DOI: 10.5061/dryad.gtht76ht3
title: Data from: Coral hypoxia response curve analysis

description: Oxygen (O2) availability is essential for healthy coral reef functioning,
 yet how continued loss of dissolved O2 via ocean deoxygenation impacts
 performance of reef building corals remains unclear. Here we examine how
 intra-colony spatial geometry of important Great Barrier Reef (GBR) coral
 species Acropora may influence variation in hypoxic thresholds for
 upregulation, to better understand capacity to tolerate future reductions
 in O2 availability. We first evaluate application of more streamlined
 models used to parameterise Hypoxia Response Curve data, models that have
 been used historically to identify variable oxyregulatory capacity. Using
 closed-system respirometry to analyse O2 drawdown rate, we show that a
 2-parameter model returns similar outputs as previous 12th order models
 for descriptive statistics such as the average oxyregulation capacity
 (Tpos) and the ambient O2 level at which the coral exerts maximum
 regulation effort (Pcmax), for diverse Acropora species. Following an
 experiment to evaluate whether stress induced by coral fragmentation for
 respirometry affected O2 drawdown rate, we subsequently identify
 differences in hypoxic response for the interior and exterior colony
 locations for the species Acropora abrotanoides, Acropora cf.
 microphthalma, and Acropora elseyi. Average regulation capacity across
 species was greater (0.78 to 1.03 ± SE 0.08) at the colony interior
 compared to exterior (0.60 to 0.85 ± SE 0.08). Moreover, Pcmax occurred at
 relatively low pO2 of &lt;30% (± 1.24; SE) air saturation for all
 species, across the colony. When compared against ambient O2 availability,
 these factors corresponded to differences in mean intra-colony
 oxyregulation, suggesting that lower variation in dissolved O2 corresponds
 with higher capacity for oxyregulation. Collectively our data shows that
 intra-colony spatial variation affects coral oxyregulation hypoxic
 thresholds, potentially driving differences in Acropora oxyregulatory
 capacity.
description: These datasets were collected in February 2022, and all fieldwork
 and collections were carried out at Opal Reef on the Great Barrier Reef
 (GBR), Australia.  Details for each dataset are
 provided in the README file.  
description: # Data from: Coral hypoxia response curve analysis
 [https://doi.org/10.5061/dryad.gtht76ht3](https://doi.org/10.5061/dryad.gtht76ht3) ## Description of the data and file structure This raw data and code has been collected and used in a recent study analysing intra-colony spatial variance of oxyregulation and hypoxic thresholds for the key coral species *Acropora* (Dilernia et al. 2024). Including algorithm evaluation and reporting selection criteria for best model choice, in conjunction with depositing data from coral hypoxia response curve analyses, allowing for reprocessing at any time using different polynomial models for comparison to optimise results, as well as *in situ* oxygen (O<sub>2</sub>) Logger Data. The raw .csv files used to run the below code, containing data for the *p*O<sub>2</sub> (ambient levels of O<sub>2</sub> (% air saturation) and VO<sub>2</sub> (patterns of O<sub>2</sub> consumption, i.e., respiration (mg h<sup>-1</sup>) values for each species and replicate, across multiple experiments (as outlined in the manuscript), have been included. Files have been separated into experiments, e.g., combined .csv files for the fragmentation experiment can be found in File entitled "Experiment 1 - fragmentation effects", etc. **Date of data collection**: February 2022 **Geographic location of data collection**: Opal Reef (GBR, Australia; 16.220 °S, 145.885 °E) **Information about funding sources that supported the collection of the data:** This research is supported by an Australian Government Research Training Program Scholarship (N.J.D.) and an Australian Research Council Discovery Project (DP230100210) (awarded to: D.J.S., E.F.C., and M.K.). M.K. also acknowledges additional support from the Gordon and Betty Moore Foundation (grant no. GBMF9206; [https://doi.org/10.37807/GBMF9206](https://doi.org/10.37807/GBMF9206). **Link to publication that uses the data**: [https://doi.org/10.1002/ece3.11100](https://doi.org/10.1002/ece3.11100) Dilernia NJ, Woodcock S, Camp EF, Hughes DJ, Kühl M, Suggett DJ (2024) Intra-colony spatial variance of oxyregulation and hypoxic thresholds for key Acropora coral species. Ecol Evol 14:e11100. doi: 10.1002/ece3.11100 **Description of the individual data files:** 1. Michaelis-Menten_Modelling.Rmd - code used in RStudio to model the hypoxia response curves, using 2nd degree Michaelis-Menten model. 