DOI: 10.5061/dryad.8cz8w9h2t
title: Data from: Male reproductive senescence in mammals is pervasive and aligned with the slow-fast continuum

description: Reproductive senescence, the decline in reproductive performance with
 increasing age, has been well documented in mammalian females. Male
 reproductive senescence, on the other hand, is much less understood,
 partly due to the past complexities of getting reliable paternity
 assignment in the wild. Through a standardized literature search, we
 compiled age-specific reproductive data on both mating and reproductive
 success on 57 species encompassing 73 populations. We then explored the
 occurrence of male reproductive senescence and sought to identify key
 ecological and evolutionary drivers modulating its intensity. We found
 evidence of reproductive senescence in 60 % of the studied species, with a
 detection probability increasing with larger sample sizes and longer
 lifespan coverage (measured as the age range studied relative to
 longevity). As expected, both the onset and the rate of male reproductive
 senescence were aligned with the species position along the slow-fast
 continuum, with fast-living species exhibiting earlier and stronger
 reproductive senescence than slow-living species. Moreover, the rate of
 reproductive senescence also increased with the level of sexual size
 dimorphism, highlighting that males from species displaying a high level
 of sexual selection suffer from a steeper rate of reproductive senescence.
description: # Data from: Male reproductive senescence in mammals is pervasive and
 aligned with the slow-fast continuum
 [https://doi.org/10.5061/dryad.8cz8w9h2t](https://doi.org/10.5061/dryad.8cz8w9h2t) ## Description of the data and file structure Read me file (scripts and data) Order in which the scripts were used and the purpose of each script: 1.      **Script_computing_new_traits**: Script used to calculate the values of traits added to the analyses, such as the number of offspring among breeders based on the data for number of offspring and paternity probability. The dataset linked to this script is `Dataset_computing_new_traits.csv`. 2.      **Script_pattern_senescence**: Script used to determine senescence patterns for each record (i.e., each trait in each population of each species). The dataset associated with this script is `Data_pattern.csv`, which corresponds to `Dataset_computing_new_traits.csv` plus the new traits calculated earlier (obtained at the end of `Script_computing_new_traits`). 3.      **Script_pglmm_article**: Script used for PGLMM analyses (probability of detecting senescence, analyses on onset and rate of senescence) as well as MCMCglmm analyses. The dataset associated with this article is `Data_meta_analyses.csv`. This script also necessitates the use of phylogeny_timetree.nwk.  ## Files and variables #### File: Data_meta_analysis.csv **Description: Data file used for the pglmm analyses**  ##### Variables * Species_valid:e xact name of the species * longevity : longevity of the species (source of the data can be found in the file Male_database) * trait_non_std: reproductive trait studied * trait_std: standardised trait studied (patern: probability of paternity per age, nb_off: mean number of offspring produced at an age x, nb_off_breeders: mean number of offspring produced at an age x among breeders ; cop: mean number of copulation per age ; litter_size ; mate: probability of mating per age) * timing: timing of sampling of the offspring (pre_weaning for offspring sampled before weaning; weaning for offspring sampled after;copulation for copulatory stage) * ref: reference * senescence: senescence observed (1) in our patterns determination or not (0) * onset: onset of senescence (in years) * onset_sd: standard deviation of the onset of senescence * longevity_observed: longevity observed of animals in the study * rate: slope/rate of senescence * rate_sd : standard deviation of the rate of senescence * order: taxonomic rank of the studied species * population: study population  * pop_status : status of popualtion (wild, semi-captive, captive) * afr: age at first reproduction (see AFR sheet in Database) * testes_mass: combined testes mass (see Testes mass sheet in Database) * mbm_testes: male body mass from the same population than the value extracted for combined testes mass * data_type: transversal or longitudinal * hunting_status: population hunted or not  * social_monogamy: species is socially monogamous (Y) or not (N) * fbm_ssd: female body mass extracted for ssd calculation (see SSD sheet in Database) * mbm_ssd: male body mass extracted for ssd calculation (see SSD sheet in Database) * nb_observations: total number of observations on which the study