Author: Tomé Neves
Keywords: Occurrence, Portugal, Macaronesia, Atlantic Ocean, Habitats, Flora, Fauna, Plants, Molluscs, Arthropods, Fish, Amphibians, Reptiles, Mammals, Habitats Directive, Natura 2000, Sites of Community Importance (SCIs), Special Areas of Conservations (SACs)

Habitats Directive Portuguese Report: Species 2007-2012

Glória Araújo^1, Tomé Neves^2

1 ICNF, , Portugal; 2 Instituto Superior de Agronomia, Lisboa, Portugal

Corresponding author(s): Glória Araújo, Tomé Neves

Received {date}; Revised {date}; Accepted {date}; Published {date}

Citation: Combination of authors, year of data paper publication (in parentheses), Title, Journal Name, Volume, Issue number (in parentheses), and doi of the data paper.

Resource Citation

Araújo G, Neves T (2021): Habitats Directive Portuguese Report: Species 2007-2012. v1. No organization. Dataset/Occurrence. http://localhost:8080/ipt-2.4.2/resource?r=especies_diretiva_habitats_07_12&amp;v=1.0

Abstract

This dataset is based on a National Report on the progress and implementation of the Habitats Directive in Portugal, concerning the 2007-2012 period. It originates from a project performed periodically (every 6 years) that aims to permit an adequate assessment of the progress, via the Natura 2000 Network, towards the goals of the Habitats Directive. 
This national reports describes conservation status for flora and fauna species in three biogeographic regions (Atlantic, Macaronesian and Mediterranean) and two marine regions (Atlantic and Macaronesian). It contains occurrence data for fauna and flora belonging to 3 kingdoms, 7 phyla, 16 classes, 52 orders, 104 families, 188 genera and 271 species.

Keywords: Occurrence, Portugal, Macaronesia, Atlantic Ocean, Habitats, Flora, Fauna, Plants, Molluscs, Arthropods, Fish, Amphibians, Reptiles, Mammals, Habitats Directive, Natura 2000, Sites of Community Importance (SCIs), Special Areas of Conservations (SACs)

Project details

Project title: Distribuição de espécies (fauna e flora) - 2007-2012
Personnel: Teresa Pimenta
Funding: This work was co-fund by ICNF, I.P. and the European Union, through the Environment Operational Programme (application 1.1/00021– Documentos Estruturantes da Conservação da Natureza e da Biodiversidade).

The preparation of this resource for publication through GBIF was supported by Project PORBIOTA—Portuguese E-Infrastructure for Information and Research on Biodiversity (POCI-01-0145-FEDER-022127), under the Operational Thematic Program for Competitiveness and Internationalization (POCI), under the PORTUGAL 2020 Partnership Agreement, through the European Regional Development Fund (FEDER) and FCT.

Data published through GBIF: http://ipt.gbif.pt/ipt/resource?r=especies_diretiva_habitats_07_12