2. PolynomialModelSelection.Rmd - code used in RStudio to originally select the most parsimonious model to analyse the hypoxia response curves, testing 1 through to 12th degree polynomials. 3. LoggerCode.Rmd - code used in RStudio to analyse and visualise the environmental O<sub>2</sub> logger data collected in the field from the experimental coral colonies. 4. Experiment_1_Fragmentation_Effects.xlsx - excel spreadsheet of raw *p*O<sub>2</sub> and VO<sub>2</sub> data from 6 reps of clipped fragments, and 6 reps of freshly fragged fragments, for Experiment 1 "fragmentation effects". See below for explanation of abbreviations and variables. The code used to analyse this data was "Michaelis-Menten_Modelling.Rmd". 5. Experiment_2_Aabrotanoides.xlsx - excel spreadsheet of raw *p*O<sub>2</sub> and VO<sub>2</sub> data from 6 reps of *A. abrotanoides* fragments collected from the inner section of the experimental coral colony, and 6 reps of of *A. abrotanoides* fragments collected from the outer section, for Experiment 2 "interior versus exterior colony variance". See below for explanation of abbreviations and variables. The code used to analyse this data was "Michaelis-Menten_Modelling.Rmd". 6. Experiment_2_Acfmicrophthalma.xlsx - excel spreadsheet of raw *p*O<sub>2</sub> and VO<sub>2</sub> data from 6 reps of *A. cf. microphthalma* fragments collected from the inner section of the experimental coral colony, and 6 reps of of *A. cf. microphthalma* fragments collected from the outer section, for Experiment 2 "interior versus exterior colony variance". See below for explanation of abbreviations and variables. The code used to analyse this data was "Michaelis-Menten_Modelling.Rmd". 7. Experiment_2_Aelseyi.xlsx - excel spreadsheet of raw *p*O<sub>2</sub> and VO<sub>2</sub> data from 6 reps of *A. elseyi* fragments collected from the inner section of the experimental coral colony, and 6 reps of of *A. elseyi* fragments collected from the outer section, for Experiment 2 "interior versus exterior colony variance". See below for explanation of abbreviations and variables. The code used to analyse this data was "Michaelis-Menten_Modelling.Rmd". 8. Model_Selection_Analysis.xlsx - excel spreadsheet of raw *p*O<sub>2</sub> and VO<sub>2</sub> data from 3 reps each of *A. hyacinthus*, *A. intermedia*, and *A. kenti* (formerly A. tenuis), originally analysed by Hughes et al. 2022, and used to re-analyse and select the most parsimonious model for analysing coral hypoxia response curves for Experiment 1 and 2. See below for explanation of abbreviations and variables. The code used to analyse this data was "PolynomialModelSelection.Rmd". 9. Logger_Data.xlsx - excel spreadsheet of raw data collected from the O<sub>2</sub> Loggers deployed in the experimental coral colonies from Experiment 2 "interior versus exterior colony variance". Including, the oxygen data for "inner" versus "outer" for each colony, as well as the temperature monitored, and the tidal height and time of day, relative to the diel cycle. The code used to analyse this data was "LoggerCode.Rmd ". **Variables, abbreviations and units of measurement used in the datasets:** * *p*O<sub>2</sub> - ambient levels of O<sub>2</sub> measured (% air sat). * VO<sub>2</sub> - standardised rate of O<sub>2</sub> consumption over time (mg O<sub>2</sub> hr<sup>-1<sup>). * mg O<sub>2</sub> hr<sup>-1<sup> or mg O<sub>2</sub> L<sup>-1<sup> - milligrams of oxygen measured per hour (for VO<sub>2</sub>) or per litre. * "% air sat" - percentage air saturation of O<sub>2</sub> measured. ***NB: missing values (empty cells/"NA") in excel spreadsheets:*** any missing values (i.e., empty cells/NA) in spreadsheets were removed during statistical analyses, i.e., using NA clean up in RStudio. ## Code/Software All statistical analyses were carried out in RStudio version 4.1.0, Build 446 (R Core Team 2021) with base packages: knitr v. 1.33 (Xie 2014, 2015, 2021), rmarkdown v. 2.20 (Xie et al. 2018, 2020; Allaire et al. 2023), and tidyverse v. 2.0.0 (Wickham et al. 2019). Additional modelling and plotting packages include: “drc” v. 3.0.1 (Ritz et al. 2015) and “ggplot2” (Wickham 2016). The prepared code used for initial model analysis and selection has been deposited as "PolynomialModelSelection.Rmd", and the code used to prepare the hypoxia response curves for the experimental corals following selection of best model has been deposited as "Michaelis-Menten_Modelling.Rmd". The code used to prepare the *in situ* O<sub>2</sub> Logger profiles has been deposited as "LoggerCode.Rmd".
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