Habitats Directive Portuguese Report: Species 2007-2012

Study Extent

The geographic area considered for the original study was Mainland Portugal and Portuguese islands.

Sampling

Species and habitats data was collected from available published and unpublished sources.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

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.

Method steps

1. 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.

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.

1. Animalia
   rank: kingdom
2. Fungi
   rank: kingdom
3. Plantae
   rank: kingdom
4. Arthropoda
   rank: phylum
5. Ascomycota
   rank: phylum
6. Bryophyta
   rank: phylum
7. Chordata
   rank: phylum
8. Marchantiophyta
   rank: phylum
9. Mollusca
   rank: phylum
10. Tracheophyta
    rank: phylum
11. Actinopterygii
    rank: class
12. Amphibia
    rank: class
13. Bivalvia
    rank: class
14. Bryopsida
    rank: class
15. Cephalaspidomorphi
    rank: class
16. Gastropoda
    rank: class
17. Insecta
    rank: class
18. Jungermanniopsida
    rank: class
19. Lecanoromycetes
    rank: class
20. Liliopsida
    rank: class
21. Lycopodiopsida
    rank: class
22. Magnoliopsida
    rank: class
23. Mammalia
    rank: class
24. Polypodiopsida
    rank: class
25. Reptilia
    rank: class
26. Sphagnopsida
    rank: class
27. Anura
    rank: order
28. Apiales
    rank: order
29. Araneae
    rank: order
30. Artiodactyla
    rank: order
31. Asparagales
    rank: order
32. Asterales
    rank: order
33. Boraginales
    rank: order
34. Brassicales
    rank: order
35. Carnivora
    rank: order
36. Caryophyllales
    rank: order
37. Caudata
    rank: order
38. Celastrales
    rank: order
39. Cetacea
    rank: order
40. Chiroptera
    rank: order
41. Clupeiformes
    rank: order
42. Coleoptera
    rank: order
43. Cyatheales
    rank: order
44. Cypriniformes
    rank: order
45. Dicranales
    rank: order
46. Dipsacales
    rank: order
47. Ericales
    rank: order
48. Fabales
    rank: order
49. Fossombroniales
    rank: order
50. Gentianales
    rank: order
51. Hymenophyllales
    rank: order
52. Isoetales
    rank: order
53. Jungermanniales
    rank: order
54. Lamiales
    rank: order
55. Lecanorales
    rank: order
56. Lepidoptera
    rank: order
57. Lycopodiales
    rank: order
58. Malpighiales
    rank: order
59. Malvales
    rank: order
60. Mantodea
    rank: order
61. Odonata
    rank: order
62. Petromyzontiformes
    rank: order
63. Poales
    rank: order
64. Polypodiales
    rank: order
65. Pottiales
    rank: order
66. Rodentia
    rank: order
67. Rosales
    rank: order
68. Salmoniformes
    rank: order
69. Salviniales
    rank: order
70. Santalales
    rank: order
71. Saxifragales
    rank: order
72. Solanales
    rank: order
73. Soricomorpha
    rank: order
74. Sphagnales
    rank: order
75. Squamata
    rank: order
76. Stylommatophora
    rank: order
77. Testudines
    rank: order
78. Unionida
    rank: order
79. Alytidae
    rank: family
80. Amaryllidaceae
    rank: family
81. Apiaceae
    rank: family
82. Arionidae
    rank: family
83. Asparagaceae
    rank: family
84. Asphodelaceae
    rank: family
85. Aspleniaceae
    rank: family
86. Asteraceae
    rank: family
87. Balaenopteridae
    rank: family
88. Blechnaceae
    rank: family
89. Boraginaceae
    rank: family
90. Bovidae
    rank: family
91. Brassicaceae
    rank: family
92. Bruchiaceae
    rank: family
93. Bufonidae
    rank: family
94. Campanulaceae
    rank: family
95. Canidae
    rank: family
96. Caprifoliaceae
    rank: family
97. Caryophyllaceae
    rank: family
98. Celastraceae
    rank: family
99. Cerambycidae
    rank: family
100. Cheloniidae
     rank: family
101. Cistaceae
     rank: family
102. Cladoniaceae
     rank: family
103. Clupeidae
     rank: family
104. Cobitidae
     rank: family
105. Coenagrionidae
     rank: family
106. Colubridae
     rank: family
107. Convolvulaceae
     rank: family
108. Corduliidae
     rank: family
109. Crassulaceae
     rank: family
110. Cricetidae
     rank: family
111. Culcitaceae
     rank: family
112. Cyperaceae
     rank: family
113. Cyprinidae
     rank: family
114. Delphinidae
