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Date of publication: August 22, 2024

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Date of publication: August 22, 2024

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Occurrence Metrics for Invasive Alien Species of Union Concern in EU27: A 10 km prototype using GBIF occurrence cubes

by Lina Estupinan-Suarez

This dataset includes GBIF occurrences of species listed under Regulation (EU) 1143/2014 on invasive alien species (IAS). The IAS list, adopted in 2016 and updated in 2017, 2019, and 2022, currently includes 88 species subject to strict environmental restrictions.

For this study, we used the most recent IAS list from the European Topic Centre on Biodiversity and Ecosystems (ETC BE) and the European Environment Agency (EEA) as of June 2 ...(continue reading)

DOI 10.25829/w0vf54
Citation
Estupinan-Suarez, L., Fernandez, M., Quoss, L., Oceguera, E. (2024). Occurrence Metrics for Invasive Alien Species of Union Concern in EU27: A 10 km prototype using GBIF occurrence cubes (Version 1) [Dataset]. German Centre for Integrative Biodiversity Research. https://doi.org/10.25829/w0vf54

Invasive alien species of union concernEuropean UnionSpecies occurrenceBasis of recordCube occurrenceGBIF records

83
The title of the dataset. Occurrence Metrics for Invasive Alien Species of Union Concern in EU27: A 10 km prototype using GBIF occurrence cubes
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A paragraph describing the dataset.
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This dataset includes GBIF occurrences of species listed under Regulation (EU) 1143/2014 on invasive alien species (IAS). The IAS list, adopted in 2016 and updated in 2017, 2019, and 2022, currently includes 88 species subject to strict environmental restrictions.

For this study, we used the most recent IAS list from the European Topic Centre on Biodiversity and Ecosystems (ETC BE) and the European Environment Agency (EEA) as of June 2024. We matched these species' scientific names with the GBIF backbone taxonomy to obtain the accepted GBIF names and species keys.

Using the GBIF API in R, we generated CSV cubes of species occurrences, applying the EEA spatial grid at a 10 km resolution. Monthly occurrence data were collected for 77 species, and the following metrics were calculated for each grid cell in the cube:
• Total number of occurrences
• Earliest date of occurrences
• Latest date of occurrences
• Basis of record for the earliest date of occurrences
• Basis of record for the latest date of occurrences

This dataset was developed by the Biodiversity Building Blocks for Policy (B3) project and was funded by the European Union’s Horizon Europe Research and Innovation Programme (ID No 101059592).
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https://doi.org/
10.15468/dl.m4694q
The method of production of the original data.
Hover to see a suggestion for a minimum description. These are the general steps to calculate the metrics of IAS of union concern based on GBIF records:

1. The field Currently valid full name from the latest IAS list by ETC in June 2024 was matched against the GBIF backbone taxonomy [1]. Thus, we obtained the accepted scientific name in GBIF and the corresponding species key. All names had an EXACT match, but four of them were considered SYNONYMS. We replaced all four SYNONYMS with the corresponding ACCEPTED scientific name and species key.

2. Using the Species occurrence cubes software developed by B3 and GBIF [2], we created species occurrence cubes in a CSV format matching the EEA grid at 10 Km for records available from 1900 until mid June 2024. The query is in a JSON file and available at GitHub as well as the R script to submit the JSON query using GBIF API [3]. Importantly only records for 77 species were found.

3. We loaded the CSV occurrence cubes using the b3gbi library, and calculated the following metrics: total number of occurrences, earliest date of records, latest date of records, basis of record of the earliest date, and basis of records of the latest date.

4. After rasterization of the metrics, data was converted to the EBVCube format.

Steps 2 to 5 were conducted in R. All scripts are available at GitHub [3]

[1]https://www.gbif.org/tools/species-lookup
[2]https://techdocs.gbif.org/en/data-use/data-cubes
[3]https://github.com/EBVcube/B-Cubed_data_mobilization
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The name of the Project.
The URL from the project website. https://b-cubed.eu/
The name of the person or other creator type principally responsible for creating this data.
The email of the person or other creator type principally responsible for creating this data. lina.estupinans@gmail.com

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lina.estupinans@idiv.de

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Essential Biodiversity Variables

