anampc / ofav_nh4_sh

Effect of elevated NH4 on Orbicella faveolata symbiont to host cell ratio (S/H)

Effect of elevated NH4 on Orbicella faveolata symbiont to host cell ratio (S/H)

This repository contains data and analysis scripts for the manuscript:

Increased Algal Symbiont Density Reduces Host Immunity in a Threatened Caribbean Coral Species, Orbicella faveolata

Authors: Lauren E. Fuess, Ana M. Palacio-Castro, Caleb C. Butler, Andrew C. Baker, Laura D. Mydlarz

Journal: Front. Ecol. Evol doi:10.3389/fevo.2020.572942

---

Description:

This repository:

• Calculates the symbiont to host cell ratio (S/H) in O. faveolata corals, and
• Tests if corals exposed to elevated NH4 (N) present higher S/H than corals maintained under ambient concentrations (C)

Contents:

Scripts:

• SH_script.Rmd: R script that imports the real-time PCR (qPCR) data and calculates the S/H cell ratio using the StepOne program (https://github.com/jrcunning/steponeR).

Data:

• Data: Folder containing the amplification CTs for each coral sample obtained from the qPCR machine.

• Outputs: Folder contained exported graphs (Figure 1), S/H cell ratio values and outputs of post-hoc Tukey comparisons.

• Sample_Plates.csv: File containing the sample treatment information (Coral colony, treatment) and the qPCR plate were each sample was run.