Data and code from Griffiths JS, Johnson KM, Sirovy KA, Yeats MS, Pan FTC, La Peyre JF, Kelly MW. 2021. Transgenerational plasticity and the capacity to adapt to low salinity in the eastern oyster, Crassostrea virginica. Proceedings of the Royal Society B. 288: 20203118. https://doi.org/10.1098/rspb.2020.3118
Script: Oyster_size_ANOVA.R
Input files: oyster_size.txt, parent_oyster_size.txt
Description: Script contains code for normalizing size data for larvae and parental adults and performing an ANOVA and a Tukey’s post-hoc test
Script: Oyster_mortality_ANOVA.R
Input files: oyster_mortality.txt
Description: Script contains code for mortality data for each cross and performing an ANVOA
Script: parent_mort.R
Input files: parent_mort.txt, cumulative_parent_mort.txt
Description: Script contains code for mortality data for adults outplanted at the two field acclimation sites. parent_mort.txt contains mortality data after two years of outplant and the cumulative_parent_mort.txt contains the mortality collected every two months for adults outplanted at the field sites.
Script: biochem_ANOVA.R
Input files: biochem_data.txt, oyster_size_eggQual.txt
Description: Script contains code for ANOVAs to determine whether egg quality differs among dam acclimation site, whether egg quality is related to a dam's successful spawn, and whether egg quality is related to size of larvae.
Script: Oyster_MCMCglmm.R
Input files: oyster_ped.txt, oyster_size.txt
Description: Script contains different models for estimating heritability and variance components for larval size. Oyster_ped.txt contains pedigree information for each family. This script also uses the breeder's equation to estimate the required mortality to return larval sizes back to ambient salinity conditions after one generation of selection.
script: Genetic_coVariation.R
Input files: family_means_v2.csv, oyster_ped_covar_matrix.txt
Description: Script contains model for estimating genetic co-variation between families reared at low and high salinity conditions. oyster_ped_covar_matrix.txt contains pedigree information for each family. family_means_v2.csv contains mean larval size for each family reared at low and high salinity.