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Genetic composition
Intraspecific genetic diversity
Genetic differentiation
Effective population size
Inbreeding
Other
Species populations
Species distributions
Species abundances
Other
Species traits
Morphology
Physiology
Phenology
Movement
Other
Community composition
Community abundance
Taxonomic and phylogenetic diversity
Trait diversity
Interaction diversity
Other
Ecosystem functioning
Primary productivity
Ecosystem phenology
Ecosystem disturbances
Other
Ecosystem structure
Live cover fraction
Ecosystem distribution
Ecosystem Vertical Profile
Other
Ecosystem services
Pollination
Other
Cross-cutting

Entity

Select the entity type of the dataset.
Species
Communities
Ecosystems
Other
None
A description of the range of taxa or ecosystem types addressed in the dataset. E.g. "300 species of mammals”, “Forests”, etc.
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Metric

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Scenario

Spatial domain

Global
Continental/Regional
National
Sub-national/Local
Name of the continent/region/country/area, separated by comma
meter
southWest lat: 700000, lon: 0
northEast lat: 7500000, lon: 8400000

Temporal domain

The targeted time period between each value in the dataset.
decadal
annually
monthly
weekly
daily
Other
Irregular
Single time
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When the dataset represents a Single time, then use the same start and end date.
__

Environmental domain *

Terrestrial
Marine
Freshwater
Miscellaneous information about the data, not captured elsewhere. Of the 87 species included in the EU list of IAS of concern, we found data for 77 species through the generation of species occurrence cubes. From the remaining ten, two are subspecies (Herpestes javanicus auropunctatus; Vespa velutina nigrithorax) and one is a variety (Pueraria montana var. lobata) that cannot be identified by the speciesKey. For the others species there is no data in GBIF and therefore they were not included.

Of the 77 species, 73 species have the same scientific name in the GBIF Backbone taxonomy and in the EEA updated offcial list. In other words the scientific name holds the category ACCEPTED. For the SYNONYMS, we used the ACCEPTED name in GBIF. Below the list of corresponding scientific names.

1. ETC SCIENTIFIC NAME: Cortaderia selloana subsp. jubata (Lemoine) Testoni & Villamil; GBIF SCIENTIFIC NAME: Cortaderia jubata (Lemoine) Stapf
2. ETC SCIENTIFIC NAME: Heracleum persicum Fischer; GBIF SCIENTIFIC NAME: Heracleum persicum Desf.
3. ETC SCIENTIFIC NAME: Neltuma juliflora (Sw.) Raf.; GBIF SCIENTIFIC NAME: Prosopis juliflora (Sw.) DC.
4. ETC SCIENTIFIC NAME: Urva auropunctata (Hodgson, 1836), GBIF SCIENTIFIC NAME: Herpestes javanicus subsp. auropunctatus (Hodgson, 1836)

The 10 species with no records via the GBIF occurrence cube software are listed using the GBIF Backbone Taxonomy. If the scientific name differs from the ETC nomenclature this is indicated in square brackets.
- Channa argus (Cantor, 1842)
- Cortaderia jubata (Lemoine) Stapf [Cortaderia selloana subsp. jubata (Lemoine) Testoni & Villamil]
- Limnoperna fortunei (Dunker, 1857)
- Morone americana (Gmelin, 1789)
- Plotosus lineatus (Thunberg, 1787)
- Pueraria montana var. lobata (Willd.) Maesen & S.M.Almeida ex Sanjappa & Predeep
- Solenopsis geminata (Fabricius, 1804)
- Solenopsis richteri Forel, 1909
- Herpestes javanicus subsp. auropunctatus (Hodgson, 1836) [Urva auropunctata (Hodgson, 1836)]
- Vespa velutina nigrithorax Buysson, 1905

