DOI: 10.5061/dryad.nk98sf848
title: The influence of relatedness on parental reproductive success and offspring fitness in Eastern chipmunks breeding in fluctuating environments

description: Mate choice and multiple paternity have been widely studied in natural
 populations, especially in research assessing inbreeding avoidance
 mechanisms. Ecological factors are expected to affect the costs and
 benefits of mate choice and multiple paternity, for instance, through
 their effects on the availability of partners. However, the relative
 importance and variation of those costs/benefits across fluctuating
 environmental contexts remain to be established. Here, we used
 reproduction data collected over 18 years on a wild population of Eastern
 chipmunks (Tamias striatus) to assess the influence of relatedness among
 mating partners on their reproductive success and on their
 offspring's fitness in different breeding contexts. In southern
 Québec, chipmunks live in a pulse resource system where they anticipate
 masting events of the American beech (Fagus grandifolia) and breed during
 the summer preceding and/or the spring following a mast. We found that,
 within a litter, less genetically related sires were assigned more
 offspring than more closely related ones. This relationship was
 significant during the summer breeding seasons only, which is
 characterized by high availability of food and mating partners in the
 environment. Multiple paternity was also more frequent during summer
 breeding than during spring breeding. We found no additional effect of
 parental relatedness on the juvenile survival, longevity, or reproductive
 success of their offspring. Our results could suggest the presence of
 context-specific inbreeding avoidance mechanisms by females or
 differential mortality of offspring at early stages linked to inbreeding
 depression. Altogether, our findings provide a better understanding of the
 influence of fluctuating environments on reproduction in small mammals.
description: ## The influence of relatedness on parental reproductive success and
 offspring fitness in Eastern chipmunks breeding in fluctuating
 environments This dataset contains 6 .csv files used to perform all
 analyses described in the paper The influence of relatedness on parental
 reproductive success and offspring fitness in Eastern chipmunks breeding
 in fluctuating environments (*Journal of Evolutionary Biology*, 2025). It
 also contains the R script that was used to run the simulation analysis.
 All methods are described in the paper. ## Description of the data and
 file structure **Data_IR_vs_Rxy.csv** This spreadsheet presents Eastern
 chipmunks' data related to juveniles and their parents (Rxy and IR).
 It contains one line per juvenile. Juvenile is a column that indicates the
 Juvenile's ID Dam is a column that indicates the Dam's ID Sire
 is a column that indicates the Sire's ID Rxy is a column that
 indicates the Parental relatedness of the juvenile's parents\ IR is a
 column that indicates the Internal relatedness of the juvenile's
 parents (IR; metric of inbreeding obtained from microsatellite multilocus
 heterozygosity data: higher IR is indicative of higher individual
 inbreeding) **Data_Longevity.csv** This spreadsheet presents Eastern
 chipmunk data related to the juvenile survival (longevity) analysis. It
 contains one line per juvenile. ID_Juv is a column that indicates the
 Juvenile's ID Rxy is a column that indicates the Parental relatedness
 of the juvenile's parents\ Year is a column that indicates the year
 the juvenile was captured Season is a column that indicates the season the
 juvenile was captured (Su=summer; Sp=spring) Survival is a column that
 indicates the number of years the juvenile has survived Sex is a column
 that indicates the juvenile's sex (F=female; M=Male) Site is a column
 that indicates the Capture site (possible values are: Site1, Site2, Site3,
 and Site4) **Data_Parent.csv** This spreadsheet presents Eastern
 chipmunks' data related to all the litters with known parents. It
 contains one line per couple of parents. Dam is a column that indicates
 the Dam's ID Sire is a column that indicates the Sire's ID Rxy
 is a column that indicates the parental relatedness Year is a column that
 indicates the year the litter was born Season is a column that indicates
 the season the litter was born (Su=summer; Sp=spring) N_Juvenile is a
 column that indicates the number of juveniles in that litter that
 descended from this couple of parents Juv_total is a column that indicates
