Abstract:
This dataset contains occurrence records for ten Southern Ocean myctophid fish species that have been downloaded and cleaned from the online biodiversity repository GBIF. As well as providing GBIF documented metadata for each occurrence record, this dataset provides environmental conditions - specifically bathymetry, temperature, salinity, dissolved oxygen and net primary productivity - for each record. Both sea-surface and depth-specific values for the temperature, salinity and oxygen variables are given in separate data files. A third data file of corresponding background points and their associated environmental conditions is also provided. Together these data were used as input files for the MaxEnt ecological niche models within the peer reviewed article: Freer JJ, Tarling GA, Collins MA, Partridge JC, Genner MJ (2020) Estimating circumpolar distributions of lanternfish using 2D and 3D ecological niche models, Marine Ecology Progress Series.
Keywords:
3D modelling, Myctophidae, ecological niche model, lanternfish, species distribution model
Freer, J. (2020). Occurrence records of ten Southern Ocean myctophid species with associated sea surface and depth-specific environmental conditions (Version 1.0) [Data set]. UK Polar Data Centre, Natural Environment Research Council, UK Research & Innovation. https://doi.org/10.5285/8e59f849-5b93-438e-a5e0-3c65636f9053
| Use Constraints: | Data are released under Open Government Licence V3.0: http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3/. |
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| Creation Date: | 2020-06-05 |
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| Dataset Progress: | Complete |
| Dataset Language: | English |
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| Parameters: |
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| Personnel: | |
| Name | UK PDC |
| Role(s) | Metadata Author |
| Organisation | British Antarctic Survey |
| Name | Dr Jennifer J Freer |
| Role(s) | Investigator |
| Organisation | British Antarctic Survey |
| Parent Dataset: | N/A |
| Reference: | 1. Freer JJ, Tarling GA, Collins MA, Partridge JC, Genner MJ (2020) Estimating circumpolar distributions of lanternfish using 2D and 3D ecological niche models, Marine Ecology Progress Series; https://doi.org/10.3354/meps13384. 2. All occurence records were obtained from the Global Biodiversity Information Facility (GBIF; http://www.gbif.org/) and were downloaded in 2015. A list of contributing datasets can be found in the file: GBIF_citations.txt 3. Interpolated climatologies for temperature, oxygen and salinity variables were extracted from the World Ocean Atlas 2013 database (https://www.nodc.noaa.gov/OC5/woa13/) at a resolution of 0.25° x 0.25° for the months October-March across the baseline temporal period 1956-2005. CITATION: Zweng, M.M., Reagan, J.R., Antonov, J.I., Locarnini, R.A., Mishonov, A.V., Boyer, T.P., Garcia, H., Baranova, O.K., Johnson, D.R., Seidov, D. & Biddle, M.M. (2013). World Ocean Atlas 2013, volume 2: salinity. NOAA Atlas NESDIS 74. CITATION: Locarnini, R.A., Mishonov, A.V., Antonov, J.I., Boyer, T.P., Garcia, H., Baranova, O.K., Zweng, M.M., Paver, C.R., Reagan, J.R., Johnson, D.R., Hamilton, M. & Seidov, D. (2013). World Ocean Atlas 2013, Volume 1: Temperature. NOAA Atlas NESDIS 73. CITATION: Garcia, H., Locarnini, R.A., Boyer, T.P., Antonov, J.I., Baranova, O.K., Zweng, M.M., Reagan, J.R. & Johnson, D.R. (2014). World Ocean Atlas 2013, volume 3: dissolved oxygen, apparent oxygen utilization, and oxygen saturation. NOAA Atlas NESDIS 75. 4. Bathymetry data (i.e. maximum water depth) were obtained from the SRTM30 global elevation and bathymetry dataset (https://topex.ucsd.edu/WWW_html/srtm30_plus.html) at the original resolution of 30 arc seconds and were re-sampled to the same resolution as the other variables using the bi-linear resample tool in ArcGIS v.10.4.1. CITATION: Becker, J.J., Sandwell, D.T., Smith, W.H.F., Braud, J., Binder, B., Depner, J., Fabre, D., Factor, J., Ingalls, S., Kim, S.H., Ladner, R., Marks, K., Nelson, S., Pharaoh, A., Trimmer, R., Von Rosenberg, J., Wallace, G. & Weatherall, P. (2009). Global bathymetry and elevation data at 30 arc seconds resolution: SRTM30_PLUS. Marine Geodesy, 32, 355-371. 5. Primary productivity is the primary organic carbon production by all types of phytoplankton and data used correspond to the ensemble mean of 1956-2005 Earth System Model historical runs. These data were extracted from the NOAA/ESRL Physical Sciences Division Climate Change Web Portal (https://www.esrl.noaa.gov/psd/ipcc/ocn/). CITATION: Scott, J.D., Alexander, M.A., Murray, D.R., Swales, D. & Eischeid, J. (2016). The Climate Change Web Portal a system to access and display climate and earth system model output from the CMIP5 archive. Bulletin of the American Meteorological Society, 97, 523-530. 6. The following software was used to match the occurrences to the environmental data: CITATION: Vignali S, Barras A, Braunisch V (2020). SDMtune: Species Distribution Model Selection. R package version 1.1.0, https://github.com/ConsBiol-unibern/SDMtune. CITATION: Duffy, Grant; L Chown, Steven (2016): Duffy_Chown_MEPS12011_model_virtualspecies. Monash University. Dataset. https://doi.org/10.4225/03/58507ddae3022. |
