Data from: A comprehensive occurrence dataset for European Ostracoda inhabiting groundwater and groundwater-dependent ecosystems
Data files
Jun 13, 2025 version files 1.21 MB
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Data_Source.csv
5.88 KB
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Dataset.csv
1.18 MB
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README.md
26.81 KB
Abstract
Motivation
Groundwater ecosystems sustain a unique and globally important biodiversity but remain understudied due to sampling and exploration challenges, as well as a shortage of taxonomic experts. Groundwater ostracods, like other groundwater taxa, exhibit a high degree of endemism, rarity, and subterranean specialisation, positioning them as potentially vulnerable organisms. To better understand biodiversity patterns and the conservation needs of this highly diverse group, we assembled a team of experts to gather the most comprehensive information available about groundwater ostracods in Europe. We present a dataset comprising 2,065 occurrence records of 110 species, 11 undescribed species, and 5 subspecies of groundwater ostracods. This open dataset may support future research on the distribution, evolutionary pathways, and conservation needs of European groundwater ostracods, as well as inspire targeted sampling efforts in regions with currently limited data available.
Main Types of Variables Contained
Occurrence records of groundwater ostracods, with details about taxonomy, source of records, occurrence locality, habitat type, and species dependence on groundwater (obligate [stygobite] versus facultative groundwater-dwellers [stygophile]).
Spatial Location and Grain
Geographical Europe, spanning 32 countries. Occurrence records were assigned decimal degrees coordinates (EPSG:4326). Most occurrence records are at 100 m resolution.
Time Period
1915–2024.
Major Taxa and Level of Measurement
Crustacea: Ostracoda. Most records have species or subspecies-level identification, while some are identified to genus or family levels.
Software Format
Comma-separated values file (.csv), with UTF-8 encoding and meta-data provided following the Darwin Core standard.
Dataset DOI: 10.5061/dryad.1g1jwsv7c
Description of the data and file structure
The European Ostracoda occurrence dataset for groundwater and groundwater-dependent ecosystems (EGWOD) was compiled from several datasets and databases: the European groundwater crustacean dataset (Zagmajster et al., 2014), the SubBioDB database (Zagmajster et al., 2008; Zagmajster et al., 2012), the Slovenian Ostracoda dataset (Mori and Šalamun, 2022), and several datasets obtained from individual researchers in the United Kingdom, Ireland, Croatia, Hungary, Romania, Italy, and Austria. Furthermore, additional data from 7 publications were included.
Main Types of Variables Contain occurrence records of groundwater ostracods, with details about taxonomy, source of records, occurrence locality, habitat type, and species dependence on groundwater (obligate [stygobiont] versus facultative groundwater-dwellers [stygophile]).
Spatial Location and Grain is geographical Europe, spanning 32 countries. Occurrence records were assigned decimal degrees coordinates (EPSG:4326). Most occurrence records are at 100 m resolution.
Time Period is 1915–2024.
Major Taxa and Level of Measurement are Crustacea: Ostracoda. Most records have species or subspecies-level identification, while some are identified to genus or family levels.
Files and variables
File: Dataset.csv
Description: The csv file Dataset contains a total of 2065 Ostracoda records across 32 countries. Forty-two records were identified only to family and 132 genus level, respectively. A total of 2022 records include precise spatial coordinates (spatial precision < 100 m), and 1902 records contain information on sampling site type.
