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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
The date on which this version of the data was created in YYYY-MM-DD format.
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

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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.
The reference as a URL. https://doi.org/10.15468/39omei

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"
kingdomphylumclassorderfamilygenusspeciesacceptedUsageKey
PlantaeTracheophytaMagnoliopsidaFabalesFabaceaeAcaciaAcacia saligna2978552
AnimaliaChordataAvesPasseriformesSturnidaeAcridotheresAcridotheres tristis2489005
PlantaeTracheophytaMagnoliopsidaSapindalesSimaroubaceaeAilanthusAilanthus altissima3190653
AnimaliaChordataAvesAnseriformesAnatidaeAlopochenAlopochen aegyptiaca2498252
PlantaeTracheophytaMagnoliopsidaCaryophyllalesAmaranthaceaeAlternantheraAlternanthera philoxeroides3084923
AnimaliaChordataSiluriformesIctaluridaeAmeiurusAmeiurus melas2340977
PlantaeTracheophytaLiliopsidaPoalesPoaceaeAndropogonAndropogon virginicus2706080
AnimaliaPlatyhelminthesTricladidaGeoplanidaeArthurdendyusArthurdendyus triangulatus2502792
PlantaeTracheophytaMagnoliopsidaGentianalesApocynaceaeAsclepiasAsclepias syriaca3170247
AnimaliaChordataMammaliaArtiodactylaCervidaeAxisAxis axis2440934
PlantaeTracheophytaMagnoliopsidaAsteralesAsteraceaeBaccharisBaccharis halimifolia3129663
PlantaeTracheophytaMagnoliopsidaNymphaealesCabombaceaeCabombaCabomba caroliniana2882443
AnimaliaChordataMammaliaRodentiaSciuridaeCallosciurusCallosciurus erythraeus2437394
AnimaliaChordataMammaliaRodentiaSciuridaeCallosciurusCallosciurus finlaysonii2437399
PlantaeTracheophytaMagnoliopsidaSapindalesSapindaceaeCardiospermumCardiospermum grandiflorum3189935
PlantaeTracheophytaLiliopsidaPoalesPoaceaeCenchrusCenchrus setaceus5828232
AnimaliaChordataAvesPasseriformesCorvidaeCorvusCorvus splendens2482499
PlantaeTracheophytaLiliopsidaPoalesPoaceaeEhrhartaEhrharta calycina2702865
PlantaeTracheophytaLiliopsidaAlismatalesHydrocharitaceaeElodeaElodea nuttallii5329212
AnimaliaArthropodaMalacostracaDecapodaVarunidaeEriocheirEriocheir sinensis2225776
AnimaliaArthropodaMalacostracaDecapodaCambaridaeFaxoniusFaxonius limosus8909595
AnimaliaArthropodaMalacostracaDecapodaCambaridaeFaxoniusFaxonius rusticus8979506
AnimaliaArthropodaMalacostracaDecapodaCambaridaeFaxoniusFaxonius virilis8971201
AnimaliaChordataCyprinodontiformesFundulidaeFundulusFundulus heteroclitus5712056
AnimaliaChordataCyprinodontiformesPoeciliidaeGambusiaGambusia affinis2350580
AnimaliaChordataCyprinodontiformesPoeciliidaeGambusiaGambusia holbrooki2350570
PlantaeTracheophytaMagnoliopsidaGunneralesGunneraceaeGunneraGunnera tinctoria2984306
PlantaeTracheophytaMagnoliopsidaAsteralesAsteraceaeGymnocoronisGymnocoronis spilanthoides6063677
PlantaeTracheophytaMagnoliopsidaProtealesProteaceaeHakeaHakea sericea7287606
PlantaeTracheophytaMagnoliopsidaApialesApiaceaeHeracleumHeracleum mantegazzianum3034825
PlantaeTracheophytaMagnoliopsidaApialesApiaceaeHeracleumHeracleum persicum3628745
PlantaeTracheophytaMagnoliopsidaApialesApiaceaeHeracleumHeracleum sosnowskyi3642949
PlantaeTracheophytaMagnoliopsidaRosalesCannabaceaeHumulusHumulus scandens2984537
PlantaeTracheophytaMagnoliopsidaApialesAraliaceaeHydrocotyleHydrocotyle ranunculoides7978544
PlantaeTracheophytaMagnoliopsidaEricalesBalsaminaceaeImpatiensImpatiens glandulifera2891770
