DOI: 10.5061/dryad.kkwh70sbw
title: Data from: Remarkable similarity of oxygen tolerance across marine taxa when standardized for temperature and body size

description: Species’ ranges are shifting in response to increasing temperature and
 decreasing oxygen in coastal oceans. Forecasting these shifts is limited
 by information on physiological oxygen thresholds and how they depend on
 temperature. Here, we adopt an ecophysiological metric, the metabolic
 index, and estimate its parameters from data collected on marine taxa
 using phylogenetic trait imputation. The metabolic index is the ratio of
 temperature-dependent rates of oxygen supply to basal oxygen demands. By
 applying a hierarchical phylogenetic model to a data set of 74 marine taxa
 that accounts for both taxonomic distance (from Linnean classification)
 and biases related to lab methods, we find that the critical oxygen
 pressure at a reference body size and temperature is remarkably consistent
 across taxa, ranging 2.9 to 4.9 kPa. In comparison, the estimated effect
 of temperature on the critical oxygen pressure was more variable among
 taxa.  These findings suggest that species-level differences in
 oxygen tolerance might be primarily related to differences in body size
 and preferred temperature. Further, this work provides data-informed
 distributions of parameters for species that lack experimental data to aid
 species distribution forecasting.
description: Data were collected via literature review or provided directly
 from authors.  Data were extracted digitally from figures when
 necessary.  
description: # Remarkable similarity of oxygen tolerance across marine taxa when
 standardized for temperature and body size # Summary of the study We used
 phylogenetic imputation on experimental data on taxonomically diverse
 marine taxa that related critical oxygen pressure (pO2crit) to temperature
 and body size. We found that once we accounted for differences in body
 size, temperatures, and the source paper, the data point to very similar
 oxygen partial pressures (generally between 3 - 5 kPa) at which oxygen
 demand exceeds supply. # Overview of folders/files and their contents The
 dryad repository contains the data used in analysis in the file
 "allmidata.csv". Each row is one experimental outcome, where
 columns indicate : 1. scientific.name: Genus species, updated January
 2023;
 [https://www.marinespecies.org/index.php](https://www.marinespecies.org/index.php) 2. Temp: experimental temperature (degrees C) 3. W: individual (or mean individual) body size (grams) 4. Pcrit: estimated critical oxygen partial pressure (kPa) 5. AphiaID: Aphia ID for species, genus, family, or order: [https://www.marinespecies.org/index.php](https://www.marinespecies.org/index.php) 6. lowest.taxon: lowest taxonomic level for taxonomic group. Usually equals "species" 7. Source: Short verson of paper citation or data source The linked Zenodo repository contains the file Archive.zip. which contains all code used in the paper.  All working R files are in subdirectory "code" in the linked Zenodo site 1. 01-configure-mi-data.R. Adds the taxonomic information by accessing the World Register of Marine Species. Does not need to be run, as results have been generated and saved in /data/alldata_taxonomy.RDS 2. 02-fit-individual-species.R. Runs linear models individually for each species. Does not need to be run, as results have been generated and saved in analysis/species_estimates.RDS 3. 03-fit_TMB_model.R. Runs Hierarchical model using TMB, and plots results for taxonomic groups. Also includes summary of data coverage by taxonomic group. 4. 04-fit_TMB_stan.R. Runs the hierarchical model using tmbstan. Does not need to be run, as results have been generated and saved in analysis/mcmcoutput.RDS 5. 05-sim_new_taxa.R. Take the output of tmbstan, and then simulates a random species within each specified taxonomic level 6. 06-summarize_sims.R. Code used to summarize results, organized by taxonomic grouping and used to create supplemental table 7. fit_model_funs.R. Contains numerous functions that are called in the above source files. It is called within those source files. Files in subdirectory "analysis" are saved products as described above. It also includes modelfit.RDS, which is a saved TMB fitted model, and modelfit_stan.RDS, which is another saved TMB model where the model code is modified to permit successful MCMC integration. All raw data are provided in subdirectory "data". The primary file is allmidata_csv. The fields are: * scientific.name: Genus species, updated January 2023; [https://www.marinespecies.org/index.php](https://www.marinespecies.org/index.php) * Temp: experimental temperature (degrees C) * W: individual (or mean individual) body size (grams) * Pcrit: estimated critical oxygen partial pressure (kPa) * AphiaID: Aphia ID for species, genus, family, or order: [https://www.marinespecies.org/index.php](https://www.marinespecies.org/index.php) * lowest.taxon: lowest taxonomic level for taxonomic group. Usually equals "species" * Source: Short verson of paper citation or data source # Instructions for users to run the software (e.g. explain the project workflow and any configuration parameters of your software) See workflow instructions above. To extract simulations for a taxa, go to the lookup_taxa sub directory and open file "lookup_taxa.R". There you can specify the taxonomic group, and source the file to see simulation medians, standard deviations, and variance - covariance matrix of metabolic index tratits