Variables
| COLUMN_NAME | DESCRIPTION | TYPE_OF_ENTRIES |
|---|---|---|
| ID | Occurrence record ID | numeric |
| datasetName | Official name of the source, if any, or unofficial name of the source | text |
| informationWithheld | Name of the owner/provider of the dataset | text |
| taxonID | Taxon ID as set in the source dataset. If an ID was not provided, the cell is left empty. | numeric |
| class | Class following nomenclature by Meisch et al., 2024 | text |
| order | Ordo following nomenclature by Meisch et al., 2024 | text |
| family | Familia following nomenclature by Meisch et al., 2024 | text |
| genus | Genus following nomenclature by Meisch et al., 2024. If identification to the genus level was not provided, the cell is left empty. | text |
| species | Species following nomenclature by Meisch et al., 2024. If identification to the species level was not provided, the cell is left empty. | text |
| scientificNameAuthorship | Author&Year following nomenclature by Meisch et al., 2024 | text |
| verbatimIdentification | Taxon/species full name as provided in the source | text |
| scientificName | Valid species full name following nomenclature by Meisch et al., 2024 | text |
| taxonRank | Taxonomic identification level. | text |
| lineage | In cases with multiple lineages, the specific lineage is indicated. If not provided, the cell is left empty. | text |
| dateIdentified | Date of survey/sampling. If not provided, the cell is left empty. | date |
| identifiedBy | Surveyers/legit. If not provided, the cell is left empty. | text |
| decimalLatitude | N - measured in degrees. If the coordinates were not provided, the cell is left empty. | numeric |
| decimalLongitude | E - measured in degrees. If the coordinates were not provided, the cell is left empty. | numeric |
| geodeticDatum | Coordinate system/georeference protocol. If the coordinates were not provided, the cell is left empty. | text |
| elevationInMeters | Defined from the source or calculated. If not avaliable, the cell is left empty. | numeric |
| verticalDatum | Predefined or calculated (def/cal). If elevationInMeters was not defined, the cell is left empty. | text |
| locationID | Locality ID if set in source dataset If an ID was not provided, the cell is left empty. | text |
| locality | Descriptive name of the exact locality. If the locality name was not provided, the cell is left empty. | text |
| municipality | Name of the municipality or nearby larger settlement. If the municipality was not provided, the cell is left empty. | text |
| stateProvince | Name of the province. If not provided, the cell is left empty. | text |
| region | Name of the region. If not provided, the cell is left empty. | text |
| country | Name of the country | text |
| locationRemarks | Sampling site type as defined in source database. If not provided, the cell is left empty. | text |
| habitat | Synchronised sampling site type : Cave; Interstitial - Hyporheic zone; Interstitial - Phreatic Zone; Spring; Well. If sampling site type was not provided, the cell is left empty. | text |
| MeasurementOrFact | Stygobiont - exclusively from GW, Stygophile - predominantly occuring in GW | text |
| references | Source reference. If not avaliable, the cell is left empty. | text |
| basisOfRecord | Literature/dataset/observation. If not avaliable, the cell is left empty. | text |
| rightsHolder | Rights holder of the data. If not provided, the cell is left empty. | text |
| Input.into.DB.-.name | Name of the person that inserted the data into the dataset | text |
File: Data_Source.csv
Description: This csv file lists all the sources from where the data on Ostracoda occurence were extracted.
Variables
| COLUMN_NAME | DESCRIPTION | TYPE_OF_ENTRIES | Explanation |
|---|---|---|---|
| Type | Type of resource | database; meta-database; dataset | |
| Name | Official name of the resource, if any | text | |
| Link | Link to the resource, if any | link | |
| Link 2 | Second link to the resource, if any | link | |
| Associated_publication | Publication describing the resource, if any | text | |
| Open_access | Is the data openly available | yes ; yes (registered); no | yes (registered): OA after registration |
| Updated | Is the resource curated and/or updated on a regularly basis | yes ; no | |
| Contact | Main contact person (with email if possible) | text ( Name Surname – email ) | |
| Accessibility_notes | Any note regarding open access and accessibility | text | |
| Temporal_span | The temporal coverage of the resource | range in years (e.g., 2005-2020) | |
| Spatial_extent | The spatial etent of the resource | punctual ; regional ; national ; transnational ; global | |
| Coordinates_x | The spatial extent of the resource | Numeric (in WGS84 decimal degrees) | |
| Coordinates_y | coordinate y (latitude) of the resource, if available | Numeric (in WGS84 decimal degrees) | |
| Subterranean_terrestrial | does the resource focus on terrestrial subterranean habitats? | yes ; no | |
| Subterranean_freshwater | does the resource focus on freshwater subterranean habitats? | yes ; no | |
| Subterranean_marine | does the resource focus on marine subterranean habitats? | yes ; no | |
| Subterranean_exclusive | is the resource solely focused on subterranean ecosystems? | yes ; no |
Code/software
Comma-separated values file (.csv) with UTF-8 encoding and meta-data provided following the Darwin Core standard.
