Nutrient and sediment loading affect multiple facets of coral functionality in a tropical branching coral.
This repository includes data and analysis for the above manuscript
Authors: Danielle M. Becker*, Nyssa J. Silbiger
Journal: Journal of Experimental Biology
Link: https://jeb.biologists.org/content/early/2020/09/15/jeb.225045
Becker, D.M. and Silbiger, N.J., 2020. Nutrient and sediment loading affect multiple facets of coral functionality in a tropical branching coral. Journal of Experimental Biology. https://doi.org/10.1242/jeb.225045
Funding: This research was funded in part by California State University, Northridge (CSUN) to NJS, U.S. National Science Foundation OCE#19-24281 to NJS, the American Academy of Underwater Sciences Foundations 2018 Masters Research Scholarship to DMB, CSUN Office of Graduate Studies, Department of Biology, Associated Students, College of Sciences and Mathematics, and Research and Graduate Studies to DMB, and the National Science Foundation 2019 Graduate Research Fellowship to DMB. Material are in this study based upon work supported by the U.S. National Science Foundation under Grant (OCE#16-37396) as well as a generous gift from the Gordon and Betty Moore Foundation. This work represents a contribution of the Mo'orea Coral Reef (MCR) LTER Site and is CSUN Marine Biology contribution #312. Research was completed under permits issued by the French Polynesian Government (De´le´gation a`la Recherche) and the Haut-commissariat de la Re´publique en Polyne´sie Francaise (DTRT) (Protocole d’Accueil 2005-2019).
Contents: There are ten folders and a README.md file.
Folders:
Correlation_Matrix
Contains data, output, and script files to compose an environmental parameters correlation matrix to compare environmental trends across our varying nutrient and sedimentation gradient within north shore fringing reef sites in Mo'orea, French Polynesia.
Effect_Sizes
Contains data, output, and script files to calculate and analyze the effect of the increasing nutrient and sediment gradient residuals on each coral, endosymbiont, and holobiont metabolic response variable
Map
Contains data, output, and script files to create a map of Mo'orea showing detailed information on the nutrient and sediment regime at each of our sampling sites. The data is represented by the average percent nitrogen content in Turbinaria ornata (macroalgal species) samples and sedimentation rates at each site.
PI_curve_sites1
Contains data, output, and script files to characterize a net photosynthesis as a function of photon flux density (commonly referred to as photosynthesis-irradiance (PI)) curve and analyze the saturating light levels for the experimental coral samples collected and sampled from sites E and F (eastern sites). Also, the output file contains a compilation plot of the three PI curves analyzed and the spectral trace of our Mars Aqua 300w LED Brand Epistar light used during experimental trials in Mo'orea.
PI_curve_sites2
Contains data, output, and script files to characterize a net photosynthesis as a function of photon flux density (commonly referred to as photosynthesis-irradiance (PI)) curve and analyze the saturating light levels for the experimental coral samples collected and sampled from sites C and D (central sites).
PI_curve_sites3
Contains data, output, and script files to characterize a net photosynthesis as a function of photon flux density (commonly referred to as photosynthesis-irradiance (PI)) curve and analyze the saturating light levels for the experimental coral samples collected and sampled from sites A and B (western sites).
Qa_Qc_Site_Data
Contains a clean data file with all average and se data for endosymbiont, coral, and holobiont metabolic response variables across our 6 northshore fringing reef sites in Mo'orea.
Respirometry
Contains data, output, and script files with all the raw respirometry files from the PreSens output, files for the raw output of the respirometry rates from the LoLinR package, and R script to take raw respirometry data and calculate photosynthesis and respiration rates.
Site_Characteristics
Contains data, output, and script files with all average and se data for biological, chemical, and physical parameters across our 6 northshore fringing reef sites in Mo'orea. Also contains plots of individual and combined parameters compared between each site and an overlayed site map and site characteristics plot.
TPC_curves
Contains data, output, and script files to characterize and analyze thermal performance curve (TPC) metrics and calculate net calcification rates. Contains all raw pH, salinity, and water volume for each sample and raw TA data and calculated net calcification rates. Also contains all the plotted TPC curves per region and by each metabolic rate process (photosynthesis, respiration, and net calcification) per coral sample.