Abstract:
This dataset contains occurrence records and associated metadata for the zooplankton species Calanus finmarchicus that were compiled from multiple open access databases. A file containing the corresponding background points is provided, along with gridded environmental variables for each season (Jan-Feb-Mar, Apr-May-Jun, Jul-Aug-Sep, Oct-Nov-Dec) and era (1955-1984, 1985-2017) that were assessed in this study. Together these data were used as input files for the MaxEnt ecological niche model within the peer reviewed article: Freer JJ, Daase, M, Tarling GA, (2021) Modelling the biogeographic boundary shift of Calanus finmarchicus reveals drivers of Arctic Atlantification by subarctic zooplankton, Global Change Biology. Finally, an R Markdown document is provided to enable data users to replicate the model optimisation and prediction steps using the input data files within this repository.
Funding was provided by:
UKRI Natural Environment Research Council (NERC): DIAPOD (NE/P006213/1),
NERC and the German Federal Ministry of Education and Research (BMBF): CHASE (NE/R012687/1),
Norwegian Research Council: Deep Impact project (300333).
Keywords:
Atlantification, Climate Warming, Ecological Niche Model, Subarctic, Zooplankton
Freer, J., Daase, M., & Tarling, G. (2021). Range-wide occurrence records of the subarctic copepod Calanus finmarchicus and associated environmental predictor variables (Version 1.0) [Data set]. NERC EDS UK Polar Data Centre. https://doi.org/10.5285/fc660bc3-09ab-4c1a-9d2a-4026951872c8
| Access Constraints: | None. |
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| Use Constraints: | Data released under Open Government Licence V3.0: http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3/. |
| Creation Date: | 2021-10-18 |
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| Dataset Progress: | Complete |
| Dataset Language: | English |
| ISO Topic Categories: |
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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 |
| Name | Dr Malin Daase |
| Role(s) | Investigator |
| Organisation | The Arctic University of Norway |
| Name | Prof Geraint A Tarling |
| Role(s) | Investigator |
| Organisation | British Antarctic Survey |
| Parent Dataset: | N/A |
| Reference: | Freer JJ, Daase, M, Tarling GA, (2021) Modelling the biogeographic boundary shift of Calanus finmarchicus reveals drivers of Arctic Atlantification by subarctic zooplankton, Global Change Biology. https://doi.org/10.1111/gcb.15937. A list of contributing datasets to the compilation of Calanus finmarchicus records can be found in the file: occurrence_dat_citations.txt. A list of the datasets and citations for the seasonal environmental climatologies we use can be found in the file: environmental_dat_citations.txt. |
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| Quality: | Occurrence records represent those remaining after undertaking quality assurance and control processes as detailed in section 6. Further actions to limit the potential for sampling bias issues were carried out and are included in the R Markdown file we provide. Due to limited data availability, seasonal environmental data during the older time period (1955-1984) are limited to: bathymetry, slope, temperature, salinity, sea-ice concentration and current velocity. Sensitivity analyses were carried out to (a) account for potential misidentification of occurrences between Calanus finmarchicus and its congener, C. glacialis, (b) account for potential bias stemming from the seasonal assignment process of occurrences to environmental, and (c) test the sensitivity of model outputs to the inclusion of sea-ice concentration. Code for these analyses is within the R Markdown file we provide. |