 the total number of juveniles in that litter Site is a column that
 indicates the capture site (possible values are: Site1, Site2, Site3, and
 Site4) N_Sire is a column that indicates the number of different sires for
 that litter Litter is a column that indicates the litter's ID
 **Data_reprod_success.csv** This spreadsheet presents Eastern chipmunk
 data related to the yearly reproductive success of an individual. It
 contains one line per reproductive event (sometimes multiple lines per
 individual). ID is a column that indicates the ID of the individual Rxy is
 a column that indicates the Parental relatedness Year is a column that
 indicates the year the juvenile was captured N_juvenile is a column that
 indicates the number of juveniles produced that year by this individual
 Season is a column that indicates the season in which this reproductive
 event occurred (Su=summer; Sp=spring) Sex is a column that indicates the
 individual's sex (F=female; M=Male) Site is a column that indicates
 the capture site (possible values are: Site1, Site2, Site3, and Site4)
 **Data_Sire.csv** This spreadsheet presents Eastern chipmunk data related
 to the litters produced by a female over her lifetime, as well as to the
 number of sires that produced these litters. It contains one line per
 litter. Dam is a column that indicates the Dam's ID Year is a column
 that indicates the year the litter was born Season is a column that
 indicates the season the litter was born (Su=summer; Sp=spring) Site is a
 column that indicates the capture site (possible values are: Site1, Site2,
 Site3, and Site4) Litter is a column that indicates the Litter's ID
 Number_Litter is a column that indicates the unique number associated with
 each litter (from 1 to 321) N_Sire is a column that indicates the number
 of different sires for that litter **Data_Survival.csv** This spreadsheet
 presents Eastern chipmunk data related to the juvenile survival (binomial)
 analysis. It contains one line per juvenile. ID_Juv is a column that
 indicates the Juvenile's ID Rxy is a column that indicates the
 parental relatedness Year is a column that indicates the year the juvenile
 was captured Season is a column that indicates the season the juvenile was
 captured (Su=summer; Sp=spring) Survival is a column that indicates the
 survival of the juvenile (A value of 0 was assigned to individuals not
 recaptured in the year following their initial capture, and a 1 to those
 captured at least once) Sex is a column that indicates the Juvenile's
 sex (F=female; M=Male) Site is a column that indicates the Capture site
 (possible values are: Site1, Site2, Site3, and Site4) **Genotypes.csv**
 This spreadsheet presents the genotype of all Eastern chipmunks captured
 in our study system. It contains one line per individual. The first column
 represents the individual's ID The following columns contain the
 whole genotype for that individual (2 columns per microsatellite,
 containing the same value for homozygotes, or different values in the case
 of a heterozygote). Missing values are represented by "NA".
 **Random_pairs_simulation.csv** This spreadsheet presents the genotype of
 100 simulated pairs of individuals for each degree of relatedness using
 the allele frequency data. It contains one line per simulated
 individual's ID. The following columns contain the whole genotype for
 that individual (2 columns per microsatellite, containing the same value
 for homozygotes, or different values in the case of a heterozygote).
 **result_sim.csv** This spreadsheet presents the estimated relatedness
 values computed from the simulated genotypes provided in
 Random_pairs_simulation.csv. It contains one line per pair. The first
 column (pair.no) corresponds to the pair number (i.e., the unique
 identifier for each pair). The second column (ind1.id) and the third
 column (ind2.id) represent the IDs of the two individuals in the pair. The
 fourth column (group) indicates the degree of relatedness of the pair
 (parent-offspring, full-sib, half-sib, or unrelated). The following
 columns contain the estimated relatedness values for each pair using
 multiple estimators. However, only the Wang estimator was actually
 computed — the other columns contain only zero values.
 **Simulation_Rxy.Rmd** This is the R Markdown script that was written to
 perform the simulation analysis described in the paper. It first performs
 the simulation (without setting the random seed number), then generates
 boxplots, density plots, and a table that contains the results of the
 analysis