is based * mass_article: if said in the reference, mean adult male body mass #### File: Data_pattern.csv **Description: data file used for the determination of senescence patterns** ##### Variables * Ref: reference from where the reproduction data were extracted from (full details in the Male_database file) * Species: studied species * Age: age in years * R: value of the reproductive trait per age class * N: sample size on the reproductive trait per age class is based * Type: trait studied (patern: probability of paternity per age, nb_off: mean number of offspring produced at an age x, nb_off_breeders: mean number of offspring produced at an age x among breeders ; cop: mean number of copulation per age ; litter_size ; mate: probability of mating per age) * Pop: population of study #### File: Dataset_*computing_new_traits*.csv **Description: data file used for the determination of new traits (e.g. number of breeders)** #### File: Male_database.xlsx **Description:** **Data files containing details of every included study as well as the origin and source of every data** The comments integrated into this table are essential for identifying the sources of the articles included in the meta-analysis and for ensuring a proper understanding of the data. These annotations provide critical context and traceability that would otherwise be lost if deleted. **NA are indicating not available data.** ##### Variables \----- Masterfile: * Included: Whether the paper has been included in our analyses or not * Life_*table*_id: corresponding ID to the record in the sheet called ‘Life_tables’ * Life_*table*_old_id: corresponding ID to the record in the sheet called ‘Life_tables’ in the old tables * Type: R = trait related to reproductive success (after mating), M = trait related to mating success * Trait: Detail of the studied trait (patern: probability of paternity per age, nb_off: mean number of offspring produced at an age x, nb_off_breeders: mean number of offspring produced at an age x among breeders ; cop: mean number of copulation per age ; litter_size ; mate: probability of mating per age) * Offspring_sampling_time_standardized : Time of sampling of the offspring for reproductive traits, standardized (infant or weaning) * Offspring_sampling_time2 : Details of the time of sampling of the offspring for reproductive traits * Type_of_record: wether the paternity is assessed through paternity analysis or through observation/monitoring * Species_id: corresponding ID of the species in the sheet called ‘Species’ * Species: Species name * Order: Order of the species * Location_id: corresponding ID of the location in the sheet called ‘Location’ * Location * Reference_id: corresponding ID of the reference in the sheet called ‘References * Reference: reference * Non_published_data: whether the data are published in the paper or not * Data_form: From where are the data extracted * Start_year: year of start of the population monitoring * Duration: duration of the population monitoring for these data * N_ind: number of individuals on which the reproductive data are based * N_capt/obs: number of observations on which the reproductive data are based * Monitoring_type: whether monitoring is longitudinal or transversal * Captivity : wild population or not * Age_type: whether age is continuous or in classes * Number_of_classes: if age is in classes, number of classes * Age_details: age range covered by the study * Exact_age_know: whether the exact age is known in this population (Y) or not (N) * Age_estimated: whether the age is estimated in this population (Y) or not (N) * Age_estimation: how the age was estimated * Left_censored: if data of young individuals were censored * Right_censored: if data of old individuals are censored * Graph_extraction: whether the data used in our analyses are extracted from a graph (Y) or not (N) * Primary_data_extracted: whether the data extracted and used in our analyses are primary data * Modelled_data_extraxted: whether the data extracted and used in our analyses are modelled data * Model_description: if the extracted data are modelled, the description of the model * Adult_mass: mean body mass of adult males reported in the article *NB: Some articles are not included in our study, if the species is a domesticated species (blue raws) of ir there is a replicate for the same trait in the same population for a same species that seems to be more adequate (in pink).