DOI: 10.5061/dryad.p2ngf1w2j
title: Data and code from: Evidence of rare occurrences of the Phoenix effect in the Hawaiian corals Porites compressa and Montipora capitata following mortality induced by a marine heatwave

description: Coral bleaching is a common stress response to extreme temperatures
 experienced during marine heatwaves. Bleached corals are left vulnerable
 without the nutritional support of their algal symbionts, and can often
 suffer partial or complete mortality. Bleaching-induced mortality is often
 accompanied by colonization of turf algae over the dead coral skeleton,
 which can be difficult for corals to regrow over. The Phoenix effect is a
 phenomenon of rapid recovery of live coral tissue following mortality,
 which is hypothesized to occur via the regrowth of tissue from deep within
 the coral skeleton that expands over the top of dead portions. Here, we
 found that the Hawaiian corals Porites compressa and Montipora capitata
 can display rapid tissue recovery suggestive of the Phoenix effect. During
 a marine heatwave that occurred in 2015 in Kāne’ohe Bay, Hawai’i, USA, 237
 individuals (including bleached and non-bleached phenotypes) were
 identified and monitored for mortality and recovery over the next 2–7
 years. Nearly 16% of P. compressa individuals and 34% of M. capitata
 exhibited substantial partial mortality, and approximately half of these
 affected individuals of each species had bleached during the heatwave.
 Partial mortality following the 2015 heatwave was followed by turf algae
 colonization over the exposed skeleton. Of the colonies with substantial
 mortality, 6 colonies (10% of affected individuals; 5 P. compressa and 1
 M. capitata) subsequently recovered to over 90% live coral tissue within
 two years (2017), with an additional 3 colonies (2 P. compressa and 1 M.
 capitata) recovering within 4 years of the 2015 marine heatwave (2019). We
 qualify colonies with rapid tissue recovery as those that meet two
 criteria: 1) substantial partial mortality (≥40%) in the first 12 months
 following the initial 2015 marine heatwave, and 2) recovery of any amount
 of live tissue at anytime before 2022. Interestingly, only colonies that
 had bleached in 2015 exhibited rapid tissue recovery. A consecutive, yet
 less severe marine heatwave occurred in 2019, and none of the previously
 recovered colonies observed experienced significant tissue loss,
 suggesting these individuals remained resilient amidst a secondary heat
 stress exposure. This phenomenon is an example of remarkable recovery and
 resilience that may be informative for further study of mechanisms of
 coral tissue regeneration in two important reef-building coral species.
description: # Data and code from: Evidence of rare occurrences of the Phoenix effect
 in the Hawaiian corals Porites compressa and Montipora capitata following
 mortality induced by a marine heatwave
 [https://doi.org/10.5061/dryad.p2ngf1w2j](https://doi.org/10.5061/dryad.p2ngf1w2j) ## Description of the data and file structure This code analyzes data from quantitatively scored mortality images for *Porites compressa* and *Montipora capitata* colonies at Kane'ohe Bay, HI, USA from 2015 to 2022. These corals experienced two marine heatwaves in 2015 and 2019 and some were marked as bleaching-susceptible in 2015. Each image was scored through ROIs drawn in ImageJ, and this code sums the areas of dead and live tissue on each individual image. Gaps in the time series within each colony tag are due to either a lost colony (from overgrowth/coverage of the tag or limitations in accessing the reef area) or poor image quality/clarity. Additional code provides statistical analysis of the recovery dynamics within our dataset. ### Files and variables #### Files: PEMortalityScores\_Mcap.csv, PEMortalityScores\_Pcom.csv, \**Description:**Raw data collection sheets from scoring individual colony photographs over time. Contains information from each ROI selection of dead and alive tissue for each colony. N/A in any cell indicates that the value is Not Applicable for that row, occurring only in columns used to calculate the overall Total Area, Dead Area, and % Live Tissue for each image and each colony.  ##### Variables * Colony: Tag number (identification number) for the specific coral colony * Date: YYYY/MM/DD the image was taken * Alive/Dead: categorical value of the subsection as either alive, dead, or no count (rulers, cards, etc that obstruct the view of the coral itself) * ROI: number of the specific selection from ImageJ * Area: calculated area of the selection from ImageJ * Mean: mean gray value of pixels in the selection from ImageJ * Min: minimum gray value of pixels in the selection from ImageJ * Max: maximum gray value of pixels in the selection from ImageJ * Total Area: sum of the area of the entire coral selection including both alive and dead fractions (ROIs) * Dead Area: sum of all the dead fractions (ROIs) * % Live Tissue: total fraction of live tissue, calculated by subtracting the ratio of (Dead Area/Total Area) from 1 #### File: Colony\_data.csv \**Description:**This sheet was used as an input for statistical tests in the file "Colony data test.R" and is a summary of existing data from the individual raw data sheets and data obtained from code. ##### Variables * Colony_ID:Tag number (identification number) for the specific coral colony * Mortality_percent: Maximum total mortality of the colony * Size_cm: Length of the colony (centimeters) * Recovery_months: Number of months between the time point with the greatest extent of partial mortality to the first time point where significant recovery to 90% live tissue was achieved ## Code/software Image ROIs and associated data were obtained throughImageJ, version 2.14.0/1.54f (Schindelin et al. 2012). To run data included in this dataset, useR version 4.2.2 (2022-10-31) (R Core Team 2022). The first code file included (Cleaned_PhoenixEffectMortality.Rmd) analyzes data from quantitatively scored mortality images for Porites compressa and Montipora capitata colonies at Kane'ohe Bay, HI, USA from 2015 to 2022. This code sums the areas of dead and live tissue on each individual image. Gaps in the time series within each colony tag are due to either a lost colony (from overgrowth/coverage of the tag or limitations in accessing the reef area) or poor image quality/clarity. The second code file included (Colony data test.R) uses summarized data from the analysis to perform statistical tests on the variables impacting recovery within our data set. ## Access information Other publicly accessible locations of the data: * GitHub: [https://github.com/katelyngracejones/PhoenixEffect](https://github.com/katelyngracejones/PhoenixEffect)