Taxonomic coverage

General taxonomic coverage description: This dataset contains occurrence data for fauna and flora belonging to 3 kingdoms, 7 phyla, 16 classes, 52 orders, 104 families, 188 genera and 271 species.
Taxonomic ranks
Kingdom: Animalia, Fungi, Plantae
Phylum: Arthropoda, Ascomycota, Bryophyta, Chordata, Marchantiophyta, Mollusca, Tracheophyta
Class: Actinopterygii, Amphibia, Bivalvia, Bryopsida, Cephalaspidomorphi, Gastropoda, Insecta, Jungermanniopsida, Lecanoromycetes, Liliopsida, Lycopodiopsida, Magnoliopsida, Mammalia, Polypodiopsida, Reptilia, Sphagnopsida
Order: Anura, Apiales, Araneae, Artiodactyla, Asparagales, Asterales, Boraginales, Brassicales, Carnivora, Caryophyllales, Caudata, Celastrales, Cetacea, Chiroptera, Clupeiformes, Coleoptera, Cyatheales, Cypriniformes, Dicranales, Dipsacales, Ericales, Fabales, Fossombroniales, Gentianales, Hymenophyllales, Isoetales, Jungermanniales, Lamiales, Lecanorales, Lepidoptera, Lycopodiales, Malpighiales, Malvales, Mantodea, Odonata, Petromyzontiformes, Poales, Polypodiales, Pottiales, Rodentia, Rosales, Salmoniformes, Salviniales, Santalales, Saxifragales, Solanales, Soricomorpha, Sphagnales, Squamata, Stylommatophora, Testudines, Unionida
Family: Alytidae, Amaryllidaceae, Apiaceae, Arionidae, Asparagaceae, Asphodelaceae, Aspleniaceae, Asteraceae, Balaenopteridae, Blechnaceae, Boraginaceae, Bovidae, Brassicaceae, Bruchiaceae, Bufonidae, Campanulaceae, Canidae, Caprifoliaceae, Caryophyllaceae, Celastraceae, Cerambycidae, Cheloniidae, Cistaceae, Cladoniaceae, Clupeidae, Cobitidae, Coenagrionidae, Colubridae, Convolvulaceae, Corduliidae, Crassulaceae, Cricetidae, Culcitaceae, Cyperaceae, Cyprinidae, Delphinidae, Dicranaceae, Emydidae, Erebidae, Ericaceae, Euphorbiaceae, Fabaceae, Felidae, Gentianaceae, Geoemydidae, Geomitridae, Gomphidae, Gymnomitriaceae, Herpestidae, Hylidae, Hymenophyllaceae, Hyperoodontidae, Iridaceae, Isoetaceae, Juncaceae, Kogiidae, Lacertidae, Lamiaceae, Lauriidae, Lucanidae, Lycopodiaceae, Macrothelidae, Mantidae, Margaritiferidae, Marsileaceae, Miniopteridae, Molossidae, Mustelidae, Nymphalidae, Oleaceae, Orchidaceae, Orobanchaceae, Pelobatidae, Petalophyllaceae, Petromyzontidae, Phocidae, Phocoenidae, Phyllodactylidae, Physeteridae, Plantaginaceae, Plumbaginaceae, Poaceae, Polygonaceae, Pottiaceae, Ranidae, Rhamnaceae, Rhinolophidae, Rosaceae, Salamandridae, Salicaceae, Salmonidae, Sapotaceae, Saxifragaceae, Scincidae, Scrophulariaceae, Sphagnaceae, Sphingidae, Talpidae, Thymelaeaceae, Unionidae, Vespertilionidae, Viperidae, Viscaceae, Viverridae
Genus: Alosa, Alyssum, Alytes, Ammi, Anaecypris, Anarrhinum, Anthyllis, Antirrhinum, Apium, Apteromantis, Arabis, Arceuthobium, Armeria, Arnica, Asphodelus, Asplenium, Avenula, Azorina, Balaenoptera, Barbastella, Barbus, Bellevalia, Biscutella, Bruchia, Bryoerythrophyllum, Bufo, Calendula, Callimorpha, Canis, Capra, Caretta, Carex, Caseolus, Centaurea, Cerambyx, Chaenorhinum, Chaerophyllum, Chalcides, Chioglossa, Chondrostoma, Cirsium, Cistus, Cladonia, Cobitis, Coenagrion, Coluber, Convolvulus, Coronella, Crepis, Culcita, Delphinus, Dianthus, Diplotaxis, Discoglossus, Discula, Doronicum, Dorycnium, Dracaena, Echium, Emys, Eptesicus, Erica, Eryngium, Euphorbia, Euphrasia, Euphydryas, Felis, Festuca, Frangula, Galemys, Genetta, Gentiana, Geomalacus, Globicephala, Gomphus, Grampus, Halimium, Herniaria, Herpestes, Holcus, Hyacinthoides, Hyla, Hyperoodon, Hypsugo, Iberis, Iris, Isoetes, Jasione, Jonopsidium, Juncus, Kogia, Lacerta, Lactuca, Lampetra, Leiostyla, Leucobryum, Leuzea, Limonium, Linaria, Lotus, Lucanus, Lutra, Lycopodiella, Lycopodium, Macromia, Macrothele, Malcolmia, Margaritifera, Marsilea, Marsupella, Martes, Mauremys, Maytenus, Megaptera, Melanoselinum, Melilotus, Mesoplodon, Microtus, Miniopterus, Monachus, Murbeckiella, Musschia, Mustela, Myosotis, Myotis, Narcissus, Nyctalus, Oenanthe, Omphalodes, Ononis, Orcinus, Oxygastra, Pelobates, Petalophyllum, Petromyzon, Phagnalon, Phocoena, Physeter, Picconia, Picris, Pipistrellus, Plantago, Plecotus, Proserpinus, Prunus, Pseudarrhenatherum, Pseudorca, Rana, Rhinolophus, Rhynchosinapis, Rumex, Ruscus, Rutilus, Salix, Salmo, Sanicula, Santolina, Saxifraga, Scabiosa, Scilla, Scrophularia, Sedum, Senecio, Sibthorpia, Sideroxylon, Silene, Spergularia, Sphagnum, Spiranthes, Stenella, Steno, Tadarida, Tarentola, Teucrium, Thorella, Thymelaea, Thymus, Trichomanes, Triturus, Tuberaria, Tursiops, Ulex, Unio, Verbascum, Veronica, Vipera, Woodwardia, Ziphius

