarily delineated). 8.      **Humans_repeatability.csv:** data file containing data collected from two different analysts on the same study, to understand the accuracy of data collection in the human dataset Variables: * Analyst: Initials of analyst who collected data * Row_withoutanalyst: Row ID without including analyst ID * Row: row ID including analyst ID * Paper: Paper/study ID * Cohort: within study cohort ID * Calculation: Effect size calculation method * Trait: Trait as classified in our study. These are categorical “words” specifying the trait and are unitless. * Broad_trait: trait binned into three broad categories in our study * Age1 to Age11: duration of sperm storage (i.e., sperm age) when study storage treatments were categorical, for each treatment category. Units are days. * x_1 to x_11: means of traits associated with each sperm storage treatment category * sd_1 to sd_11: standard deviations of traits associated with each sperm storage treatment category * se_1 to se_11: standard errors of traits associated with each sperm storage treatment category * n_1 to n_11: numbers of (sperm storing) individuals sampled by the study/effect size, associated with each treatment category * N_unique: number of unique individuals sampled in the effect size * N_total: number of total individuals sampled in the effect size, including repeated sampling of the same individuals * Test_stat: type of test statistic used by the study * Value: value of the test_statistic that tested how sperm storage duration impacted traits * Multiplier: Multiplier to multiply the final effect size with, such that negative effect sizes convey deleterious effects of sperm storage and positive effect sizes show beneficial effects * Sampling: whether individuals were sampled cross-sectionally or longitudinally 9.      **abstinence-code.html:** R markdown HTML output for our entire code and analysis related to the animal dataset. Associated data file is “Humans_abstinence.csv”. 10.  **Repeatability.html:** R markdown HTML output for our entire code and analysis related to the repeatability of data extraction for the humans dataset. Associated data file is “Humans_repeatability.csv”. 11.     **README_sperm_storage_meta.docx** - Word file copy of this README.