***Coding for Basis of record
[1] "HUMAN_OBSERVATION"
[2] "LIVING_SPECIMEN"
[3] "MACHINE_OBSERVATION"
[4] "MATERIAL_CITATION"
[5] "MATERIAL_SAMPLE"
[6] "OBSERVATION"
[7] "OCCURRENCE"
[8] "PRESERVED_SPECIMEN"
SpeciesGenusFamilyOrderClassPhylumKingdom
Acacia salignaAcaciaFabaceaeFabalesMagnoliopsidaTracheophytaPlantae
Acridotheres tristisAcridotheresSturnidaePasseriformesAvesChordataAnimalia
Ailanthus altissimaAilanthusSimaroubaceaeSapindalesMagnoliopsidaTracheophytaPlantae
Alopochen aegyptiacaAlopochenAnatidaeAnseriformesAvesChordataAnimalia
Alternanthera philoxeroidesAlternantheraAmaranthaceaeCaryophyllalesMagnoliopsidaTracheophytaPlantae
Ameiurus melasAmeiurusIctaluridaeSiluriformesChordataAnimalia
Andropogon virginicusAndropogonPoaceaePoalesLiliopsidaTracheophytaPlantae
Arthurdendyus triangulatusArthurdendyusGeoplanidaeTricladidaPlatyhelminthesAnimalia
Asclepias syriacaAsclepiasApocynaceaeGentianalesMagnoliopsidaTracheophytaPlantae
Axis axisAxisCervidaeArtiodactylaMammaliaChordataAnimalia
Baccharis halimifoliaBaccharisAsteraceaeAsteralesMagnoliopsidaTracheophytaPlantae
Cabomba carolinianaCabombaCabombaceaeNymphaealesMagnoliopsidaTracheophytaPlantae
Callosciurus erythraeusCallosciurusSciuridaeRodentiaMammaliaChordataAnimalia
Callosciurus finlaysoniiCallosciurusSciuridaeRodentiaMammaliaChordataAnimalia
Cardiospermum grandiflorumCardiospermumSapindaceaeSapindalesMagnoliopsidaTracheophytaPlantae
Cenchrus setaceusCenchrusPoaceaePoalesLiliopsidaTracheophytaPlantae
Corvus splendensCorvusCorvidaePasseriformesAvesChordataAnimalia
Ehrharta calycinaEhrhartaPoaceaePoalesLiliopsidaTracheophytaPlantae
Elodea nuttalliiElodeaHydrocharitaceaeAlismatalesLiliopsidaTracheophytaPlantae
Eriocheir sinensisEriocheirVarunidaeDecapodaMalacostracaArthropodaAnimalia
Faxonius limosusFaxoniusCambaridaeDecapodaMalacostracaArthropodaAnimalia
Faxonius rusticusFaxoniusCambaridaeDecapodaMalacostracaArthropodaAnimalia
Faxonius virilisFaxoniusCambaridaeDecapodaMalacostracaArthropodaAnimalia
Fundulus heteroclitusFundulusFundulidaeCyprinodontiformesChordataAnimalia
Gambusia affinisGambusiaPoeciliidaeCyprinodontiformesChordataAnimalia
Gambusia holbrookiGambusiaPoeciliidaeCyprinodontiformesChordataAnimalia
Gunnera tinctoriaGunneraGunneraceaeGunneralesMagnoliopsidaTracheophytaPlantae
Gymnocoronis spilanthoidesGymnocoronisAsteraceaeAsteralesMagnoliopsidaTracheophytaPlantae
Hakea sericeaHakeaProteaceaeProtealesMagnoliopsidaTracheophytaPlantae
Heracleum mantegazzianumHeracleumApiaceaeApialesMagnoliopsidaTracheophytaPlantae
Heracleum persicumHeracleumApiaceaeApialesMagnoliopsidaTracheophytaPlantae
Heracleum sosnowskyiHeracleumApiaceaeApialesMagnoliopsidaTracheophytaPlantae
Humulus scandensHumulusCannabaceaeRosalesMagnoliopsidaTracheophytaPlantae
Hydrocotyle ranunculoidesHydrocotyleAraliaceaeApialesMagnoliopsidaTracheophytaPlantae
Impatiens glanduliferaImpatiensBalsaminaceaeEricalesMagnoliopsidaTracheophytaPlantae
Koenigia polystachyaKoenigiaPolygonaceaeCaryophyllalesMagnoliopsidaTracheophytaPlantae
