## 2 Materials and Methods
### Coral Sample Analysis  
RNAs, DNAs, and proteins were extracted from the small (50-100 mg) precollopridoral biopsies (\(n=110\)) as in prior works [26; 27; 28]. It is worth emphasizing that a standard operating procedure was used for all LOF-GRE samples to improve data comparability across research missions. In addition to genotyping the dinoflagellate communities to genus-level and host corals to species-level from the co-extracted DNAs as in prior work [18], 13 additional response variables were measured for each colony: an in situ, qualitative coral health assessment based on pigmentation and disease presence (either \"normal\" or \"abnormal\"), maximum colony length (cm), surface area (cm\({}^{2}\); via ImageJ analysis of underwater imagery), the Symbiodiniaceae geometry copy proportion (GCP; a molecular proxy for dinoflagellate endosymbiont density [29]), the RNA/DNA ratio, and the expression of four Symbiodiniaceae and four host coral genes. The former included the large subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase (_trclL_), ubiquitin ligase (_ubiq-lig_), heat shock protein 90 (_lsp90_), and zinc-induced facilitator-like 1-like (_zifl1_). The coral genes included green fluorescent protein (GFP)-like chromoprotein (_gfp-cp_), _lectin_, carbonic anhydrase (_ca_), and copper-zinc superoxide dismutase (_cu-zn-sod_); all eight mRNAs have been shown previously to be thermosensitive [30; 31]. Since surface area inherently covariates with colony length, it was excluded from the analysis. The qualitative color health assessment data were recoded as 0 and \(-1\) for normal and abnormal colonies, respectively, and these \"qualitative color scores\" were added to the standardized values of the Symbiodiniaceae GCP (the more quantitative measure of endosymbiont density) for those standardized values between \(-2\) and \(2\) (the stress tolerance threshold; described below); standardized GCP values \(\geq\)2 were first converted to negative values as a penalty for aberrant behavior. In other words, the penalty-weighted and standardized Symbiodiniaceae GCP values were added to the qualitative color scores to create a new response metric called the \"mean color score\". Higher values of this parameter were hypothesized to reflect healthier corals. In analyses that featured 12 physiological response variables (see table and figure captions for details. ), these included the eight genes, mean color score, RNA/DNA ratio, colony length, and Symbiodiniaceae GCP. In addition to the mean color score, three additional measures of aberrancy were derived. First, the \"heat map score\" [32] was calculated. This is simply the summed total of all response variables whose standardized levels fell below two standard deviations below the mean or above two standard deviations above the mean. The response variables included were the Symboliniaceae GCP, the RNA/DNA ratio, and the eight target genes. For instance, if a sample's standardized values (i.e., \(z\)-scores) for these parameters were \(-2.5\) (+1), \(-1.9\) (0), \(-1\) (0), 0 (0), 1 (0), 1.2 (0), 1.5 (0), 1.9 (0), 2.3 (+1), and 3 (+1), respectively, it would be given a heat map score of 3. Higher heat map scores are indicative of more stressed corals. To assess intrasample variability, the variability index [33] was calculated. This is simply the standard deviation calculated across the \(z\)-scores for the same 10 response variables used for the heat map score calculation, and high variability index scores are hypothesized to be evidence for the loss of control of homeostasis and therefore putative stress. To assess inter-sample aberrancy, the Mahalanobis distance was calculated across the same 10 response variables; as per the variability index, high values (i.e., significant deviation from normal behavior) were presumed to reflect the loss of control of homeostasis.