Coral_DNAMethylation_Plasticity
This repository includes data and analysis scripts to accompany: Ocean acidification influences host DNA methylation and phenotypic plasticity in environmentally susceptible corals
Authors: Putnam, Hollie M., Davidson, Jennifer M., Gates, Ruth D. Journal: Evolutionary Applications Link: Description: This repository provides data and scripts to analyze the influence of ocean acidification on host DNA methylation and phenotypic plasticity. Clonal coral fragments from Montipora capitata and Pocillopora damicornis were exposed to ambient and low fluctuating pH treatments for 6 weeks. Coral growth was measured every 2 weeks and samples were taken after 6 weeks of exposure for analysis of host DNA methylation and HNMR metabolomic profiling.
Contents: RAnalysis file containing three folders (Scripts, Data, Output)
Scripts: Coral_DNA_Methylation.R: A R script that imports all data and runs all analyses for the maniscript and generates all figures and tables opls.R: A R script required for the metabolomic profiling analysis (orthogonal partial least squares discriminate analysis). OPLS DA analysis script by Paul Anderson published in Sogin et al 2014 (http://birg.cs.cofc.edu/index.php/O-PLS)
Data: BM_Light_Calibration_Data.csv BM_Acclimation.csv BM_Field_Temp.csv BM_Tank_Temp.csv BM_Tank_light.csv BM_Daily_Measurements.csv BM_SWChem.csv BM_NBS_pH.csv BM_NMR_Data_0.04binned_truncated_nowater.csv BM_NMR_sample_info pH probe calibration files : Coral_DNAMethylation_Plasticity/R_Analysis/Data/pH_Calibration_Files/ BM_Methylation.csv BM_Buoyant_Weight.csv
Output: The directory containing the analysis results, figures, tables, and supplementary material.