Data from: Mother of all bonds: influences on spatial association across the lifespan in capuchins
Data files
Feb 29, 2024 version files 6.54 MB
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data_1_matProx_sub.csv
5.68 MB
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data_2_extra_group.csv
749.25 KB
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data_3_extra_early.csv
4.31 KB
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README.md
9.37 KB
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soc_scores_mothers1.csv
36.35 KB
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soc_scores_offspring.csv
58.20 KB
Abstract
In humans, being more socially integrated is associated with better physical and mental health and/or with lower mortality. This link between sociality and health may have ancient roots: sociality also predicts survival or reproduction in other mammals, such as rats, dolphins, and non-human primates. A key question, therefore, is which factors influence the degree of sociality over the life course. Longitudinal data can provide valuable insight into how environmental variability drives individual differences in sociality and associated outcomes. The first year of life—when long-lived mammals are the most reliant on others for nourishment and protection—is likely to play an important role in how individuals learn to integrate into groups. Using behavioral, demographic, and pedigree information on 376 wild capuchin monkeys (Cebus imitator) across 20 years, we address how changes in group composition influence spatial association. We further try to determine the extent to which early maternal social environments have downstream effects on sociality across the juvenile and (sub)adult stages. We find a positive effect of early maternal spatial association, where female infants whose mothers spent more time around others also later spent more time around others as juveniles and subadults. Our results also highlight the importance of kin availability and other aspects of group composition (e.g. group size) in dynamically influencing spatial association across developmental stages. We bring attention to the importance of—and difficulty in—determining the social versus genetic influences that parents have on offspring phenotypes.
README: Data from: Mother of all bonds: influences on spatial association across the lifespan in capuchins
https://doi.org/10.5061/dryad.h70rxwdqw
Included here are all data and code necessary to replicate findings from “Mother of all bonds: influences on spatial association across the lifespan in capuchins” by Irene Godoy, Peter Korsten, and Susan E. Perry.
You will need to have R installed. All analyses were conducting using R version 4.3.1.
Download all files into one folder and set it as your working directory.
You can create a subfolder ‘objects’ to save model objects in.
We used the following R packages:
brms (Version 2.19.0)
tidyverse (Version 2.0.0)
The following files were used for visualisation but are not required for analyses:
rethinking
ggplot2
ggthemes
cowplot
bayesplot
THE FOLLOWING DATASETS ARE PROVIDED AS .CSV FILES:
“data_1_matProx_sub.csv” - file containing data on early maternal social environments
Columns:
- Year: year of data collection
- infant_age: age of infant, in years, when data point on the mother was taken
- rad_366: day of data collection (as radian)
- mins: time of day, as minutes into the day
- type: whether instantaneous point sample was from a focal follow (Y) or focal scan (P)
- inf_CC: whether the infant was in proximity to the mother (TRUE) or not (FALSE)
- social: whether or not the mother was in proximity of another capuchin (1) or not (0) (response variable)
- sex: sex of infant (“f” for female, “m” for male)
- id_mom: identity of mother
- id_infant: identity of infant
“data_2_extra_group.csv” - file containing data on group composition
Columns:
- id: identity of focal (offspring)
- Year: year of data collection
- Month: month of data collection (string)
- MM: month of data collection (integer)
- Group: primary group of residence of the focal
- offspring: number of offspring of any age (for females) present in group
- n_fems: number of (sub)adult females (>= 5 years of age) in the group of residence of the focal
- n_mals: number of (sub)adult males (>= 5 years of age) in the group of residence of the focal
- n_juvs: number of juveniles (< 5 years of age) in the group of residence of the focal
- mat_kin: number of maternal kin (mother, maternal siblings) present in the group of residence of the focal
- members: group size of the group of residence of the focal
“data_3_extra_early.csv” - file containing information on early maternal rank
Columns:
- id: identity of focal (offspring)
- mat_rank: average rank (0 lowest, 1 highest) of the focal’s mother during that focal’s first year of life (average early maternal rank)
THE FOLLOWING DATASETS ARE ACCESSED THROUGH DRYAD IN THE R SCRIPTS (from Godoy et al. 2022):
Behavioural data file:
Godoy, Irene; Korsten, Peter; Perry, Susan (2022). Data from: Genetic, maternal, and environmental influences on sociality in a pedigreed primate population [Dataset]. Dryad.
https://doi.org/10.5061/dryad.mkkwh7136
File “cebusData.csv”
Columns:
- id: identity of focal
- Year: year of data collection
- Month: month of data collection (string)
- n: number of focal scans for the focal in the month
- animal: identity of focal (for linking to population pedigree)
- Mother: identity of mother (for estimating maternal effects)
- Sex: sex of focal (“Female” or “Male”)
- age: age of focal in years
- Group: primary group of residence of the focal, and identity of alpha male of the group of residence
- social: number of focal scans where the focal was in proximity of another capuchin
Pedigree data file:
Godoy, Irene; Korsten, Peter; Perry, Susan (2022). Data from: Genetic, maternal, and environmental influences on sociality in a pedigreed primate population [Dataset]. Dryad.
