Data and data analysis for: Variation in susceptibility among three Caribbean coral species and their algal symbionts indicates Acropora cervicornis is particularly susceptible to elevated nutrients and heat stress

Changes in this release:

• Added color to all graphs to make it easier to track the nutrient treatments
• Did not drop replicate tank from the models when it was not significant

This repository contains data and data analysis for the manuscript:

Variation in susceptibility among three Caribbean coral species and their algal symbionts indicates the threatened Acropora cervicornis is particularly susceptible to elevated nutrients and heat stress

Authors: Ana M. Palacio-Castro, Caroline E. Dennison, Stephanie M. Rosales, Andrew C. Baker

Journal: Coral Reefs doi:XXX

Description:

In this study, we examined the effects of pre-exposure to elevated nutrients (NH4 and NH4 + PO4 for >2 months at 26 °C), followed by heat stress (31.5 °C for 3-weeks) on three Caribbean corals: A. cervicornis, O. faveolata, and S. siderea.

We aimed to compare the effects of these combined stressors on coral survivorship, and associated algal symbiont communities (community composition, abundance, and function).

Repository content:

0.LabNotebooks: Contains daily note entries during the experiment

• Acer_Nut- Notebook.pdf: Pdf document with A. cervicornis notes (collection, maintenance, molecular work... )
• Nut_Ofav-Ssid_NoteBook.pdf: Pdf document with O. faveolata and S. siderea notes (collection, maintenance, molecular work... )

1.Temperature:

• Contains raw temperature data (Day_Tem.csv) and code (Temperature.Rmd) for Figure 1

2.Mortality: Contains raw mortality data and code for Figure 2

• Mortatily_Script.Rmd: code for survivorship analysis and Figure 2
• Data/Acer_Mortality.csv: Raw mortality data for A. cervicornis
• Data/Ofav_Mortality.csv: Raw mortality data for O. faveolata
• Data/Ssid_Mortality.csv: Raw mortality data for S. siderea

3.YII:

• Contains raw photochemical efficiency (Fv/Fm) data and code for Figure 3

• YII_Script.Rmd: code for Fv/Fm analysis and Figure 3

• YII_Data/All_YII_data.csv: YII values for all coral species

4.Chla_Sym2: Contains raw values of Chlorophyll-a and Symbiodiniaceae cell counts, as well as code for Figure 4 and 5

• Blasting.Rmd: code for Chlorophyll-a and Symbiodiniaceae areal density analysis (Figures 4 and 5)
• Data/data.csv: Data and metadata with Chlorophyll-a values (ug Chlorophyll-a cm^-2^ [Chl_a]) and Symbiodiniaceae areal density values (Symbiodiniaceae cells cm^-2^ [Sym.cm2])

5.SH: Contains raw qPCR values and code to produce the Symbiont to Host cell ratio (S/H). Inside each species folder (Acer, Ofav and Ssid) you can find:

• 1.spp_SH_calculation.Rmd: code to calculate the symbiont to host cell ratio using files in qPCR-Raw/, and metadata in Sample_Plates.csv

• 2.Spp_Nut_SH_analysis.Rmd: data analysis of the symbiont to host cell ratio, Durusdinium proportion and figures S1 (O.faveolata) and S1 (S. siderea)

• qPCR-Raw/: Contains the outputs from each plate run in qPCR