Spatial coverage

General spatial coverage: Mainland Portugal and Portuguese islands.
Coordinates: 29°13'30''N and 42°7'8.4''N Latitude; 33°6'21.6''W and 6°12'36''W Longitude 

Temporal coverage: 1975 - 2012

Methods

Method step description: Preparation of the dataset for GBIF publication used as source the geographic layer in shapefile format. The data layer was a vector layer containing polygons with various sizes. The following steps were performed:
- Intersected the layer with the EEA reference grid (10km);
- Created a joinID column with the row numbers;
- Calculated the WKTs for each polygon in the original (EPSG:3035) projection;
- Calculated the centroids for each polygon in both WGS84 and the original (EPSG:3035) projection.;
- Calculated the distance of the centroids to the farthest point in the envolving polygon (coordinate accuracy) in both WGS84 and the original (EPSG:3035) projection.;
- Used the centroids (in the original projection) with intersect to get the marine regions from (Marine regions (ETRS) 10x10km grid) http://cdr.eionet.europa.eu/help/habitats_art17/Reporting2019 ;
- Produced another shapefile by clipping it with the dissolved biogeographic regions obtained from BiogeoRegions2016_shapefile.zip https://www.eea.europa.eu/data-and-maps/data/biogeographical-regions-europe-3 ;
- Calculated the inside centroids of the clipped layer;
- Used the inside centroids (with intersect) to get the biogeographical regions from the previously mentioned layer;
- Joined the results obtained from the clipped layer to the original layer via the joinID;
- For polygons that possessed both a marine a biogeographical region, the appropriate one was chosen based on the species on the polygon and the PT_species_reports.xml obtained from http://cdr.eionet.europa.eu/pt/eu/art17/envuc2hfw/index_html?&page=3 (which I converted into a csv). As such, similarly placed polygons can have different regions.;
- All species/regions combos were cross referenced with the XML, as if the species did not have the corresponding region, it was changed to the correct match (happened in frontier zones)1;
- Used the WGS84 centroids to extract the locations from the CAOP2020;
- exported to csv and reinterpreted attributes matching to DwC standard terms.
Study extent description: The geographic area considered for the original study was Mainland Portugal and Portuguese islands.
Sampling description: Species and habitats data was collected from available published and unpublished sources. Expert opinion was also used as a source of information. Data for each species and habitats was organised in specific data sheets that combine different ecological and biological parameters.
Quality control description: All initial data was inserted in a specific relational database built specifically for the project, which implemented several quality control methods. In the preparation of the dataset for GBIF publication, data consistency was verified using cluster algorithms using OpenRefine.

Datasets

Dataset description
Object name: Darwin Core Archive Habitats Directive Portuguese Report: Species 2007-2012
Character encoding: UTF-8
Format name: Darwin Core Archive format
Format version: 1.0
Distribution: http://ipt.gbif.pt/ipt/archive.do?r=especies_diretiva_habitats_07_12
Publication date of data: 2021-09-03
Language: English
Licences of use: Creative Commons Attribution (CC-BY) 4.0 License

External datasets

Dataset description
Object name: WMS
Character encoding: UTF-8
Format name: Raster
Distribution: http://si.icnf.pt/wms/especies_diretiva_habitats_07_12

Dataset description
Object name: WFS
Character encoding: UTF-8
Format name: Shapefile
Distribution: http://si.icnf.pt/wfs/especies_diretiva_habitats_07_12

Dataset description
Object name: National Report Resources
Character encoding: Various
Format name: Various
Distribution: http://cdr.eionet.europa.eu/pt/eu/art17/envuc2hfw

Metadata language: English
Date of metadata creation: 2021-08-20
Hierarchy level: Dataset