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Date of publication: August 22, 2024

Version 1

Date of publication: August 22, 2024

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Occurrence Metrics for the Birds Directive Annex I Species in EU27: A 10 km prototype using GBIF occurrence cubes

by Lina Estupinan-Suarez

This dataset includes GBIF occurrences of 193 species listed in Annex I of the Birds Directive, subject to special conservation measures. The scientific names, updated by the EEA, were cross-referenced with the GBIF backbone taxonomy, yielding accepted GBIF scientific names and corresponding acceptedUsageKeys for these species. Using these names and the EEA spatial grid at a 10 km resolution, we generated the occurrence cube via the GBIF API in R ...(continue reading)

DOI 10.25829/mbw554
Citation
Estupinan-Suarez, L., Fernandez, M., Oceguera, E., Quoss, L. (2024). Occurrence Metrics for the Birds Directive Annex I Species in EU27: A 10 km prototype using GBIF occurrence cubes (Version 1) [Dataset]. German Centre for Integrative Biodiversity Research. https://doi.org/10.25829/mbw554

Birds Directive Annex IEuropean UnionSpecies occurrenceSeasonality occurrenceCube occurrenceGBIF records

82
The title of the dataset. Occurrence Metrics for the Birds Directive Annex I Species in EU27: A 10 km prototype using GBIF occurrence cubes
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A paragraph describing the dataset.
Hover to see a suggestion for a good description. Allowed:
This dataset includes GBIF occurrences of 193 species listed in Annex I of the Birds Directive, subject to special conservation measures. The scientific names, updated by the EEA, were cross-referenced with the GBIF backbone taxonomy, yielding accepted GBIF scientific names and corresponding acceptedUsageKeys for these species. Using these names and the EEA spatial grid at a 10 km resolution, we generated the occurrence cube via the GBIF API in R (DOI: https://doi.org/10.15468/dl.43ydtq). A total of 168 species met the criteria for inclusion in the cube. The following preliminary occurrence metrics were calculated for each grid cell in the cube:
• Total number of occurrences
• Earliest month with occurrences across all years
• Latest month with occurrences across all years
• Month with the highest total number of occurrences across all years
• Month with the second-highest total number of occurrences across all years
• Month with the third-highest total number of occurrences across all years.

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.43ydtq
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 species listed in the Annex I of the Birds Directive:
1. The scientific name of species in the Annex I was matched against the GBIF backbone taxonomy to obtain the accepted scientific name in GBIF and the corresponding acceptedSpeciesKey.
2. A JSON query was prepared for the corresponding species. The acceptedSpeciesKey was used as speciesKey for all records available until 2024 and with a coordinate uncertainty of 10000m. The complete query specifications is available at https://doi.org/10.15468/dl.43ydtq.
3. Using the Species occurrence cubes software developed by B3 and GBIF [1], we created species occurrence cubes in a CSV format matching the EEA grid at 10 Km.
4. We loaded the CSV occurrence cubes using the b3gbi library in R, and calculated the following metrics:
- Total number of occurrences
- Earliest month with occurrences across all years
- Latest month with occurrences across all years
- Month with the highest total number of occurrences across all years
- Month with the second-highest total number of occurrences across all years
- Month with the third-highest total number of occurrences across all years
5. After rasterization of the metrics, data was converted to the EBVCube format.

All scripts are available at GitHub https://github.com/EBVcube/B-Cubed_data_mobilization
[1] https://techdocs.gbif.org/en/data-use/data-cubes
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The URL from the project website. https://b-cubed.eu/
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The email of the person or other creator type principally responsible for creating this data. lina.estupinans@idiv.de
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

Biological entity

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Species
Communities
Ecosystems
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None
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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
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Single time
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Environmental domain *

Terrestrial
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Freshwater
Miscellaneous information about the data, not captured elsewhere. From 193 species listed in the Annex I of the Birds Directive, we found data for 168 species through the species occurrence cubes generation. The 25 remaining species, using the GBIF Backbone Taxonomy, are:
- Subspecies that are not identified by the speciesKey in the JSON query (20 species; Accipiter gentilis, Accipiter nisus, Anser albifrons, Calidris alpina, Certhia brachydactyla, Columba palumbus, Dendrocopos major, Dendrocopos major, Ardea alba, Fringilla coelebs, Gelochelidon nilotica, Lagopus muta, Lagopus muta, Periparus ater, Perdix perdix, Perdix perdix, Phalacrocorax aristotelis, Lyrurus tetrix, Troglodytes troglodytes, Uria aalge). - Species from the Canary Islands (4 species; Columba bollii, Columba junoniae, Fringilla teydea, Saxicola dacotiae) or the Azores (1 species; Pyrrhula murina).

25 species were considered SYNONYMS by the GBIF Backbone Taxonomy, so we used the acceptedUsageKey that corresponds to the ACCEPTED scientific name by GBIF. Below the list of scientific names by the GBIF Backbone Taxonomy and in square brackets the name by the Birds Directive:
- Bonasa bonasia (Linnaeus, 1758) [Bonasa bonasia]
- Charadrius morinellus morinellus [Charadrius morinellus (Eudromias morinellus)]
- Cygnus bewickii Yarrell, 1830 [Cygnus bewickii (Cygnus columbianus bewickii)]
- Dendrocopos medius (Linnaeus, 1758) [Dendrocopos medius]
- Egretta alba alba [Egretta alba (Ardea alba)]
- Hieraaetus fasciatus (Vieillot, 1822) [Hieraaetus fasciatus]
- Hoplopterus spinosus Linnaeus, 1758 [Hoplopterus spinosus]
- Lagopus mutus helveticus [Lagopus mutus helveticus]
- Lagopus mutus pyrenaicus Hartert, 1921 [Lagopus mutus pyrenaicus]
- Larus audouinii Payraudeau, 1826 [Larus audouinii]
- Larus genei Brème, 1839 [Larus genei]
- Larus melanocephalus Temminck, 1820 [Larus melanocephalus]
- Larus minutus Pallas, 1776 [Larus minutus]
- Mergus albellus albellus [Mergus albellus (Mergellus albellus)]
- Nyctea scandiaca (Linnaeus, 1758) [Nyctea scandiaca]
- Parus ater cypriotes Dresser, 1888 [Parus ater cypriotes]
- Phalacrocorax pygmeus (Pallas, 1773) [Phalacrocorax pygmeus]
- Philomachus pugnax (Linnaeus, 1758) [Philomachus pugnax]
- Puffinus puffinus mauretanicus Lowe, 1921 [Puffinus puffinus mauretanicus (Puffinus mauretanicus)]
- Sterna albifrons Pallas, 1764 [Sterna albifrons]
- Sterna caspia Pallas, 1770 [Sterna caspia]
- Sterna sandvicensis Latham, 1787 [Sterna sandvicensis]
- Sylvia rueppelli Temminck, 1823 [Sylvia rueppelli]
- Tetrao tetrix tetrix [Tetrao tetrix tetrix]
- Uria aalge ibericus Bernis, 1948 [Uria aalge ibericus]

Note: We manually changed the acceptedUsageKey of two species due to inconsistencies with the match tool. The replaced acceptedUsageKey are:
- Cygnus columbianus (Ord, 1815) from 6178421(old) to 2498338 (new)
- Sternula albifrons (Pallas, 1764) from 7192406 (old) to 5789279 (new)