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| Lineage: | Occurrence records and environmental data were downloaded from online and open access sources (see section Reference). After identifying overlapping datasets between repositories, remaining occurrence records were thinned to retain only one occurrence per season per grid cell (resolution: 0.25° x 0.25°) using the "spThin" R package (Aiello-Lammens et al. 2015). This removes the fewest records necessary to substantially reduce the effects of sampling bias, while simultaneously retaining the greatest amount of useful information. This left a total of 27,727 occurrence records and this cleaned dataset is version provided here. Occurrence and background points were matched to the conditions from the season and era from which they were collected. This was done using an adapted version of the "depth_extract" R function available from: https://figshare.com/articles/Duffy_Chown_MEPS12011_model_virtualspecies/4315052. The adapted version we use is available in the R Markdown file we provide. The steps that followed included optimising Maxent model settings, using the final model to predict habitat suitability across the study region, and running several sensitivity analyses. These processes are documented in the R Markdown file provided. - Folder: env_dat_rasters, Volume: 193 megabytes Contents: This folder contains the gridded environmental data. Each subfolder contains the raster files (ascii format) for a particular time period (era) and season. E.g. subfolder "era1_amj" contains the raster data during April-May-June of era 1 (1955-1984). Data files and units: bathy.asc = bathymetry (metres) chla.asc = sea surface chlorophyll a concentration (mg.m-3) par.asc = sea surface photosynthetically active radiation (einstein.m-2.day-1) ph.asc = sea surface ph (total scale) salinity.asc = sea surface salinity (psu) seaicecon.asc = sea-ice concentration (%) silicate.asc = sea surface molar concentration of silicate (µmol.kg-1) slope.asc = bathymetric slope (degrees) temp.asc = sea surface temperature (degrees celsius) velocity.asc = sea surface current velocity (m.s-1) - File: occurrence_dat_cleaned.csv, Volume: 4.9 megabytes Contents: This file contains the cleaned and processed occurrence records of Calanus finmarchicus and the season-and-era-specific environmental conditions assigned to each presence locality. Data columns and units: NAME = identifier for species "Calanus_finmarchicus" LON = longitude (decimal degrees) LAT = latitude (decimal degrees) MONTH_COLLECTED = month of sample collection (1=Jan, 2=Feb etc.) SEASON = season assigned to each point (1=Jan-Feb-Mar, 2=Apr-May-Jun, 3=Jul-Aug-Sep, 4=Oct-Nov-Dec) MINIMUM_DEPTH = minimum vertical depth of sample (metres from sea surface) MAXIMUM_DEPTH = maximum vertical depth of sample (metres from sea surface) MIN_MAX_DEPTH_RANGE = vertical range of sample (metres) YEAR_COLLECTED = year of sample collection TIME_PERIOD = era assigned to each point (1=1955-1984, 2=1985-2017) LIFESTAGE = copepodite life stage assigned to the record at collection (CI-Adult) DATASET = dataset/cruise from which sample was collected (see file "occurrence_dat_citations.txt" for full list) DATABASE = database from which sample was archived (see file "occurrence_dat_citations.txt" for full list) BATHY = bathymetry (metres) CHLA = sea surface chlorophyll a concentration (mg.m-3) PAR = sea surface photosynthetically active radiation (einstein.m-2.day-1) PH = sea surface pH (total scale) SALINITY = sea surface salinity (psu) SEAICECON = Sea-ice concentration (%) SILICATE = sea surface molar concentration of silicate (µmol.kg-1) SLOPE = Bathymetric slope (degrees) TEMP = sea surface temperature (degrees Celsius) VELOCITY = sea surface current velocity (m.s-1) Abbreviations: CI - CVI = lifestage Copepodite I - VI, where C5 = CV and C6 = CVI NA = Not Available AF = Adult Female F = Female M = Male - File: background_dat.csv, Volume: 1.3 megabytes Contents: This file contains the coordinates of the background data generated for the study and the season-and-era-specific environmental conditions assigned to each point. Data columns and units: NAME = identifier for background data "bg" LON = longitude (decimal degrees) LAT = latitude (decimal degrees) TIME_PERIOD = era assigned to each point (1=1955-1984, 2=1985-2017) SEASON = season assigned to each point (1=Jan-Feb-Mar, 2=Apr-May-Jun, 3=Jul-Aug-Sep, 4=Oct-Nov-Dec) BATHY = bathymetry (metres) CHLA = sea surface chlorophyll a concentration (mg.m-3) PAR = sea surface photosynthetically active radiation (einstein.m-2.day-1) PH = sea surface pH (total scale) SALINITY = sea surface salinity (psu) SEAICECON = Sea-ice concentration (%) SILICATE = sea surface molar concentration of silicate (µmol.kg-1) SLOPE = Bathymetric slope (degrees) TEMP = sea surface temperature (degrees Celsius) VELOCITY = sea surface current velocity (m.s-1) - File: occurrence_dat_sens1.csv, Volume: 4.9 megabytes Contents: This file contains the amended occurrence records used in the 1st sensitivity analysis we report - replacing 10% of C. finmarchicus records with C. glacialis. As in the original occurrence data file, the season-and-era-specific environmental conditions assigned to each presence locality are also given. Data columns and units: same as in occurrence_dat_cleaned.csv. - File: occurrence_dat_sens2.csv, Volume: 4.9 megabytes Contents: This file contains the amended and processed occurrence records used in the 2nd sensitivity analysis we report - replacing 20% of C. finmarchicus records with C. glacialis. As in the original occurrence data file, the season-and-era-specific environmental conditions assigned to each presence locality are also given. Data columns and units: same as in occurrence_dat_cleaned.csv. - File: occurrence_dat_sens3.csv, Volume: 4.9 megabytes Contents: This file contains the amended occurrence records used in the 3rd sensitivity analysis we report - assigning 50% of occurrences collected at months 1, 4, 7, 10 to environmental conditions one season earlier and assigning 50% of occurrences collected at months 3, 6, 9, 12 to environmental conditions one season later. As in the original occurrence data file, the season-and-era-specific environmental conditions assigned to each presence locality are also given. Data columns and units: same as in occurrence_dat_cleaned.csv. - File: occurrence_dat_citations.txt, Volume: 14 kilobytes Contents: A citation list of all contributing datasets for occurrence records compiled from openly accessible online databases and repositories. - File: environmental_dat_citations.txt, Volume: 4 kilobytes Contents: Citations, URL links and parameter information for each contributing dataset used to create seasonal climatologies. - File: GCB-21-1892_Freer.rmd, Volume: 19 kilobytes Contents: An R Markdown file that provides the code necessary to produce the habitat suitability predictions of C. finmarchicus, using the input files provided within this repository. An html file that shows the complete output of the .rmd file is also provided. |
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| Temporal Coverage: | |
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| Start Date | 1985-01-01 |
| End Date | 2017-12-31 |
| Start Date | 1955-01-01 |
| End Date | 1984-12-31 |
| Spatial Coverage: | |
| Latitude | |
| Southernmost | 30 |
| Northernmost | 90 |
| Longitude | |
| Westernmost | -180 |
| Easternmost | 180 |
| Altitude | |
| Min Altitude | N/A |
| Max Altitude | N/A |
| Depth | |
| Min Depth | 0 m |
| Max Depth | 0 m |
| Data Resolution: | |
| Latitude Resolution | 0.25 decimal degree |
| Longitude Resolution | 0.25 decimal degree |
| Horizontal Resolution Range | N/A |
| Vertical Resolution | N/A |
| Vertical Resolution Range | N/A |
| Temporal Resolution | N/A |
| Temporal Resolution Range | N/A |
| Location: | |
| Location | N/A |
| Detailed Location | Arctic |
| Location | N/A |
| Detailed Location | Subarctic |
| Location | N/A |
| Detailed Location | North Atlantic |
| Data Collection: | All analyses were carried out in R version 3.4.1. |
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| Data Storage: | For details see the section Lineage. Folder: env_dat_rasters, Volume: 193 megabytes File: occurrence_dat_cleaned.csv, Volume: 4.9 megabytes File: background_dat.csv, Volume: 1.3 megabytes File: occurrence_dat_sens1.csv, Volume: 4.9 megabytes File: occurrence_dat_sens2.csv, Volume: 4.9 megabytes File: occurrence_dat_sens3.csv, Volume: 4.9 megabytes File: occurrence_dat_citations.txt, Volume: 14 kilobytes File: environmental_dat_citations.txt, Volume: 4 kilobytes File: GCB-21-1892_Freer.rmd, Volume: 19 kilobytes |
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