Access information
Other publicly accessible locations of the data:
- Hazelton https://bcra.org.uk/biology/
Data was derived from the following sources:
| Type | Name | Link |
|---|---|---|
| database | European Groundwater Crustacea Database | https://opennetzero.org/freshwater-research-resources-and-tools/european-groundwater-crustacea-database |
| database | SubBioDB - Subterranean Biodiversity Database | https://db.subbio.net/ |
| database | Slovenian Ostracoda Dataset | https://www.ckff.si/zbirka.php |
| meta-database | GBIF | https://www.gbif.org/ (not presented in the Dryad due to licence limitation) |
| dataset | Romanian Ostracoda Dataset | n/a (not available online) |
| dataset | Hungarian Ostracoda Dataset | n/a (not available online) |
| article | Klie, W. (1937). Weitere Ostracoden aus dem Grundwasser von Belgien. Bulletin of the Royal Belgian Natural History Museum, 13(4). | https://biblio.naturalsciences.be/rbins-publications/bulletin-of-the-royal-belgian-natural-history-museum/13-1937/irscnb_p4087_00f27dp_13_bulletin-4-red.pdf |
| database | Hazelton Database | https://bcra.org.uk/biology/ |
| article | Rossetti, G., Martens, K., Meisch, C., Tavernelli, S., & Pieri, V. (2006). Small is beautiful: Diversity of freshwater ostracods (Crustacea, Ostracoda) in marginal habitats of the province of Parma (Northern Italy). Journal of Limnology, 65(2), 121-131. https://doi.org/10.4081/jlimnol.2006.121 | https://doi.org/10.4081/jlimnol.2006.121 |
| article | Pieri, V., Martens, K., Meisch, C., & Rossetti, G. (2015). An annotated checklist of the Recent non-marine ostracods (Ostracoda: Crustacea) from Italy. Zootaxa, 3919(2), 271–305. https://doi.org/10.11646/zootaxa.3919.2.3 | https://mapress.com/zt/article/view/zootaxa.3919.2.3 |
| article | Pendino, V., Vecchioni, L., Stoch, F., & Marrone, F. (2024). Checklist and distribution of the groundwater crustacean fauna from Sicily, Italy. Journal of Limnology, 83(1), 1-19. https://doi.org/10.4081/jlimnol.2024.2199 | https://www.jlimnol.it/jlimnol/article/view/2199 |
| article | Mazzini, I., Marrone, F., Arculeo, M., & Rossetti, G. (2017). Revision of Recent and fossil Mixtacandona Klie 1938 (Ostracoda, Candonidae) from Italy, with description of a new species. Zootaxa, 4221(3), 323–340. https://doi.org/10.11646/zootaxa.4221.3.3 | https://www.mapress.com/zt/article/view/zootaxa.4221.3.3 |
| dataset | Scotland Ostracoda Dataset | n/a (not available online) |
| article | Knight, L. R. F. D., Mori, N. & Brancelj, A. (2022). A preliminary survey of the aquatic invertebrate fauna of Scottish caves. Cave and Karst Science, 49(1), 3–13. | https://bcra.org.uk/pub/candks/index.html?j=145 |
| article | Pociecha, A., Karpowicz, M., Namiotko, T., Dumnicka, E., & Galas, J. (2021). Diversity of Groundwater Crustaceans in Wells in Various Geologic Formations of Southern Poland. Water, 13(16), 2193. https://doi.org/10.3390/w13162193 | https://www.mdpi.com/2073-4441/13/16/2193 |
| dataset | Austrian Ostracoda dataset | n/a (not available online) |
- Mori, Nataša; Vehovar, Živa; Brad, Traian et al. (2025). A Comprehensive Occurrence Dataset for European Ostracoda Inhabiting Groundwater and Groundwater‐Dependent Ecosystems. Global Ecology and Biogeography. https://doi.org/10.1111/geb.70065