This repository contains code to accompany the manuscript titled Exploring mechanisms that affect coral cooperation: symbiont transmission mode, cell density and community composition by Carly D. Kenkel and Line K. Bay 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 Symbiodinium 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 per se that influences host-symbiont cooperation, but genetic uniformity of the symbiont community. Repository contents: TraitDataAnalysis.R: Annotated R script for generating figures and re-creating statistical analyses RsquaredGLMM.R: Accessory R script for running RsquaredGLMM analyses, called by TraitDataAnalysis.R NSF_RunningPam.csv: 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=A. millepora, Maqe=M. aequituberculata, Gast=G. astreata, Gach=G. acrhelia, Plob=P. lobata, Gcol=G. columna) 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 Symbiodinium 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 TraitData.csv: 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. TraitData_DaysAsCols.csv: Reformatted input file with trait data split by sampling day across columns DADA2Analysis.R: 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

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