/CaribbeanSST

GitHub repository containing data and code accompanying the Caribbean SST and MHW manuscript (Bove et al XXX; DOI: XXX)

Primary LanguageHTMLMIT LicenseMIT

A century of warming on Caribbean reefs

GitHub repository containing data and code accompanying the Caribbean warming and MHW manuscript (Bove et al 2022; DOI: https://doi.org/10.1371/journal.pclm.0000002)

Repository DOI: DOI

Authors: Colleen B. Bove, Laura Mudge & John F Bruno

Abstract: The world’s oceans are warming at an unprecedented rate, causing dramatic changes to coastal marine systems, especially on coral reefs. We used three complementary ocean temperature databases (HadISST, Pathfinder, and OISST) to quantify change in thermal characteristics of Caribbean coral reefs over the last 150 years (1871–2020). These sea surface temperature (SST) databases included combined in situ and satellite-derived SST (HadISST, OISST), as well as satellite-only observations (Pathfinder) at multiple spatial resolutions. We also compiled a Caribbean coral reef database identifying 5,326 unique reefs across the region. We found that Caribbean reefs began warming in 1915 and have warmed on average by 0.19 °C per decade since 1994 (the calculated year that warming accelerated). Geographic variation in warming rates ranged from 0.17 °C per decade on Bahamian reefs to 0.26 °C per decade on reefs within the Southern and Eastern Caribbean ecoregions. If this linear rate of warming continues, these already threatened ecosystems would warm by an additional 1.5°C on average by 2100. We also found that marine heatwave (MHW) events are increasing in both frequency and duration across the Caribbean. Caribbean coral reefs now experience on average 5 MHW events annually, compared to 1 per year in the early 1980s, with recent events lasting on average 14 days. These changes in the thermal environment, in addition to other stressor including fishing and pollution, have caused a dramatic shift in the composition and functioning of Caribbean coral reef ecosystems.

Citation: Bove CB, Mudge L, Bruno JF (2022) A century of warming on Caribbean reefs. PLOS Climate 1(3): e0000002. DOI: https://doi.org/10.1371/journal.pclm.0000002

Repository contains the following:

  1. R markdown script and html output with all code and analyses included in manuscript (CaribbeanSST_manuscript)
  2. code
    • External R script used to extract SST from netCDF files using coral reef GPS coordinates to run remotely (SSTExtraction_ReefGPS.R)
    • External R script used to clip Pathfinder netCDF and calculate rates of warming to run remotely (Pathfinder_RasterCalculations.R)
    • Functions from Gavin Simpson (GitHub: gavinsimpson) for calculating significant slopes from a GAM (GSimpsonFunctions.R)
  3. data
    • EcoRegions
      • Caribbean ecoregion shapefiles (Caribbean_ecoregions.)
    • HadISST
      • SST from the HadISST database extracted by reefs within each ecoregion (HadISST_ecoregion_sst.Rdata)
      • Extracted SST from HadISST database for all coral reefs (HadISST_reefs_SST_update.Rdata)
      • Calculated HadISST pvalues of the GLS model per map pixel for rate of change (HadISST_pvals.Rdata)
      • Calculated HadISST slope (rate of change) from the GLS model per map pixel (HadISST_slopes.Rdata)
      • Time information for the HadISST raster layers (HadISST_times.Rdata)
    • Pathfinder
      • Ecoregion extracted SST data from Pathfinder database (Pathfinder_ecoregion_sst; both .csv and .rds files)
      • P-values from the raster slope calculation through time for the Patherdiner database (Pathfinder_pval; both .csv and .rds files)
      • Extracted SST from Pathfinder database for all coral reefs (Pathfinder_reefs_SST.rds)
      • Slope (rate) of SST temperature change based on the Pathfinder database for whole region (Pathfinder_slope; both .csv and .rds files)
      • Time information for the Pathfinder raster layers (Pathfinder_times.Rdata)
      • Folder containing old versions of calculated data being saved temporarily (Old Files)
    • ReefData
      • CSV containing the GPS coordinates of Caribbean coral reefs (CaribbeanReef_points.csv)
      • Caribbean region shapefile cropped from the WCMC008_CoralReef2018_Py_v4 files (Caribbean_reefs.)
      • MHW specific reef locations file (MHW_reefs.csv)
    • Supplemental tables as an excel file produced in the markdown file (Supplemental_Tables.xlsx)
  4. figures
    • Manuscript
      • Fig1_ReefMap.pdf (both PDF and PNG versions)
      • Fig2_SST_trends (both PDF and PNG versions)
      • Fig3_Ecoregion_SST_trends (both PDF and PNG versions)
      • Fig4_SST_MHW_map (both PDF and PNG versions)
      • Fig5_MHW_metrics (both PDF and PNG versions)
      • Fig6_ClimateStripes (both PDF and PNG versions)
    • Supplemental
      • FigS1_HadISST_GAM_slopes (both PDF and PNG versions)
      • FigS2_Pathfinder_SST_trends (both PDF and PNG versions)
      • FigS3_PathVhadISST (both PDF and PNG versions)
      • FigS4_Both_SST_trends (both PDF and PNG versions)
      • FigS5_Ecoregion_MapSST (both PDF and PNG versions)
      • FigS6_SST_MHW_significance_map (both PDF and PNG versions)
      • FigS7_HadISST_map (both PDF and PNG versions)
      • FigS8_HadISST_subset_map (both PDF and PNG versions)
      • FigS9_MHW_metrics_ecoregions (both PDF and PNG versions)
      • HadISST.gif (both PDF and PNG versions)

NOTE: The original OISST database compilation and MHW analyses were all performed by Laura Mudge (GitHub: Lmudge13). This repository includes the previously compiled/calculated OISST and MHW parameters for simplicity. To find the code and data used to compile the datasets for Caribbean MHWs in this repository, please visit Laura's GitHub or email me (colleenbove@gmail.com).