* \----- Life tables * Reference * Trait (patern: probability of paternity per age, nb_off: mean number of offspring produced at an age x, nb_off_breeders: mean number of offspring produced at an age x among breeders ; cop: mean number of copulation per age ; litter_size ; mate: probability of mating per age) * Life_tablenew_id * Start_age: starting age of the age class (when m written, the values are in months, otherwise in years) * End_age: ending age of the age class * Mean_par: mean value of the reproductive trait per age class * N_alive: number of observations on which the data are based per age class \----- Weaning age * Species * Weaning age * Source \----- Longevity source * Species * Longevity in article: whether the maximum longevity of males in this population is specified in the article * On who : On which sex were retreived the data (M=males, x=undetermined) * Longevity: longevity value used in our analyses * Source: source of this latter value * Ref: if the source is a database, specific reference * Order \----- Missing age-specific sample size : source of the lx data when age-specific sample size is missing * Species * Pop * Ref: reference of the article from which the age-specific sample size is unkown * Missing age-specific sample size: whether the age-specific sample size is unknown in the study * Population lx: population of extraction of lx values * Lx reference: article of extraction of lx values \----- Species * Species_id * Genus * Species * Sub_species * Included * Data_available * COL_id \----- Localisations * Localisation_id * Name: name of the study site * Country * Lat_D: latitude * Lat_M: latitude * Long_D: longitude * Long_M: longitude \----- References * Reference_id * Pop duplicates: whether the study population of the paper has a duplicate in the dataset * Included: whether this paper was included in our analyses * First_author * Authors * Year * Type * Journal * Title * DOI * APA \----- Testes mass * Species * Order * Combined_testes_mass * Male_body_mass * References_RTM: source of combined testes mass and male body mass data \----- AFR * Species * Ref * Pop * Trait (patern: probability of paternity per age, nb_off: mean number of offspring produced at an age x, nb_off_breeders: mean number of offspring produced at an age x among breeders ; cop: mean number of copulation per age ; litter_size ; mate: probability of mating per age) * Captive: whether the studied population is captive of not * Age class: whether the data extracted are in continuous age or in age classes * AFR: value of AFR kept in the analyses * Ref_AFR: Source of extraction of the AFR \------ SSD * Species * FBM_ssd: female body mass used in the calculation of ssd * MBM_ssd: male body mass used in the calculation of ssd * Ref_ssd: reference for those body masses \------ Screen total Detail of the second step of screening and reasons why articles were excluded from our selection 
 
 #### File: Male_database.zip **Description:** **Exact same data as
 Male_database.csv,** **ZIP folder containing all the sheets from the Male
 Database XLSX file, this time provided in CSV format to ensure easier
 access and usability.** --- ## Code/software 1.     
 **Script_computing_new_traits**: Script used to calculate the values of
 traits added to the analyses, such as the number of offspring among
 breeders based on the data for number of offspring and paternity
 probability. The dataset linked to this script is
 `Dataset_computing_new_traits.csv`. 2.      **Script_pattern_senescence**:
 Script used to determine senescence patterns for each record (i.e., each
 trait in each population of each species). The dataset associated with
 this script is `Data_pattern.csv`, which corresponds to
 `Dataset_computing_new_traits.csv` plus the new traits calculated earlier
 (obtained at the end of `Script_computing_new_traits`). 3.     
 **Script_pglmm_article**: Script used for PGLMM analyses (probability of
 detecting senescence, analyses on onset and rate of senescence) as well as
 MCMCglmm analyses. The dataset associated with this article is
 `Data_meta_analyses.csv`. **Analyses were performed under R version 4.2.3
 (2023-03-15 ucrt)** Devices, utils, datasets, methods, base other attached
 packages: rr2_1.1.1, phyr_1.1.0, phytools_2.4-4, maps_3.4.2,
 orthopolynom_1.0-6.1 MCMCglmm_2.35, coda_0.19-4.1, adephylo_1.1-13,
 ade4_1.7-22, ggpubr_0.6.0, report_0.5.8, ghibli_0.3.4, rptR_0.9.22,
 optimx_2023-10.21, cowplot_1.1.3, plotrix_3.8-4, lmodel2_1.7-3,
 caper_1.0.3, mvtnorm_1.2-4, ape_5.8, lmtest_0.9-40, zoo_1.8-12,
 lmerTest_3.1-3, Rmisc_1.5.1, plyr_1.8.8, lattice_0.20-45, carData_3.0-5,
 MuMIn_1.47.5, lme4_1.1-35.3, Matrix_1.6-5, rmarkdown_2.27,
 lubridate_1.9.3, forcats_1.0.0, purrr_1.0.1, readr_2.1.5, tidyr_1.3.0,
 tibble_3.2.1, ggplot2_3.5.2, tidyverse_2.0.0, stringr_1.5.1, dplyr_1.1.1,
 ggeffects_2.2.1, mgcv_1.8-42, segmented_2.1-0, nlme_3.1-164,
 MASS_7.3-58.2, phylobase_0.8.10 ## Access information Data was derived
 from the following sources: * See file Database for the sources