Data Package: |
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Local Identifier: | edi.1355.2 |
Title: | Datasets for: A global review of pyrosomes: Shedding light on the ocean’s elusive gelatinous ‘fire-bodies’ |
Alternate Identifier: | DOI PLACE HOLDER |
Abstract: | These are the datasets used to create all figures included in: "Lilly, L.E., Suthers, I.M., Everett, J.D., Richardson, A.J. (2023). A Global Review of Pyrosomes: Shedding light on the ocean’s elusive gelatinous ‘fire-bodies’. Limnology & Oceanography Letters."
The review presents a comprehensive global description of the body of current knowledge on pyrosomes, a zooplanktonic tunicate taxon closely related to salps, doliolids, and appendicularians.
For review analyses, we used pyrosome observations and associated information from literature-published studies and four databases: NOAA COPEPOD Urochordates database (NOAA, 2022; https://www.st.nmfs.noaa.gov/copepod/atlas/html/taxatlas_4350000.html), BCO-DMO Jellyfish Database Initiative (JeDI; Condon et al., 2014; https://www.bco-dmo.org/dataset/526852), Global Biodiversity Information Facility (GBIF; https://doi.org/10.15468/dl.a8phvp), and Ocean Biodiversity Information System (OBIS; https://obis.org/taxon/137216). We matched pyrosome observations to corresponding satellite-measured sea surface temperature (NOAA Optimum Interpolation Sea Surface Temperature, V2, high-resolution, https://psl.noaa.gov/data/gridded/data.noaa.oisst.v2.highres.html) and chlorophyll-a (MODIS-AQUA, 4 km^2 resolution, Melin, 2013; http://data.europa.eu/89h/10161412-a76c-42b0-b4e1-5fcccdc412b2). The files included in this metadata record have been subsetted from all original file sources. Our subsetted files are designed to run with the associated MATLAB scripts to recreate all manuscript files.
We include seven MATLAB scripts: 1) A four-part script to clean up all pyrosome observations, divide to species level, and remove duplicate records from multiple databases and within each database, and 2) Three standalone scripts to plot Figs. 1, 2, and 3.
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Publication Date: | 2023-05-24 |
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Data Entities |
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Data Table Name:
| GBIF_Pyrosoma
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Description:
| All records of global occurrences of the 'Pyrosoma' genus available through the Global Biodiversity Information Facility. One of three datafiles for GBIF. |
Data Table Name:
| GBIF_Pyrosomella
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Description:
| All records of global occurrences of the 'Pyrosomella' genus available through the Global Biodiversity Information Facility. Two of three datafiles for GBIF. |
Data Table Name:
| GBIF_Pyrostremma
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Description:
| All records of global occurrences of the 'Pyrostremma' genus available through the Global Biodiversity Information Facility. Three of three datafiles for GBIF. |
Data Table Name:
| JeDI_Pyro_All
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Description:
| All records of global pyrosome occurrences entered into the Jellyfish Database Initiative (JeDI). One of one records from JeDI. |
Data Table Name:
| LiteratureStudies_PyrosomeObs_All
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Description:
| Records of all published literature studies from which pyrosome data (observations - species, location, time, depth, etc.; associated habitat data) have been extracted for Figs. 1 and 2 |
Data Table Name:
| OBIS_Pyro_All
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Description:
| All records of global pyrosome occurrences available through the Ocean Biodiversity Information System (OBIS) database. One of one records for OBIS. |
Data Table Name:
| Pyros_Chla_match
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Description:
| List of all records of pyrosomes from compiled databases (COPEPOD, JeDI, GBIF, OBIS) and matching closest chlorophyll-a value (log10[mg m-3]) measured by the MODIS-AQUA satellites. Chlorophyll-a measurements are gridded at a resolution of 0.04 x 0.04 degrees (4 km^2). |
Data Table Name:
| Pyros_Temp_match
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Description:
| List of all records of pyrosomes from compiled databases (COPEPOD, JeDI, GBIF, OBIS) and matching closest sea surface temperature value (degrees Celsius) measured by the NOAA Optimum Interpolation SST, v2 (high-resolution). Chlorophyll-a measurements are gridded at a resolution of 0.25 x 0.25 degrees. |
Other Name:
| Lilly_etal_PyrosRev_St1a_DataIn
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Description:
| MATLAB script to code the first of a four-part data cleanup of pyrosome records from literature studies and four databases (COPEPOD, JeDI, GBIF, OBIS). STEP 1 of 4: This step loads all datafiles and assigns variable names. |
Other Name:
| Lilly_etal_PyrosRev_St1b_SppDivs
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Description:
| MATLAB script to code the second of a four-part data cleanup of pyrosome records from literature studies and four databases (COPEPOD, JeDI, GBIF, OBIS). STEP 2 of 4: This step compiles all databases and sections them by species. |
Other Name:
| Lilly_etal_PyrosRev_St1c_DupRmv
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Description:
| MATLAB script to code the third of a four-part data cleanup of pyrosome records from literature studies and four databases (COPEPOD, JeDI, GBIF, OBIS). STEP 3 of 4: This step removes duplicate records from multiple databases using a hierarchy of: Literature > COPEPOD > JeDI > GBIF > OBIS, where the leftmost database that contains a record retains that record, and all databases listed to the right have that record removed. |
Other Name:
| Lilly_etal_PyrosRev_St1d_DupRmv2
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Description:
| MATLAB script to code the fourth of a four-part data cleanup of pyrosome records from literature studies and four databases (COPEPOD, JeDI, GBIF, OBIS). STEP 4 of 4: This step removes all remaining duplicate records from within each database, after Step 3 removes duplicates from multiple databases. |
Other Name:
| Lilly_etal_PyrosRev_St2_Fig1
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Description:
| MATLAB script to code Fig. 1 from Lilly et al. (2023). Figure 1 creates a global map of species-level distributions for all available pyrosome data from Literature and four databases (COPEPOD, JeDI, GBIF, OBIS). NOTE: Must run scripts 'St1a'-'St1d' prior to running this script. |
Other Name:
| Lilly_etal_PyrosRev_St2_Fig2
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Description:
| MATLAB script to code Fig. 2 from Lilly et al. (2023). Figure 2 creates temperature and chlorophyll-a habitat envelopes for all avalable pyrosome species, based on matchups of Literature/Database pyrosome observations with satellite-measured sea surface temperature (NOAA OISST) or chlorophyll (MODIS-AQUA). NOTE: Must run scripts 'St1a'-'St1d' prior to running this script. |
Other Name:
| Lilly_etal_PyrosRev_St2_Fig3
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Description:
| MATLAB script to code Fig. 3 from Lilly et al. (2023). Figure 3 histograms of depth distributions for all available pyrosome species from Literature/Databases. NOTE: Must run scripts 'St1a'-'St1d' prior to running this script. |
Other Name:
| NOAA_COPEPOD_Urochordates
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Description:
| All samples of urochordate sightings archived in the NOAA COPEPOD Database. Source: https://www.st.nmfs.noaa.gov/copepod/atlas/html/taxatlas_4350000.html |