DOI: 10.5281/zenodo.1208684
title: Exploring Mechanisms That Affect Coral Cooperation: Symbiont Transmission Mode, Cell Density And Community Composition

description: This repository contains code to accompany the manuscript titled

<strong>Exploring mechanisms that affect coral cooperation: symbiont transmission mode, cell density and community composition</strong>

by <strong>Carly D. Kenkel and Line K. Bay</strong><br>
 

In this study, we used a phylogenetically controlled design to investigate the role of vertical symbiont transmission, an evolutionary mechanism predicted to enhance cooperation and holobiont fitness of reef-building corals. Six species of coral, three vertical transmitters and their closest horizontally transmitting relatives, were fragmented and subjected to a two-week thermal stress experiment. Symbiont cell density, photosynthetic function and translocation of photosynthetically fixed carbon between symbionts and hosts were quantified to assess changes in physiological metrics of fitness and cooperation. Amplicon sequencing of the <em>Symbiodinium</em> ITS-2 locus was used to investigate differences in symbiont community composition among focal species. We did not observe universally higher levels of cooperation in vertically transmitting species. However, the reduction in cooperation at the onset of bleaching was marginally associated with symbiont community diversity. Analysis of ITS2 amplicon sequence data suggest that it may not be vertical transmission <em>per se</em> that influences host-symbiont cooperation, but genetic uniformity of the symbiont community.

Repository contents:


	
	<strong>TraitDataAnalysis.R:</strong> Annotated R script for generating figures and re-creating statistical analyses

	
		
		<strong>RsquaredGLMM.R:</strong> Accessory R script for running RsquaredGLMM analyses, called by <strong>TraitDataAnalysis.R</strong>
		
		
		<strong>NSF_RunningPam.csv</strong>: Input file for statistical analysis. Contains photophysiological data. Column headers are as follows:

		
			
			Tank: Number of experimental tank in which experimental coral fragment was held
			
			
			Treatment: short-hand notation for sample treatments (e.g. ctrl1-5 = control temperature, genotypes 1-5)
			
			
			Water: source sump for temperature controlled water jackets for each set of treatment tanks
			
			
			Position: numerical rack position of coral fragment within experimental treatment tank
			
			
			Species: Coral species (Amil=<em>A. millepora</em>, Maqe=<em>M. aequituberculata</em>, Gast=<em>G. astreata</em>, Gach=<em>G. acrhelia</em>, Plob=<em>P. lobata</em>, Gcol=<em>G. columna</em>)
			
			
			Genotype: source colony origin of individual coral fragments within species
			
			
			Temp: experimental temperature treatment (ctrl: 27°C ; heat: 31°C)
			
			
			Treat: whether experimental corals received C14-labeled bicarbonate (bicarb), artemia or were sampled separately for Gene Expression Analysis (not presented in this manuscript)
			
			
			EQY: Effective quantum yield of <em>Symbiodinium</em> photosystem II as measured using PAM fluorometry
			
			
			Date: Actual calendar date of measure
			
			
			Transmission: coral symbiont transmission mode
			
			
			Reef: reef site of original coral collection
			
			
			Date: experimental date of measure
			
		
		
		
		<strong>TraitData.csv:</strong> Input file for statistical analysis. Contains all physiological trait data.

		
			
			Includes columns as described above for the Running_Pam file in addition to columns containing raw trait data as described in the manuscript.
			
		
		
		
		<strong>TraitData_DaysAsCols.csv:</strong> Reformatted input file with trait data split by sampling day across columns
		
	
	
	
	<strong>DADA2Analysis.R:</strong> Annotated R script for generating figures and running ITS2 amplicon analyses

	
		
		GeoSymbio_ITS2_LocalDatabase_verForPhyloseq.fasta: FASTA file of the GeoSymbio ITS2 reference database https://sites.google.com/site/geosymbio/, formatted for use with the R prograom Phyloseq
		
		
		SeqVars_6Feb.fasta: FASTA file of identified sequence variants resulting from DADA2 analysis
		
		
		OutputDADA_6Feb.csv: Counts of sequence variants by sample
		
		
		Raw FASTQ paired end read files can be downloaded from NCBI's SRA: PRJNA338365
description: An NSF International Postdoctoral Research Fellowship, DBI-1401165, to Carly D Kenkel and funding from the Australian Institute of Marine Science to Line K Bay, supported this work.

Please contact ckenkel@usc.edu with any questions