DOI: 10.5061/dryad.2bv13
title: Data from: Gene expression plasticity as a mechanism of coral adaptation to a variable environment

description: Local adaptation is ubiquitous, but the molecular mechanisms that give
 rise to this ecological phenomenon remain largely unknown. A year-long
 reciprocal transplant of mustard hill coral (Porites astreoides) between a
 highly environmentally variable inshore habitat and a more stable offshore
 habitat demonstrated that populations exhibit phenotypic signatures that
 are consistent with local adaptation. We characterized the genomic basis
 of this adaptation in both coral hosts and their intracellular symbionts
 (Symbiodinium sp.) using genome-wide gene expression profiling.
 Populations differed primarily in their capacity for plasticity: following
 transplantation to a novel environment, inshore-origin coral expression
 profiles became significantly more similar to the local population's
 profiles than those in offshore-origin corals. Furthermore, elevated
 plasticity of the environmental stress response expression was correlated
 with lower susceptibility to a natural summer bleaching event, suggesting
 that plasticity is adaptive in the inshore environment. Our results reveal
 a novel genomic mechanism of resilience to a variable environment,
 demonstrating that corals are capable of a more diverse molecular response
 to stress than previously thought.
description: R script for statistical
 analysesAnnotated R script for
 completing statistical analyses as described in the publication (e.g.
 WGCNA, DAPC, etc).WGCNA_DFA_final.RR script for plotsAnnotated R script for obtaining gene lists from gene ontology enrichement analyses (completed using the GO_MWU package - https://github.com/z0on/GO_MWU) and plotting heatmaps.go_plotresults_versionCarl.RCoral Host Physiological Trait Data.csv file of physiological trait data for coral host samples, used as input for the WGCNA R script.WGCNA_traitsHost.csvGene Ontology Annotations for Porites astreoides transcriptome.tab file of GO term annotations for isogroups in the Porites astreoides transcriptome. Used as input for the statistical and plots R scripts.past2digNvecManual_apr2014_iso2go_ckupdate.tabDAPC assignments for host cellular response to stress genes.csv file of DAPC assignments for environmental stress response genes - i.e. those annotated with the GO terms 'cellular response to stress' and 'ribosome biogenesis'. Used as input for statistical R script.Host_IndividCoord_DFA_CRSgenes.csvStandardized traits in coral host.csv file of standardized gene expression and fitness-related traits (percent weight gain) for the coral host. Used to calculate the costs of expression plasticity using the selection gradient method. Used as input for the statistical R script.PlasticityCosts.csvNormalized expression data for ESR genes in the coral host.csv file of normalized expression data by sample for genes annotated with either the 'cellular response to stress' or 'ribosome biogenesis' GO term. Used as input for R statistical script.Host_annotESRgenes_CRSriboBiogen.csvDAPC assignments for all Symbiodinium genes.csv file of DAPC assignments for all high expression Symbiodinium genes. Used as input for statistical R script.Sym_IndividCoord_DFA_1174genes.csvDAPC assignments for all coral host genes.csv file of DAPC assignments for all high expression coral host genes. Used as input for statistical R script.Host_IndividCoord_DFA_7008genes.csvGene Ontology Annotations for Symbiodinium Clade A transcriptome (kb8).tab file of GO term annotations for isogroups in the Symbiodinium Clade A transcriptome (strain kb8). Used as input for the statistical and plots R scripts.kb8_mar2014_iso2go.tabRaw expression counts for coral hostTable of raw read count data for the coral host by sample (ii=inshore to inshore; io=inshore to offshore; oi=offshore to inshore; oo=offshore to offshore; number indicates genotype). Used as input for the R statistical script.allcountsHostOnly_Bowtie2.txtRaw expression counts for SymbiodiniumTable of raw read count data for in hospite Symbiodinium by sample (ii=inshore to inshore; io=inshore to offshore; oi=offshore to inshore; oo=offshore to offshore; number indicates genotype). Used as input for the R statistical script.allcountsSymOnly_Bowtie2.txtGene Name Annotations for Porites astreoides transcriptome.tab file of gene name annotations for isogroups in the Porites astreoides transcriptome. Used as input for the statistical and plots R scriptspast_apr2014_iso2gene.tabGene Name Annotations for Symbiodinium Clade A transcriptome (kb8).tab file of gene name annotations for isogroups in the Symbiodinium Clade A (strain kb8) transcriptome. Used as input for the statistical and plots R scriptskb8_mar2014_iso2gene.tab