Dataset DOI: 10.5061/dryad.cjsxksnn2

Description of the data and file structure

As climate change accelerates, characterizing metabolic scaling in corals is essential to forecasting which species are most physiologically vulnerable to environmental shifts. While body size is a fundamental driver of metabolism, it remains unclear whether colonial organisms such as corals conform to universal scaling laws.

We characterized the relationship between polyp morphological traits and aerobic metabolism across 13 diverse reef-building coral species from the Red Sea. We measured dark respiration rates and paired them with polyp-level morphological traits, including biovolume, surface area, and corallite width. This dataset consists of two primary components:

1. Empirical physiological and morphological measurements collected from 156 coral fragments across a wide range of polyp sizes.
2. A predictive expansion where we applied our derived scaling models to 727 coral species using the Coral Trait Database.

Files and variables

File: Supplementary_Data_1.csv

Description: Primary empirical dataset containing respiration rates and morphological metrics (biovolume, surface area, corallite width) for 156 coral fragments across 13 species.

Variables

• Species : Scientific name of the coral species.
• Polyp_count: Number of individual polyps on the coral fragment.
• Raw_respiration: Initial oxygen consumption rate measured.
• Blank_respiration: Oxygen consumption of the seawater control (microbial background).
• Respiration_blanked: Final respiration rate after background correction.
• Incubation_volume: Volume of the glass vial used for respiration measurements (mL).
• Absolute_respiration: The absolute value of the blank-corrected oxygen consumption rate (expressed in mg O₂​ L⁻¹ h⁻¹).
• Resp_F1: The respiration rate converted from mass to molar units (μmol O₂​ L⁻¹ h⁻¹).
• Respiration_fragment: The total respiration rate of the entire coral fragment (μmol O₂​ L⁻¹ h⁻¹), calculated by multiplying the molar rate (Resp_F1) by Incubation_volume.
• Respiration_per_polyp: Normalized dark respiration rate per number of polyps in the fragment (μmol O₂​ polyp⁻¹ h⁻¹).
• Specific_RR: Size-specific metabolic rate normalized to polyp biovolume (μmol O2​ mm−3 h−1). Calculated as μmol O₂​ polyp⁻¹ h⁻¹/Average_Biovolume
• Random_Biovolume: Biovolume of a randomly selected individual polyp from the fragment (mm³).
• Average_Biovolume: The mean biovolume calculated for the species across all sampled fragments (mm³).
• Surface_area_per_polyp: Mean surface area of polyps for that fragment (mm²).
• Average_SA: The mean surface area calculated for the species across all sampled fragments (mm²).
• Median_CW: Median corallite width (mm) for the species.
• Max_CW: Maximum corallite width (mm) for the species.
• Min_CW: Minimum corallite width (mm) for the species.
• AFDW: Ash-free dry weight of the fragment tissue (g). Data represent a subsample of 5 fragments per species.

File: Supplementary_Data_2.csv

Description: Morphological dataset containing corallite width measurements compiled from the Coral Trait Database. The dataset includes the minimum and maximum reported corallite width values for coral species used to estimate polyp size during model predictions.

Variables

• specie_id: Unique identifier assigned to each coral species in the Coral Trait Database.

• specie_name: Scientific name of the coral species.

• subclass: Taxonomic subclass of the organism.

• resource_id: Unique identifier assigned to the original data source in the Coral Trait Database.

• trait_name: Name of the recorded trait (e.g., maximum or minimum corallite width).

• trait_class_name: Category of the trait within the Coral Trait Database trait classification system.

• standard_unit: Standardized unit in which the trait measurement is reported (mm for corallite width).

• methodology_name: Description of the methodology used to obtain the trait measurement as recorded in the Coral Trait Database.

• value: Numerical value of the recorded trait measurement.

File: Supplementary_Data_3.csv

Description: Theoretical expansion dataset providing predicted respiration rates for 727 species based on corallite width data from the Coral Trait Database.

