DOI: 10.5061/dryad.w9ghx3g1s
title: Data from: Inbreeding depression across multiple life history traits in a long-lived mammal

description: Inbreeding depression is widely recognized as a near-universal phenomenon
 of high conservation concern, particularly as wild populations continue to
 decline. However, most research to date has focused on early life stages,
 leaving later-life effects comparatively understudied, especially for wild
 populations of long-lived species. The Pyrenean brown bear (Ursus arctos),
 characterized by a small population, high levels of inbreeding, and
 conflicts with human activities, embodies the conservation challenges
 faced by many large mammals. We analyzed 27 years of monitoring data to
 quantify inbreeding depression across multiple life stages on survival,
 reproduction and dispersal. Our results reveal strong inbreeding
 depression effects, particularly in early life stages, including reduction
 in litter size and in natal dispersal distance. In adults, more inbred
 mothers exhibit lower cub survival. The cumulative effect of inbreeding,
 as measured by lifetime breeding success, also shows a negative impact.
 These findings highlight the necessity of assessing inbreeding depression
 across the entire life cycle to accurately evaluate its threat to
 population dynamics and viability. Such comprehensive assessments will
 become increasingly essential for wild plant and animal populations
 constrained by habitat destruction, human-wildlife conflict, and
 harvesting pressures.
description: README for the paper: Inbreeding depression across multiple life history
 traits in a long-lived mammal GENETIC DATA Dataset:
 genotypes_founders_new_set.txt File Format: ``` Name:
 genotypes_founders_new_set.txt Type: txt Delimiter: tabulation ``` This
 dataset gives the genotypes for 23 microsatellite markers of 9 founders of
 the population. The missing values are coded as 0. Dataset:
 genotypes_founders_old_set.txt File Format: ``` Name:
 genotypes_founders_old_set.txt Type: txt Delimiter: tabulation ``` This
 dataset gives the genotypes for 11 microsatellite markers of 8 founders of
 the population. The missing values are coded as 0. DEMOGRAPHIC DATA
 Dataset: litter_size_dt.csv File Format: ``` Name: litter_size_dt.csv
 Type: CSV (Comma-Separated Values) Delimiter: , ``` Variables description:
 ``` -Birth_year (numeric): Year of birth of the bear. -Id_mother
 (categorical): Anonymized identifier of the mother of the bear.
 -Litter_size (numeric): Number of cubs in the litter. -Id_father
 (categorical): Anonymized identifier of the father of the bear.
 -Inbreeding_individual (numeric): Inbreeding coefficient of the cubs from
 the litter. -Primiparity (categorical): Whether the litter was the
 mother’s first. True if the litter is the first one detected for the
 mother otherwise False. -Inbreeding_mother (numeric): Inbreeding
 coefficient of the mother of the bear calculated from the pedigree, with
 the relatedness of the founders and half-founders corrected by
 microsatellite data. -Mother_age (numeric): Age of the mother in the year
 of the litter’s birth. -Complete_litter (categorical): True if all the
 cubs from the litter have been genotyped and therefore have a known
 father. -Diff_detect_litter (numeric): Time is measured as the number of
 days between March 15 of the birth year and the detection of the litter,
 which allowed for determining its size (i.e, picture or direct
 observation). -Male_density (numeric): Number of adult males with
 overlapping home range with the mother at the year of the litter’s birth.
 ``` Dataset: survival_dt.csv File Format: ``` Name: survival_dt.csv Type:
 CSV (Comma-Separated Values) Delimiter: , ``` Variables description: ```
 -Id_bear (categorical): Anonymized identifier of bears. -Sex
 (categorical): Sex of the bear (M = Male, F = Female). -X1996 to X2023:
 Detection status of the bear for each year. 0 indicates no detection, 1 a
 detection of the bear alive, 2 a dead recovery of the bear only and 3 a
 detection of the bear alive followed by a dead recovery that year.
 -Inbreeding_individual (numeric): Inbreeding coefficient of the bear
 calculated from the pedigree, with the relatedness of the founders and
 half-founders corrected by microsatellite data. Some litters have not been
 genotyped, resulting in missing inbreeding coefficient values (NA) for
 those individuals. -Inbreeding_mother (numeric): Inbreeding coefficient of
 the mother of the bear calculated from the pedigree, with the relatedness
 of the founders and half-founders corrected by microsatellite data. As the
 mother is unknown for founders, the inbreeding of mother is missing (NA
 values). -Age_first_detection (numeric): Age of the bear when it was first
 detected. ``` Dataset: Natal_dispersal_dist.csv File Format: ``` Name:
 Natal_dispersal_dist.csv Type: CSV (Comma-Separated Values) Delimiter: ,
 ``` Variables description: ``` -Id_bear (categorical): Anonymized
 identifier of bears. -Id_mother (categorical): Anonymized identifier of
 the mother of the bear. -Sex (categorical): Sex of the bear (M = Male, F =
 Female). -Sexual_maturity (numeric): Year when theoretical sexual maturity
 is reached for the bear (3 years old). -Inbreeding_individual (numeric):
 Inbreeding coefficient of the bear calculated from the pedigree, with the
 relatedness of the founders and half-founders corrected by microsatellite
 data. -Distance (numeric): Shortest distance in meters between the
 centroids of the natal and adult home ranges on the WGS84 ellipsoid.