PlantaeTracheophytaMagnoliopsidaCaryophyllalesPolygonaceaeKoenigiaKoenigia polystachya8848208
PlantaeTracheophytaLiliopsidaAlismatalesHydrocharitaceaeLagarosiphonLagarosiphon major2865565
AnimaliaChordataSquamataColubridaeLampropeltisLampropeltis getula9799308
AnimaliaChordataPerciformesCentrarchidaeLepomisLepomis gibbosus2394486
PlantaeTracheophytaMagnoliopsidaFabalesFabaceaeLespedezaLespedeza cuneata8114276
AnimaliaChordataAmphibiaAnuraRanidaeLithobatesLithobates catesbeianus2427091
PlantaeTracheophytaMagnoliopsidaMyrtalesOnagraceaeLudwigiaLudwigia grandiflora5421039
PlantaeTracheophytaMagnoliopsidaMyrtalesOnagraceaeLudwigiaLudwigia peploides5420991
PlantaeTracheophytaPolypodiopsidaSchizaealesLygodiaceaeLygodiumLygodium japonicum2650436
PlantaeTracheophytaLiliopsidaAlismatalesAraceaeLysichitonLysichiton americanus2869311
PlantaeTracheophytaLiliopsidaPoalesPoaceaeMicrostegiumMicrostegium vimineum5289808
AnimaliaChordataMammaliaArtiodactylaCervidaeMuntiacusMuntiacus reevesi2440946
AnimaliaChordataMammaliaRodentiaMyocastoridaeMyocastorMyocastor coypus4264680
PlantaeTracheophytaMagnoliopsidaSaxifragalesHaloragaceaeMyriophyllumMyriophyllum aquaticum5361785
PlantaeTracheophytaMagnoliopsidaSaxifragalesHaloragaceaeMyriophyllumMyriophyllum heterophyllum5361762
AnimaliaChordataMammaliaCarnivoraProcyonidaeNasuaNasua nasua2433536
PlantaeTracheophytaMagnoliopsidaFabalesFabaceaeProsopisProsopis juliflora5358460
AnimaliaChordataMammaliaCarnivoraCanidaeNyctereutesNyctereutes procyonoides2434552
AnimaliaChordataMammaliaRodentiaCricetidaeOndatraOndatra zibethicus5219858
AnimaliaChordataAvesAnseriformesAnatidaeOxyuraOxyura jamaicensis2498305
AnimaliaArthropodaMalacostracaDecapodaAstacidaePacifastacusPacifastacus leniusculus2226990
PlantaeTracheophytaMagnoliopsidaAsteralesAsteraceaePartheniumParthenium hysterophorus3086784
AnimaliaChordataPerciformesOdontobutidaePerccottusPerccottus glenii2390064
PlantaeTracheophytaMagnoliopsidaCaryophyllalesPolygonaceaePersicariaPersicaria perfoliata4033648
PlantaeTracheophytaLiliopsidaAlismatalesAraceaePistiaPistia stratiotes2870583
PlantaeTracheophytaLiliopsidaCommelinalesPontederiaceaePontederiaPontederia crassipes2765942
AnimaliaArthropodaMalacostracaDecapodaCambaridaeProcambarusProcambarus clarkii2227300
AnimaliaArthropodaMalacostracaDecapodaCambaridaeProcambarusProcambarus virginalis9442269
AnimaliaChordataMammaliaCarnivoraProcyonidaeProcyonProcyon lotor5218786
AnimaliaChordataCypriniformesCyprinidaePseudorasboraPseudorasbora parva2362868
AnimaliaChordataAvesPasseriformesPycnonotidaePycnonotusPycnonotus cafer2486131
ChromistaOchrophytaPhaeophyceaeDictyotalesDictyotaceaeRugulopteryxRugulopteryx okamurae5824863
PlantaeTracheophytaPolypodiopsidaSalvinialesSalviniaceaeSalviniaSalvinia molesta5274863
AnimaliaChordataMammaliaRodentiaSciuridaeSciurusSciurus carolinensis5219681
AnimaliaChordataMammaliaRodentiaSciuridaeSciurusSciurus niger5219683
AnimaliaArthropodaInsectaHymenopteraFormicidaeSolenopsisSolenopsis invicta5035230
AnimaliaChordataMammaliaRodentiaSciuridaeTamiasTamias sibiricus2437450
AnimaliaChordataAvesPelecaniformesThreskiornithidaeThreskiornisThreskiornis aethiopicus2480764
AnimaliaChordataTestudinesEmydidaeTrachemysTrachemys scripta2443002
PlantaeTracheophytaMagnoliopsidaMalpighialesEuphorbiaceaeTriadicaTriadica sebifera3054399
AnimaliaArthropodaInsectaHymenopteraFormicidaeWasmanniaWasmannia auropunctata1315391
AnimaliaChordataAmphibiaAnuraPipidaeXenopusXenopus laevis5217334