HiDaFernPT: Historical data of spore availability for 121 fern and lycopod taxa in Portugal (1926 – 2013)
Citation
Timóteo S, Heleno R, Covelo F, Santos J, Lopes P, Gouveia A C, Matos A, Salgado A, Girão da Cruz M T, Farminhão J, Horta M, Barreto G, Marques A V, Craveiro L, Pinto P, Santos M, Nunes B, Barreiro M, Dias A, Rodrigues G, Esteves L, Wanderley M, Santos I, Artiaga J P, Veríssimo J, Vilhena I, Moniz L, Leão A, Couras M, Mendes S B, Nereu M, Silva A M D D, Sales F, Gonçalves M T, Coutinho A, Freitas H, Silva J S, Ramos J, Marchante E, Costa J M (2024). HiDaFernPT: Historical data of spore availability for 121 fern and lycopod taxa in Portugal (1926 – 2013). Version 1.2. Jardim Botânico da Universidade de Coimbra. Occurrence dataset https://doi.org/10.15468/6gp2ha accessed via GBIF.org on 2024-12-01.Description
This dataset provides information on the exact day and site where spores of 121 taxa of ferns and lycopos were collected for the Index Seminum (seed exchange catalogue) of the Botanic Garden of the University of Coimbra, between 1926 and 2013. Spores were collected from spontaneous and cultivated individuals across Portugal, including both native and introduced taxa. The database consists of 3,383 curated records with information on the species, or infraspecific taxa (including authority), and the day and site where spores were collected. All records are georeferenced and provided with a confidence interval for the collection site.Sampling Description
Study Extent
Data covers mainland Portugal.Sampling
This dataset includes the records of ferns and lycopods spores collected since 1926 by the staff of the Botanic Garden of the University of Coimbra. It includes the date, location, and species or infraspecific taxa for the spores collected every year to integrate the Botanic Garden of the University of Coimbra Index Seminum.Quality Control
Intermediate quality checks at data entry, taxonomic harmonization and georeferencing stages to detect and correct errors.Method steps
- Taxonomic harmonization: - initial verification by botanist from the Herbarium of the University of Coimbra, to check small typos and authorities misspellings; - harmonization through the Global Name Resolver using function gnr_resolve from the R (R Core Team 2023) package taxixe 0.9.9 (Chamberlain & Szöcs 2013, Chamberlain et al. 2020), against the Global Biodiversity Information Facility - GBIF backbone, accessed on 2023-03-01; - species classification as native or introduced to Portugal based on the World Checklist of Vascular Plants - WCVP (Govaerts et al. 2021), using function wcvp_distribution from the R package rWCVP (Brown et al. 2023), accessed on 2023-06-28. The data set includes the original name, and the harmonized taxonomy based on GBIF and WCVP. Georeferencing protocol: - original record of collection localities clustered based on textual description using OpenRefine, followed by manual inspection; - locations georeferenced with point-radius georeferencing method (Chapman & Wieczorek 2020, Zermoglio et al. 2020), with geographic coordinates, and corresponding confidence intervals, obtained with Maps.ie (Maps.ie 2023), and uncertainty obtained with Georeferencing Calculator (Bloom et al. 2020; Wieczorek et al. 2021); - administrative levels obatined with Google Geocoding API through the Reverse Geocoding Service (Google 2022); - elevation retrieved with Google Elevation API.
Taxonomic Coverages
Plants identified to species or infraspecific level.
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Plantaerank: kingdom
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Tracheophytarank: phylum
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Lycopodiopsidarank: class
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Polypodiopsidarank: class
Geographic Coverages
Mainland Portugal
Bibliographic Citations
- R Core Team. (2023). R: A language and environment for statistical computing. -
- Chamberlain, S.A. & Szöcs, E. (2013). taxize: taxonomic search and retrieval in R. F1000Research. - 10.12688/f1000research.2-191.v2
- Chamberlain, S., Szoecs, E., Foster, Z., Arendsee, Z., Boettiger, C., Ram, K., Bartomeus, I., Baumgartner, J., O’Donnell, J. & Oksanen, J. (2020). taxize: Taxonomic information from around the web. R package version 0.9, 92. -
- Govaerts, R., Nic Lughadha, E., Black, N., Turner, R. & Paton, A. (2021). The World Checklist of Vascular Plants, a continuously updated resource for exploring global plant diversity. Scientific Data 8, 215. - 10.1038/s41597-021-00997-6
