DOI: 10.5061/dryad.z8w9ghx8s
title: Data from: Measuring the effect of environmental stress on inbreeding depression alone obscures the relative importance of inbreeding-stress interactions on overall fitness in Callosobruchus maculatus

description: Environmental stress can have a profound effect on inbreeding depression.
 Quantifying this effect is of particular importance in threatened
 populations, which are often simultaneously subject to both inbreeding and
 environmental stress. But while the prevalence of inbreeding-stress
 interactions is well known, the importance and broader applicability of
 such interactions in conservation are not clearly understood. We used seed
 beetles, Callosobruchus maculatus, as a model system to quantify how
 environmental stressors (here host quality and temperature stress)
 interact with inbreeding as measured by changes in the magnitude
 of8inbreeding depression, δ, as well as the relative importance of
 inbreeding-stress interactions to overall fitness. We found that while
 both environmental stressors caused substantial inbreeding-stress
 interactions as measured by change in δ, the relative importance of these
 interactions to overall survival was modest. This suggests that assessing
 inbreeding-stress interactions within the framework of δ alone may give an
 inaccurate representation of the relevance of interactions to population
 persistence. Furthermore, we found that the effect of environmental stress
 on fitness, but not inbreeding depression, varied strongly among
 populations. These results suggest that the outcomes of inbreeding-stress
 interactions are not easily generalized, an important consideration in
 conservation settings.
description: Survival and mass data were collected from inbred and outbred
 seed beetles from different lines and stress treatments.
description: Below is a description of the files contained in this compressed
 directory, as well as a description of how the analyses based on these
 files were run.<br> The programs R, jags, and Rjags are needed for
 this analysis. This folder contains eight
 files: Abbreviations used in these files
 include: 
 BF = the Burkina Faso seed
 beetle lineage CA = the California seed beetle
 lineage SI =
 the South India seed beetle lineage<br> H = heat treatment (37
 C) R = regular
 incubation temperature (27 C) M = mung bean host (native host
 for SI) C =
 cowpea host (native host for CA and BF) P = green pea host (stressful
 host for all lineages) DATA
 FILES The five data files include data_mass_BF.csv,
 data_mass_CA.csv, data_survival_BF.csv, data_survival_CA.csv, and
 data_survival_SI.csv<br> These files include the raw data from the
 inbreeding-stress seed beetle experiment. MASS DATA
 FILES Each row in the two 'mass' data files
 represents the data for a single beetle. Each of the 'mass' data
 files contains eight columns: The two full-sibling families
 within each block treatment were assigned either a capital or lowercase
 letter. For
 example, block A would contain two unrelated full-sibling families:
 'A' and 'a'.<br> These families were used for
 each of the four crosses within each block: inbred (i.e. 'AA' or
 'aa') or outbred ('Aa' or 'aA').
 ALL of the beetles weighed for the mass files were female as we
 were using female mass as a proxy for fecundity.
 SURVIVAL DATA FILES The three
 'survival' data files contain the same first seven columns as
 the mass data, but with 8 additional columns: MODEL
 FILES The file
 "model_mass.txt"; contains the linear mass model used to analyze
 the raw mass data using jags.<br> NOTE: Because the CA lineage had
 no female beetles survive in the host+temp and inbreeding+host+temp
 treatment groups, the sample sizes for these treatments are both zero.
 Thus, to run the analysis for CA, the model must be altered to comment out
 lines 56 (del[4]), 66 (HLE[4]), 75 (deldif[4]) and 84 (HLEdif[4]) as these
 are undefined for CA The file
 'model_survival.txt" contains the linear survival model used to
 analyze the raw survival data using jags.<br> NOTE: Again, because
 the CA lineage had no beetles survive in the inbreeding+host+temp
 treatment group, the percent survival for this treatment was zero. Thus,
 to run the analysis for CA without problems, the survival model must be
 altered to comment out line 56 (HLE[4]) as this is undefined for
 CA. R SCRIPT The file
 named 'script_filter_data_run_model' contains the R code to
 compile and run the statistical analyses for each of the raw data files.
 Additional details for how the data were formatted for analysis are found
 in this file. Lines 1 through 300 in this script can be
 run as-is with no alterations needed. Before running
 lines 301 through 325, both the mass model and survival model text files
 (see 'MODEL FILES' above) must be altered to remove undefined
 variables for the CA lineage. After changing the model
 text files for the CA lineage, lines 301 through 325 can be run
 as-is. The output of running this R-script (in two
 segments) includes the following: D.BF, D.CA, and D.SI: these three
 lists contain the raw survival data formatted for use in jags
 D.BF.M, and D.CA.M: these
 two lists contain the raw mass data formatted for use in jags
 BF.surv.out, CA.surv.out,
 and SI.surv.out: these are MCMC lists containing the thinned MCMC output
 from each of the three MCMC chains in the survival model BF.mass.out and CA.mass.out:
 These are MCMC lists containing the MCMC output from the mass
 model BF.surv.summary, CA.surv.summary,
 and SI.surv.summary: these three matrices contain the summarized MCMC
 output<br> (95% equal-tail probabilities from the posterior
 distributions of the tracked variables in the linear model)
 BF.mass.summary and
 CA.surv.summary: these two matrices contain the summarized MCMC
 output<br> (95% equal-tail probabilities from the posterior
 distributions of the tracked variables in the mass model)