Data repository for study on dinoflagellate bioluminescence and toxicity in response to copepodamides

Overview

This repository contains the datasets and analysis code for the manuscript "Grazer-induced bioluminescence and toxicity in marine dinoflagellates" by Gonzalo-Valmala and colleagues, which has been submitted as an original research article/report to the journal Limnology & Oceanography.

Analysis code and output

This repository includes an R Markdown file (Supplementary_Code.Rmd) containing all code used for data analysis and visualization. It provides a fully reproducible workflow for statistical analyses, correlation assessments, effect size calculations, and figure generation. The corresponding Supplementary_Code.html file is the compiled output of the R Markdown file, displaying both the code and its execution results.

Data sets

P.reticulatum_Bioluminescence.csv: This dataset is used for Michaelis-Menten curve fitting and statistical analysis of the bioluminescence induction response observed in Protoceratium reticulatum under increasing copepodamide concentrations. It also provides the data for the correlation analysis between net bioluminescence production rates and net growth rates, as well as for generating figures 1b, d, and f of the main manuscript.

A.catenella_Bioluminescence.csv: This dataset is used for Michaelis-Menten curve fitting and statistical analysis of the bioluminescence induction response observed in Alexandrium catenella under increasing copepodamide concentrations. It also provides the data for the correlation analysis between net bioluminescence production rate and net growth rates, as well as for generating figures 1a, c, and e of the main manuscript.

G.catenatum_Toxins.csv: Contains the primary data used for the statistical analysis and correlation analysis (net toxicity production rate vs. net growth rates) for the toxin production in Gymnodinium catenatum upon increasing copepodamide concentrations. It is also used to produce figures 2a, c, and e of the main manuscript.

A.catenella_Toxin_Wide.csv: Contains the primary data used for the statistical analysis and correlation analysis (net toxicity production rate vs. net growth rates) for the toxin production in Alexandrium catenella upon increasing copepodamide concentrations, as well as to produce figures 2d and 2f of the main manuscript and figure S1 of the supplementary information.

A.catenella_Toxins_Long.csv: Provides the data to produce figure 2b.

Both_species_bioluminescence.csv: Contains the data to compute the summary statistics (number of replicates, mean, standard deviation, standard error, 95% confidence intervals, and lower and higher confidence intervals) used for the effect size calculations in the bioluminescence induction experiments of Protoceratium reticulatum and Alexandrium catenella (Table 3).

EffectSizeBiolum_Data.csv: Contains the data needed to produce the percent effect size calculations between treatment and control groups for the bioluminescence induction experiment in Protoceratium reticulatum and Alexandrium catenella, as well as the rest of the elements observed in Table 2.

Both_species_Toxins.csv: Contains the necessary data to compute the summary statistics (number of replicates, mean, standard deviation, standard error, 95% confidence intervals, and lower and higher confidence intervals) used for the effect size calculations in the toxin induction experiments of Alexandrium catenella and Gymnodinium catenatum (Table 3).

EffectSizeTox_Data.csv: Contains the data needed to produce the percent effect size calculations between treatment and control groups for the bioluminescence induction experiment in Alexandrium catenella and Gymnodinium catenatum, as well as the rest of the elements observed in Table 3.

Alexandrium_catenella_(1).PNG: This .png file contains a dinoflagellate drawing of Alexandrium catenella used in figures 1a and 2b.

Protoceratium_reticulatum_(1).PNG: This .png file contains a dinoflagellate drawing of Protoceratium reticulatum used in figure 1b.

Gymnodinium_catenatum_(1).PNG: This .png file contains a dinoflagellate drawing of Gymnodinium catenatum inserted in figure 2a.