Variables

• Species Name: Scientific name of the coral species.
• Median corallite width (mm): Median corallite width (mm) for the species. The predictor variable used for the scaling expansion.
• Calculated Respiration rates (μmol O₂​ polyp⁻¹ h⁻¹): Predicted respiration (μmol O₂​ polyp⁻¹ h⁻¹) based on the empirical power law model.
• Coral Trait Database ID: Unique identifier for cross-referencing with the public database.

Code/software

Software Requirements

The data and analysis included in this submission were processed using R (version 4.3.2), a free and open-source software environment for statistical computing and graphics. To view the raw data files (.csv), any standard spreadsheet software (e.g., Microsoft Excel, LibreOffice Calc, or Google Sheets) or a text editor can be used. See 'Software' Related Work link for R script.

R Packages Used

To run the included analysis script (Polyp size predicts metabolic rates across diverse tropical coral species.R), the following R packages must be installed and loaded:

• Data Manipulation & Transformation: dplyr, readr, readxl, openxlsx, caret.
• Statistical Analysis: stats, lme4 and lmerTest (for Linear Mixed-Effects Models), car, dunn.test.
• Visualization & Plotting: ggplot2, ggpmisc, scales, RColorBrewer, patchwork, gtable.
• Package Management: pacman (used in the script to automate the loading of the above libraries).

Workflow and Script Description The provided R script follows a structured workflow to reproduce the study’s results:

1. Data Import: The script reads the empirical measurements from Supplementary_Data_1.csv.
2. Processing: It performs log-transformations (base 10 ) on morphological and metabolic variables to prepare them for scaling analysis.
3. Statistical Modeling:
   • It executes linear regressions to determine the scaling exponents (b) for respiration against biovolume and surface area.
   • It utilizes Linear Mixed-Effects Models (via lmer) to account for species-level random effects when analyzing the relationship between polyp traits and metabolism.
4. Visualization: The script generates all figures presented in the manuscript, including the scaling plots and comparative species analyses.

Relationship of Files

• Input files for the script: Supplementary_Data_1.csv.
• Output: Statistical summaries (printed to console) and visualizations of coral metabolic scaling.

Access information

Other publicly accessible locations of the corallite width data:

• https://coraltraits.org

Corallite width data was derived from the following sources:

• Madin, J. S. et al. The Coral Trait Database, a curated database of trait information for coral species from the global oceans. Sci. Data. 3, 1–22 (2016).
• Cairns, S. D. A revision of the Ahermatypic Scleractinia of the Galapagos and Cocos Islands. http://dx.doi.org/10.5479/si.00810282.504 (1991).
• Veron, J. E. N. & Stafford-Smith, M. Corals of the World Australian Institute of Marine Science. (CCR Old Ptv Ltd., Townsville, 2000).
• Zapata, F. A., Rodríguez-Ramírez, A., Rodríguez-Moreno, M., Muñoz, C. G. & López-Victoria, M. Confirmation of the occurrence of the coral Pavona chiriquiensis Glynn, Maté and Stemann (Cnidaria: Anthozoa: Agariciidae) in the Colombian Pacific. Boletín de Investigaciones Marinas y Costeras 36, 307–312 (2007).
• Veron, J. E. N. New Species Described in Corals of the World. vol. 11(Australian Institute of Marine Science Townsville, 2002).
• Pichon, M., Chuang, Y.-Y. & Chen, C. A. Pseudosiderastrea formosa sp. nov. (Cnidaria: Anthozoa: Scleractinia) a New Coral Species Endemic to Taiwan.
• Ditlev, H. New Scleractinian corals (Cnidaria: Anthozoa) from Sabah, North Borneo. Description of one new genus and eight new species, with notes on their taxonomy and ecology. Zoologische Mededelingen 77, 193–219 (2003).
• Veron, J. E. N. New Scleractinia from Australian Coral Reefs. (Records of the Western Australian Museum, 1985).
• Wallace, C., Done, B. & Muir, P. Revision and catalogue of worldwide staghorn corals Acropora and Isopora (Scleractinia: Acroporidae) in the Museum of Tropical Queensland. MQMN 57, 1–255 (2012).
• https://www.aims.gov.au