Lagarosiphon majorLagarosiphonHydrocharitaceaeAlismatalesLiliopsidaTracheophytaPlantae
Lampropeltis getulaLampropeltisColubridaeSquamataChordataAnimalia
Lepomis gibbosusLepomisCentrarchidaePerciformesChordataAnimalia
Lespedeza cuneataLespedezaFabaceaeFabalesMagnoliopsidaTracheophytaPlantae
Lithobates catesbeianusLithobatesRanidaeAnuraAmphibiaChordataAnimalia
Ludwigia grandifloraLudwigiaOnagraceaeMyrtalesMagnoliopsidaTracheophytaPlantae
Ludwigia peploidesLudwigiaOnagraceaeMyrtalesMagnoliopsidaTracheophytaPlantae
Lygodium japonicumLygodiumLygodiaceaeSchizaealesPolypodiopsidaTracheophytaPlantae
Lysichiton americanusLysichitonAraceaeAlismatalesLiliopsidaTracheophytaPlantae
Microstegium vimineumMicrostegiumPoaceaePoalesLiliopsidaTracheophytaPlantae
Muntiacus reevesiMuntiacusCervidaeArtiodactylaMammaliaChordataAnimalia
Myocastor coypusMyocastorMyocastoridaeRodentiaMammaliaChordataAnimalia
Myriophyllum aquaticumMyriophyllumHaloragaceaeSaxifragalesMagnoliopsidaTracheophytaPlantae
Myriophyllum heterophyllumMyriophyllumHaloragaceaeSaxifragalesMagnoliopsidaTracheophytaPlantae
Nasua nasuaNasuaProcyonidaeCarnivoraMammaliaChordataAnimalia
Prosopis julifloraProsopisFabaceaeFabalesMagnoliopsidaTracheophytaPlantae
Nyctereutes procyonoidesNyctereutesCanidaeCarnivoraMammaliaChordataAnimalia
Ondatra zibethicusOndatraCricetidaeRodentiaMammaliaChordataAnimalia
Oxyura jamaicensisOxyuraAnatidaeAnseriformesAvesChordataAnimalia
Pacifastacus leniusculusPacifastacusAstacidaeDecapodaMalacostracaArthropodaAnimalia
Parthenium hysterophorusPartheniumAsteraceaeAsteralesMagnoliopsidaTracheophytaPlantae
Perccottus gleniiPerccottusOdontobutidaePerciformesChordataAnimalia
Persicaria perfoliataPersicariaPolygonaceaeCaryophyllalesMagnoliopsidaTracheophytaPlantae
Pistia stratiotesPistiaAraceaeAlismatalesLiliopsidaTracheophytaPlantae
Pontederia crassipesPontederiaPontederiaceaeCommelinalesLiliopsidaTracheophytaPlantae
Procambarus clarkiiProcambarusCambaridaeDecapodaMalacostracaArthropodaAnimalia
Procambarus virginalisProcambarusCambaridaeDecapodaMalacostracaArthropodaAnimalia
Procyon lotorProcyonProcyonidaeCarnivoraMammaliaChordataAnimalia
Pseudorasbora parvaPseudorasboraCyprinidaeCypriniformesChordataAnimalia
Pycnonotus caferPycnonotusPycnonotidaePasseriformesAvesChordataAnimalia
Rugulopteryx okamuraeRugulopteryxDictyotaceaeDictyotalesPhaeophyceaeOchrophytaChromista
Salvinia molestaSalviniaSalviniaceaeSalvinialesPolypodiopsidaTracheophytaPlantae
Sciurus carolinensisSciurusSciuridaeRodentiaMammaliaChordataAnimalia
Sciurus nigerSciurusSciuridaeRodentiaMammaliaChordataAnimalia
Solenopsis invictaSolenopsisFormicidaeHymenopteraInsectaArthropodaAnimalia
Tamias sibiricusTamiasSciuridaeRodentiaMammaliaChordataAnimalia
Threskiornis aethiopicusThreskiornisThreskiornithidaePelecaniformesAvesChordataAnimalia
Trachemys scriptaTrachemysEmydidaeTestudinesChordataAnimalia
Triadica sebiferaTriadicaEuphorbiaceaeMalpighialesMagnoliopsidaTracheophytaPlantae
Wasmannia auropunctataWasmanniaFormicidaeHymenopteraInsectaArthropodaAnimalia
Xenopus laevisXenopusPipidaeAnuraAmphibiaChordataAnimalia