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| Quality: | Occurrence records for all ten species were downloaded from the Global Biodiversity Information Facility (GBIF). These occurrence records represent those remaining after undertaking following quality assurance and control processes. Unreliable data, which included records with identical latitude and longitude, and records with a latitude and longitude corresponding to a terrestrial location, were removed. Due to high sampling bias towards austral spring and summer seasons, only records from the months October-March were kept for analyses. Furthermore, only occurrence records from 1960 to 2010 were retained, to correspond to a similar baseline period of available environmental data. Duplicate records were excluded from model runs. Citations for all data (occurrence and environmental data) are given in the Reference section. |
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| Lineage: | Occurrence records and environmental data were downloaded from online and open access sources (see the Reference section). For the 2D model approach, occurrence and background points were matched to the appropriate environmental conditions using the "prepareSWD" function from the R package "SDMtune". Sea surface conditions are matched to all records, regardless of the depth they were caught at. For the 3D model approach, occurrence and background points were matched to the appropriate environmental conditions using the "depth_extract" function from Duffy and Chown (2017) source code available at: https://figshare.com/articles/Duffy_Chown_MEPS12011_model_virtualspecies/4315052. This ensures each occurrence or background point is only matched to the environmental conditions from the depth closest to the depth from which the record came from. File: occurrence_data_2D.csv Volume: 6 megabytes Contents: This file contains the cleaned and processed occurrence records of the ten myctophid species modelled in the study and the sea surface environmental conditions associated to each presence locality. Data columns and units: NAME = species LON = longitude (decimal degrees) LAT = latitude (decimal degrees) DEPTH = depth of catch information (metres) BATHYMETRY = bathymetry (metres) O2 = dissolved oxygen at the sea surface (mmol-m3) PP = primary organic carbon production by all types of phytoplankton in the upper 150m (nmol m-2 s-1) SAL = sea surface salinity (PSU) TEMP = sea surface temperature (degrees celcius) ALL OTHER COLUMNS = STANDARD GBIF METADATA File: occurrence_data_3D.csv Volume: 4.5 megabytes Contents: This file contains the cleaned and processed occurrence records of the ten myctophid species modelled in the study and the depth-specific environmental conditions associated to each presence locality. Data columns and units: NAME = species LON = longitude (decimal degrees) LAT = latitude (decimal degrees) DEPTH = depth of catch information (metres) BATHYMETRY = bathymetry (metres) O2 = depth-specific dissolved oxygen at (mmol-m3) PP = primary organic carbon production by all types of phytoplankton in the upper 150m (nmol m-2 s-1) SAL = depth-specific salinity (PSU) TEMP = depth-specific temperature (degrees celcius) ALL OTHER COLUMNS = STANDARD GBIF METADATA File: background_data_2D_AND_3D.csv Volume: 1.2 megabytes Contents: This file contains the coordinates of the background data generated for the study. Both the 2D (suface) and 3D (depth-specific) environmental conditions are given for each point. Data columns and units: NAME = identifier for background data "bg" LON = longitude (decimal degrees) LAT = latitude (decimal degrees) DEPTH = depth assigned to each point (metres) BATHYMETRY = bathymetry (metres) PP = primary organic carbon production by all types of phytoplankton in the upper 150m (nmol m-2 s-1) O2_2D = dissolved oxygen at the sea surface (mmol-m3) SAL_2D = sea surface salinity (PSU) TEMP_2D = sea surface temperature (degrees celcius) O2_3D = depth-specific dissolved oxygen (mmol-m3) SAL_3D = depth-specific salinity (PSU) TEMP_3D = depth-specific temperature (degrees celcius) File: GBIF_citations.txt Volume: 6 kilobytes Contents: A citation list of all contributing datasets for occurrence records downloaded from GBIF, generated in 2020 via R package "rgbif". |
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| Temporal Coverage: | |
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| Start Date | 1962-10-01 |
| End Date | 2010-03-01 |
| Start Date | 1956-10-01 |
| End Date | 2005-03-31 |
| Spatial Coverage: | |
| Latitude | |
| Southernmost | -75 |
| Northernmost | -35 |
| Longitude | |
| Westernmost | -180 |
| Easternmost | 180 |
| Altitude | |
| Min Altitude | N/A |
| Max Altitude | N/A |
| Depth | |
| Min Depth | 0 m |
| Max Depth | 1000 m |
| Data Resolution: | |
| Latitude Resolution | 0.25 DD |
| Longitude Resolution | 0.25 DD |
| Horizontal Resolution Range | N/A |
| Vertical Resolution | 0,50,100,200,500,800,1000 m |
| Vertical Resolution Range | N/A |
| Temporal Resolution | N/A |
| Temporal Resolution Range | N/A |
| Location: | |
| Location | Southern Ocean |
| Detailed Location | circumpolar |
| Data Collection: | All analyses were carried out in R version 3.5.3. |
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