https://doi.org/10.5061/dryad.mkkwh7136
File “cebusPedigree.csv”
Columns:
- animal: identity of focal
- Mother: identity of mother
- Father: identity of father
BLUPs generated by the Mother models and Offspring models are also provided as .csv files:
“soc_scores_mothers1.csv”
Columns:
- id: identity of offspring
- Mother: identity of mother
Early maternal scores:
- mom_mu: mean, early maternal spatial association score (probability scale)
- mom_sd: standard deviation, early maternal spatial association score (probability scale)
- mom_scale_mu: mean, standardised early maternal spatial association score
- mom_scale_sd: standard deviation, standardised early maternal spatial association score
“soc_scores_offspring.csv”
Columns:
- id: identity of offspring
Juveniles scores:
- juv_mu: mean, juvenile spatial association score (probability scale)
- juv_sd: standard deviation, juvenile spatial association score (probability scale)
- juv_scale_mu: mean, standardised juvenile spatial association score
- juv_scale_sd: standard deviation, standardised juvenile spatial association score
Subadult scores:
- mid_mu: mean, subadult spatial association score (probability scale)
- mid_sd: standard deviation, subadult spatial association score (probability scale)
- mid_scale_mu: mean, standardised subadult spatial association score
- mid_scale_sd: standard deviation, standardised subadult spatial association score
Adult scores:
- adu_mu: mean, adult spatial association score (probability scale)
- adu_sd: standard deviation, adult spatial association score (probability scale)
- adu_scale_mu: mean, standardised adult spatial association score
- adu_scale_sd: standard deviation, standardised adult spatial association score
Code/Software
Code used to run the main models are in the associated .R files. The code is written assuming at least 4 cores for running models in parallel.
- “code_1_mods_soc_maternal.R” requires the use of “data_1_matProx_sub.csv”
- “code_2_mods_soc_juv_mid_adu.R” requires the use of “data_2_extra_group.csv”
- Access behavioural data from Dryad from Godoy et al. 2022 for file “code_2b_mods_soc_juv_mid_adu.R”
Supplementary analyses
Requires the use of the following data files:
- “data_2_extra_group.csv”
- Access behavioural data from Dryad from Godoy et al. 2022
- “code_3_mods_earlyEffects.R” requires the use of “data_3_extra_early.csv”
- Access pedigree data from Dryad from Godoy et al. 2022
Code used to produce Figures are in the following .Rmd files
- “figures_code_1.Rmd” - Figures produced from data or output from “code_1_mods_soc_maternal.R”
- “figures_code_2.Rmd” - Figures produced from data or output from “code_2_mods_soc_juv_mid_adu.R” and “code_2b_mods_soc_juv_mid_adu.R”
- To reproduce Fig 2, you will need the image file “2022.03.13.rf.igo_3311.JPG”
- “figures_code_3.Rmd” - Figures produced from data or output from “code_3_mods_earlyEffects.R”
Model outputs (objects) have also been saved as .rds files
Mother models (generated by “code_1_mods_soc_maternal.R”):
- mod_mom1_bernoulli.rds - early maternal spatial association - to generate early maternal BLUPs for early maternal spatial association phenotypes
Offspring models (generated by “code_2_mods_soc_juv_mid_adu.R” and “code_2b_mods_soc_juv_mid_adu.R”):
To generate offspring BLUPS for spatial association phenotypes
- mod_juv_BB1.rds - juveniles spatial association
- mod_juv_BB2.rds - Supplementary analysis, juvenile spatial association
- mod_juv_BB3.rds - Supplementary analysis, juvenile spatial association
- mod_mid_BB1.rds - subadult spatial association
- mod_mid_BB2.rds - Supplementary analysis, subadult spatial association
- mod_mid_BB3.rds - Supplementary analysis, subadult spatial association
- mod_adu_BB1.rds - adult spatial association
- mod_adu_BB2.rds - Supplementary analysis, adult spatial association
- mod_adu_BB3.rds - Supplementary analysis, adult spatial association
Maternal effects on offspring models (generated by “code_3_mods_earlyEffects.R”):
To asses influence of early maternal spatial association (early maternal BLUPs) on later offspring spatial association (offspring BLUPs)
- mod_juv_0.rds - juveniles, random effects only
- mod_juv_1.rds - juveniles, early maternal spatial association and early maternal rank (interactions)
- mod_juv_2.rds - juveniles, early maternal spatial association and early maternal rank (weak interactions removed)
- mod_juv_3.rds - juveniles, early maternal rank
- mod_mid_0.rds - subadults, random effects only
- mod_mid_1.rds - subadults, early maternal spatial association and early maternal rank (interactions)
- mod_mid_2.rds - subadults, early maternal spatial association and early maternal rank (weak interactions removed)
- mod_mid_3.rds - subadults, early maternal rank
- mod_adu_0.rds - adults, random effects only
- mod_adu_1.rds - adults, early maternal spatial association and early maternal rank (interactions)
- mod_adu_2.rds - adults, early maternal spatial association and early maternal rank (weak interactions removed)
- mod_adu_3.rds - adults, early maternal rank