     rank: family
115. Dicranaceae
     rank: family
116. Emydidae
     rank: family
117. Erebidae
     rank: family
118. Ericaceae
     rank: family
119. Euphorbiaceae
     rank: family
120. Fabaceae
     rank: family
121. Felidae
     rank: family
122. Gentianaceae
     rank: family
123. Geoemydidae
     rank: family
124. Geomitridae
     rank: family
125. Gomphidae
     rank: family
126. Gymnomitriaceae
     rank: family
127. Herpestidae
     rank: family
128. Hylidae
     rank: family
129. Hymenophyllaceae
     rank: family
130. Hyperoodontidae
     rank: family
131. Iridaceae
     rank: family
132. Isoetaceae
     rank: family
133. Juncaceae
     rank: family
134. Kogiidae
     rank: family
135. Lacertidae
     rank: family
136. Lamiaceae
     rank: family
137. Lauriidae
     rank: family
138. Lucanidae
     rank: family
139. Lycopodiaceae
     rank: family
140. Macrothelidae
     rank: family
141. Mantidae
     rank: family
142. Margaritiferidae
     rank: family
143. Marsileaceae
     rank: family
144. Miniopteridae
     rank: family
145. Molossidae
     rank: family
146. Mustelidae
     rank: family
147. Nymphalidae
     rank: family
148. Oleaceae
     rank: family
149. Orchidaceae
     rank: family
150. Orobanchaceae
     rank: family
151. Pelobatidae
     rank: family
152. Petalophyllaceae
     rank: family
153. Petromyzontidae
     rank: family
154. Phocidae
     rank: family
155. Phocoenidae
     rank: family
156. Phyllodactylidae
     rank: family
157. Physeteridae
     rank: family
158. Plantaginaceae
     rank: family
159. Plumbaginaceae
     rank: family
160. Poaceae
     rank: family
161. Polygonaceae
     rank: family
162. Pottiaceae
     rank: family
163. Ranidae
     rank: family
164. Rhamnaceae
     rank: family
165. Rhinolophidae
     rank: family
166. Rosaceae
     rank: family
167. Salamandridae
     rank: family
168. Salicaceae
     rank: family
169. Salmonidae
     rank: family
170. Sapotaceae
     rank: family
171. Saxifragaceae
     rank: family
172. Scincidae
     rank: family
173. Scrophulariaceae
     rank: family
174. Sphagnaceae
     rank: family
175. Sphingidae
     rank: family
176. Talpidae
     rank: family
177. Thymelaeaceae
     rank: family
178. Unionidae
     rank: family
179. Vespertilionidae
     rank: family
180. Viperidae
     rank: family
181. Viscaceae
     rank: family
182. Viverridae
     rank: family
183. Alosa
     rank: genus
184. Alyssum
     rank: genus
185. Alytes
     rank: genus
186. Ammi
     rank: genus
187. Anaecypris
     rank: genus
188. Anarrhinum
     rank: genus
189. Anthyllis
     rank: genus
190. Antirrhinum
     rank: genus
191. Apium
     rank: genus
192. Apteromantis
     rank: genus
193. Arabis
     rank: genus
194. Arceuthobium
     rank: genus
195. Armeria
     rank: genus
196. Arnica
     rank: genus
197. Asphodelus
     rank: genus
198. Asplenium
     rank: genus
199. Avenula
     rank: genus
200. Azorina
     rank: genus
201. Balaenoptera
     rank: genus
202. Barbastella
     rank: genus
203. Barbus
     rank: genus
204. Bellevalia
     rank: genus
205. Biscutella
     rank: genus
206. Bruchia
     rank: genus
207. Bryoerythrophyllum
     rank: genus
208. Bufo
     rank: genus
209. Calendula
     rank: genus
210. Callimorpha
     rank: genus
211. Canis
     rank: genus
212. Capra
     rank: genus
213. Caretta
     rank: genus
214. Carex
     rank: genus
215. Caseolus
     rank: genus
216. Centaurea
     rank: genus
217. Cerambyx
     rank: genus
218. Chaenorhinum
     rank: genus
219. Chaerophyllum
     rank: genus
220. Chalcides
     rank: genus
221. Chioglossa
     rank: genus
222. Chondrostoma
     rank: genus
223. Cirsium
     rank: genus
224. Cistus
     rank: genus
225. Cladonia
     rank: genus
226. Cobitis
     rank: genus
227. Coenagrion
     rank: genus
228. Coluber
     rank: genus
229. Convolvulus
     rank: genus
230. Coronella
     rank: genus
231. Crepis
     rank: genus
232. Culcita
     rank: genus
233. Delphinus
     rank: genus
234. Dianthus
     rank: genus
235. Diplotaxis
     rank: genus
236. Discoglossus
     rank: genus
237. Discula
     rank: genus
238. Doronicum
     rank: genus