 -Mother_age (numeric): Age of the mother in the year of the litter birth.
 -Number_cubs (numeric): Number of cubs in the litter of the bear.
 -Nb_points (numeric): Number of samples associated with spatial
 coordinates used to define the centroid of the adult home range. ```
 Dataset: Age_first_repro.csv File Format: ``` Name: Age_first_repro.csv
 Type: CSV (Comma-Separated Values) Delimiter: , ``` Variables description:
 ``` -Id_bear (categorical): Anonymized identifier of bears. -Sex
 (categorical): Sex of the bear (M = Male, F = Female).
 -Inbreeding_individual (numeric): Inbreeding coefficient of the bear
 calculated from the pedigree, with the relatedness of the founders and
 half-founders corrected by microsatellite data. -Age_first_repro
 (numeric): Age of the bear at the first successful copulation, defined as
 one year before the first cubs are detected. If the bear never reproduced,
 the value is missing (NA). -Reproduction (categorical): Indicates whether
 the bear reproduced successfully: True if cubs were detected, False
 otherwise. -Number_potential_repro_partner (numeric): Number of adult
 bears (older than 3 years old) from the opposite sex with an overlapping
 home range at the year of sexual maturity (3 years old).
 -First_Reproduction_censored (numeric): If the bear has a reproduction
 detected: age of the bear at the first successful copulation otherwise,
 the number of years of monitoring without reproduction (from birth to last
 observation). ``` Dataset: yearly_breeding_success_dt.csv File Format: ```
 Name: yearly_breeding_success_dt.csv Type: CSV (Comma-Separated Values)
 Delimiter: , ``` Variables description: ``` -Id_bear (categorical):
 Anonymized identifier of bears. -Sex (categorical): Sex of the bear (M =
 Male, F = Female). -Inbreeding_individual (numeric): Inbreeding
 coefficient of the bear calculated from the pedigree, with the relatedness
 of the founders and half-founders corrected by microsatellite data. -Year
 (numeric): Year when the number of cubs produced is measured
 -Nb_repro_year_cub (numeric): Number of offspring detected each year over
 an individual’s reproductive period (from the age of two until the last
 observed year of the individual’s life, removing for females, the first
 year after they were observed with cubs). -Number_potential_repro_partner
 (numeric): Number of adult bears (older than 3 years old) from the
 opposite sex with an overlapping home range in the year of sexual maturity
 (3 years old). -Age (numeric): Age of the bear at the year of birth of the
 cubs -Age_2 (numeric): Age of the bear at the year of birth of the cubs to
 the power of two ``` Dataset: life_time_breeding_success.csv File Format:
 ``` Name: life_time_breeding_success.csv Type: CSV (Comma-Separated
 Values) Delimiter: , ``` Variables description: ``` -Id_bear
 (categorical): Anonymized identifier of bears. If the bear is a cub added
 to complete a litter to three cubs, the value is missing (NA). -Id_mother
 (categorical): Anonymized identifier of the mother of the bear.
 -Birth_year (numeric): Year of birth of the bear. -Inbreeding_individual
 (numeric): Inbreeding coefficient of the bear calculated from the
 pedigree, with the relatedness of the founders and half-founders corrected
 by microsatellite data. -number_cubs (numeric): The number of a
 bear's offspring that survived to at least one year old
 -Additional_cubs (categorical): True if the cub was observed, False if the
 cub was never observed but added to fill each litter to three offspring to
 take into account cubs that may have died before being detected and the
 potential impact of inbreeding on litter size. -censored (categorical): 0
 if the bear was dead at the end of the data sample (2023), 1 otherwise.
 ``` Script: RScript File Format: ``` Name: RScript.R Type: R (version
 4.3.3) ``` Purpose: The R script reproduces the analyses performed in the
 paper "Inbreeding depression across multiple life history traits in a
 long-lived mammal". It includes: ``` -Data Preparation (Standardizing
 numerical predictors, filtering data to create subsets for specific
 analyses (e.g., capture-mark-recapture analyses), etc.), -Model Building
 -Diagnostics and Model Checking: checking multicollinearity and residual
 diagnostics with the DHARMa package. ```