Data for: Patterns of bleaching and recovery of Montipora capitata in Kāneʻohe Bay, Hawaiʻi, USA

This repository includes data and analysis scripts to accompany:

Patterns of bleaching and recovery of Montipora capitata in Kāneʻohe Bay, Hawaiʻi, USA

Authors: Ross Cunning, Raphael Ritson-Williams, Ruth D. Gates

Journal: Marine Ecology Progress Series

Link: doi:10.3354/meps11733

Description:

This work analyzes bleaching and recovery dynamics of Symbiodinium in Montipora capitata corals following a thermal stress event in Kāneʻohe Bay, Oʻahu (Hawaiʻi, USA) in late 2014. Corals were tagged and resampled 6 times between October 2014 and May 2015, and extracted DNA from each sample was used to measure symbiont to host cell ratios for both clade C and clade D Symbiodinium.

Contents:

Scripts:

• setup.R: R script that imports and quality controls qPCR data in preparation for analysis.

• analysis.R: R script for all data analyses and figures presented in the manuscript.

• suppmethods.R: R script for analyses presented in the Supplement (fluorescence normalization, copy number estimation, ITS2 analysis, environmental data analysis).

• ITS2_analysis.txt: Shell script for bioinformatic analysis of Symbiodinium ITS2 data.

Data:

• data/coast_n83.shp/: Hawaii coastline shapefile, originally downloaded from here

• data/bleachedpair.png: Photograph of a bleached and non-bleached pair of M. capitata colonies used in Figure 1 (photo credit: R. Ritson-Williams).

• data/qPCR/: Directory containing .csv files of symbiont and host quantification data exported directly from Applied Biosystems StepOnePlus Software qPCR platform.

• data/ITS2/: Directory containing ITS2 sequence data .fastq files (raw data) and OTU tables (final result of bioinformatic analysis). Note that intermediate/temporary data files in bioinformatic analysis are not included in the repository.

• data/supp/: Directory containing data for fluorescence normalization and gene copy number estimation, presented in the Supplement.

• data/temp_light/: Directory containing temperature and light data recorded during the study, originally downloaded from Zenodo.
  • Links to Zenodo data repositories:
    • Temperature data: doi:10.5281/zenodo.53226
    • Light data: doi:10.5281/zenodo.53227

Output:

• output/: Directory containing the figures and tables produced by the analysis scripts and presented in the manuscript and the Supplement.