README

Author: Marta Mosna Date: 22.04.2026

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Files Overview

File	Type
main_script.R	R Script
hyena_reproduction_dataset.csv	Dataset
maternal_lineage_with_ranks.csv	Dataset
paternal_lineage_with_ranks.csv	Dataset
res_rep_1000_app.rds	Data saved as R Data Object
LICENSE.md	License file

R Scripts

main_script.R

The main script to be used for running all the analyses.

Data

hyena_reproduction_dataset.csv

This dataset contains life-history, reproductive, social rank, and genetic contribution data for all individuals included in the study. All reproductive counts and genetic contribution metrics are computed up to January 1st, 2023.

Variable Description

Variable	Description
ID	Unique individual identifier.
birth_date	Date of birth of the individual.
death_date	Date of death of the individual (NA if still alive at the end of the study period).
selection_first	Date when the individual begins its reproductive career.
sex	Biological sex of the individual.
tenure	Duration (in years) during which the individual was reproductively active within the study population (from selection_first to death or end of the study period).
n_off_type	Number of offspring genetically typed for both mother and father.
n_g_off	Number of grandoffspring (offspring of genetically typed offspring).
n_gg_off	Number of great-grandoffspring (grand-offspring of genetically typed offspring).
n_alive_genotyped_offspring	Number of genetically typed offspring alive at end of the study period.
rank_maternal.std	Standardized maternal social rank at the time of the individual's birth.
n_off_obs	Total number of offspring observed, regardless of genetic typing.
n_g_off_obs	Total number of grandoffspring observed (includes those from non-genotyped offspring).
gen_cont	Long-term genetic contribution (gᵢ): expected number of gene copies present in the population at the end of the study period.

maternal_lineage_with_ranks.csv & paternal_lineage_with_ranks.csv

These datasets summarize the genealogical lineages and parental ranks of spotted hyenas used in the study. Each table contains information on all individuals with known ancestry in the population, including the rank of their ancestors across multiple generations.

• maternal_lineage_with_ranks.csv tracks maternal ancestry (mother, maternal grandmother, etc.).

• paternal_lineage_with_ranks.csv tracks paternal ancestry (father, paternal grandfather, etc.).

These tables form the basis for analyses of rank inheritance and sex-biased lineage effects across generations.

Variable Description

Variable	Description
ID	Unique individual identifier.
n_generation	Number of generations including the focal individual (G0) known for the ID.
rank_G0	Maternal rank of the focal individual.
rank_G1, rank_G2, ...	Maternal rank of the individual's ancestors in generations G1, G2, ... respectively.

res_rep_1000_app.rds

This file contains results from 1,000 permutation simulations, used to test the effect of disrupting maternal lineage continuity while preserving the empirical variation in reproductive output. It allows testing whether social rank inheritance significantly affects the overrepresentation of alpha-descendant lineages across generations.

Structure

A list of 1,000 elements, each corresponding to a single permutation simulation. Each element is itself a list with two components:

• geometric_mean — Geometric mean of fold-changes in the proportion of alpha-ranked mothers across consecutive generations (same number as with the real data).

• long_data_proportions — A tidy data frame containing:

Column	Description
generation	Generation relative to the focal individual (G0, G-1, ...).
rank	Maternal rank of each ancestor in that generation.
n	Number of individuals with that rank in the permutation.
proportion	Proportion of individuals with that rank within the generation.
total_n	Total number of individuals in the generation.

Software

Package	Version
R	4.5.0 (2025-04-11 ucrt)
ggplot2	4.0.3
patchwork	1.3.2
ragg	1.5.2
dplyr	1.2.1
tidyr	1.3.2
lubridate	1.9.5
tibble	3.3.1
SkewCalc	1.0 (install via remotes::install_github("Ctross/SkewCalc"))
DescTools	0.99.60
flextable	0.9.11
glmmTMB	1.1.14
DHARMa	0.4.7
car	3.1.5
broom.mixed	0.2.9.7
diffcor	0.8.4
officer	0.7.3
ggbreak	0.1.7