239. Dorycnium
     rank: genus
240. Dracaena
     rank: genus
241. Echium
     rank: genus
242. Emys
     rank: genus
243. Eptesicus
     rank: genus
244. Erica
     rank: genus
245. Eryngium
     rank: genus
246. Euphorbia
     rank: genus
247. Euphrasia
     rank: genus
248. Euphydryas
     rank: genus
249. Felis
     rank: genus
250. Festuca
     rank: genus
251. Frangula
     rank: genus
252. Galemys
     rank: genus
253. Genetta
     rank: genus
254. Gentiana
     rank: genus
255. Geomalacus
     rank: genus
256. Globicephala
     rank: genus
257. Gomphus
     rank: genus
258. Grampus
     rank: genus
259. Halimium
     rank: genus
260. Herniaria
     rank: genus
261. Herpestes
     rank: genus
262. Holcus
     rank: genus
263. Hyacinthoides
     rank: genus
264. Hyla
     rank: genus
265. Hyperoodon
     rank: genus
266. Hypsugo
     rank: genus
267. Iberis
     rank: genus
268. Iris
     rank: genus
269. Isoetes
     rank: genus
270. Jasione
     rank: genus
271. Jonopsidium
     rank: genus
272. Juncus
     rank: genus
273. Kogia
     rank: genus
274. Lacerta
     rank: genus
275. Lactuca
     rank: genus
276. Lampetra
     rank: genus
277. Leiostyla
     rank: genus
278. Leucobryum
     rank: genus
279. Leuzea
     rank: genus
280. Limonium
     rank: genus
281. Linaria
     rank: genus
282. Lotus
     rank: genus
283. Lucanus
     rank: genus
284. Lutra
     rank: genus
285. Lycopodiella
     rank: genus
286. Lycopodium
     rank: genus
287. Macromia
     rank: genus
288. Macrothele
     rank: genus
289. Malcolmia
     rank: genus
290. Margaritifera
     rank: genus
291. Marsilea
     rank: genus
292. Marsupella
     rank: genus
293. Martes
     rank: genus
294. Mauremys
     rank: genus
295. Maytenus
     rank: genus
296. Megaptera
     rank: genus
297. Melanoselinum
     rank: genus
298. Melilotus
     rank: genus
299. Mesoplodon
     rank: genus
300. Microtus
     rank: genus
301. Miniopterus
     rank: genus
302. Monachus
     rank: genus
303. Murbeckiella
     rank: genus
304. Musschia
     rank: genus
305. Mustela
     rank: genus
306. Myosotis
     rank: genus
307. Myotis
     rank: genus
308. Narcissus
     rank: genus
309. Nyctalus
     rank: genus
310. Oenanthe
     rank: genus
311. Omphalodes
     rank: genus
312. Ononis
     rank: genus
313. Orcinus
     rank: genus
314. Oxygastra
     rank: genus
315. Pelobates
     rank: genus
316. Petalophyllum
     rank: genus
317. Petromyzon
     rank: genus
318. Phagnalon
     rank: genus
319. Phocoena
     rank: genus
320. Physeter
     rank: genus
321. Picconia
     rank: genus
322. Picris
     rank: genus
323. Pipistrellus
     rank: genus
324. Plantago
     rank: genus
325. Plecotus
     rank: genus
326. Proserpinus
     rank: genus
327. Prunus
     rank: genus
328. Pseudarrhenatherum
     rank: genus
329. Pseudorca
     rank: genus
330. Rana
     rank: genus
331. Rhinolophus
     rank: genus
332. Rhynchosinapis
     rank: genus
333. Rumex
     rank: genus
334. Ruscus
     rank: genus
335. Rutilus
     rank: genus
336. Salix
     rank: genus
337. Salmo
     rank: genus
338. Sanicula
     rank: genus
339. Santolina
     rank: genus
340. Saxifraga
     rank: genus
341. Scabiosa
     rank: genus
342. Scilla
     rank: genus
343. Scrophularia
     rank: genus
344. Sedum
     rank: genus
345. Senecio
     rank: genus
346. Sibthorpia
     rank: genus
347. Sideroxylon
     rank: genus
348. Silene
     rank: genus
349. Spergularia
     rank: genus
350. Sphagnum
     rank: genus
351. Spiranthes
     rank: genus
352. Stenella
     rank: genus
353. Steno
     rank: genus
354. Tadarida
     rank: genus
355. Tarentola
     rank: genus
356. Teucrium
     rank: genus
357. Thorella
     rank: genus
358. Thymelaea
     rank: genus
359. Thymus
     rank: genus
360. Trichomanes
     rank: genus
361. Triturus
     rank: genus
362. Tuberaria
     rank: genus
363. Tursiops
     rank: genus
364. Ulex
     rank: genus
365. Unio
     rank: genus
366. Verbascum
     rank: genus
367. Veronica
     rank: genus
368. Vipera
     rank: genus
369. Woodwardia
     rank: genus
370. Ziphius
     rank: genus

Mainland Portugal and Portuguese islands.