- Brown, M.J.M., Walker, B.E., Black, N., Govaerts, R.H.A., Ondo, I., Turner, R. & Nic Lughadha, E. (2023). rWCVP: a companion R package for the World Checklist of Vascular Plants. New Phytologist, 1–10. - 10.1111/nph.18919
- Chapman, A. D. & Wieczorek, J. R. (2020). Georeferencing best practices. Version 1.0. - 10.15468/doc-gg7h-s853
- Zermoglio P.F., Chapman A.D., Wieczorek J.R., Luna M.C. & Bloom D.A. (2020). Georeferencing Quick Reference Guide. Copenhagen: GBIF Secretariat - 10.35035/e09p-h128
- Maps.ie. (2023). https://www.maps.ie/draw-radius-circle-map. Accessed on 2023-03-20. -
- Bloom, D. A., Wieczorek, J. R. & Zermoglio, P. F. (2020). Georeferencing Calculator Manual. Copenhagen: GBIF Secretariat. Version 1.0. - 10.35035/gdwq-3v93
- Wieczorek, C. & Wieczorek, J. (2020). Georeferencing Calculator; http://georeferencing.org/georefcalculator/gc.html. Accessed on 2022-08-29, 2021. -
- Google. (2022). Google Geocoding API https://developers.google.com/maps/documentation/geocoding/start. Accessed on 2022-08-29. -
Contacts
Sérgio Timóteooriginator
position: Researcher
Centre for Functional Ecology, Associate Laboratory TERRA, Department of Life Sciences, University of Coimbra
Calçada Martim de Freitas, 3000-456 Coimbra
Coimbra
3000-456
PT
email: sergio.timoteo@uc.pt
userId: https://orcid.org/0000-0003-2417-3259
Ruben Heleno
originator
position: Professor
Centre for Functional Ecology, Associate Laboratory TERRA, Department of Life Sciences, University of Coimbra
Calçada Martins de Freitas
Coimbra
3000-456
PT
email: rheleno@uc.pt
userId: https://orcid.org/0000-0002-4808-4907
Filipe Covelo
originator
position: Collection Manager
Centre for Functional Ecology, Associate Laboratory TERRA, Department of Life Sciences, University of Coimbra
Calçada Martins de Freitas
Coimbra
3000-456
PT
email: fcovelo@uc.pt
userId: https://orcid.org/0000-0003-0432-2843
Joaquim Santos
originator
position: Collection Manager
Centre for Functional Ecology, Associate Laboratory TERRA, Department of Life Sciences, University of Coimbra
Calçada Martins de Freitas
Coimbra
3000-456
PT
email: joaquimsantos@gmail.com
userId: https://orcid.org/0000-0002-2160-4968
Pedro Lopes
originator
position: Technician
Centre for Functional Ecology, Associate Laboratory TERRA, Department of Life Sciences, University of Coimbra
Calçada Martins de Freitas
Coimbra
3000-456
PT
email: pedro.lopes275@gmail.com
userId: https://orcid.org/0000-0002-5078-0602
António Carmo Gouveia
originator
position: Researcher
Centre for Functional Ecology, Associate Laboratory TERRA, Department of Life Sciences, University of Coimbra
Calçada Martins de Freitas
Coimbra
3000-456
PT
email: gouveia.ac@uc.pt
userId: https://orcid.org/0000-0002-7175-0365
Arménio Matos
originator
position: Gardener
Botanic Garden of the University of Coimbra, University of Coimbra
Calçada Martins de Freitas
Coimbra
3000-456
PT
Agostinho Salgado
originator
position: Gardener
Botanic Garden of the University of Coimbra, University of Coimbra
Calçada Martins de Freitas
Coimbra
3000-456
PT
Maria Teresa Girão da Cruz
originator
position: Director
Botanic Garden of the University of Coimbra, University of Coimbra
Calçada Martins de Freitas
Coimbra
3000-456
PT
email: teresa.girao@uc.pt
userId: https://orcid.org/0000-0003-2625-2567
João Farminhão
originator
position: Researcher
Centre for Functional Ecology, Associate Laboratory TERRA, Department of Life Sciences, University of Coimbra
Calçada Martins de Freitas
Coimbra
3000-456
PT
email: joao.farminhao@uc.pt
userId: https://orcid.org/0000-0002-8811-9895
Marta Horta
originator
position: BSc Student
Centre for Functional Ecology, Associate Laboratory TERRA, Department of Life Sciences, University of Coimbra
Calçada Martins de Freitas
Coimbra
3000-456
PT
email: martahortauc@gmail.com
Guilherme Barreto
originator
position: BSc Student
Centre for Functional Ecology, Associate Laboratory TERRA, Department of Life Sciences, University of Coimbra
Calçada Martim de Freitas
Coimbra
3000-456
email: guilherme.barreto@live.com.pt
userId: https://orcid.org/0000-0002-6226-0567
Ana V. Marques
originator
position: BSc Student
Centre for Functional Ecology, Associate Laboratory TERRA, Department of Life Sciences, University of Coimbra
Calçada Martim de Freitas
Coimbra
3000-456
PT
email: anamarques110301@gmail.com
Leonardo Craveiro
originator
position: BSc Student
Centre for Functional Ecology, Associate Laboratory TERRA, Department of Life Sciences, University of Coimbra
Calçada Martim de Freitas
Coimbra
3000-456
PT
email: leonardocraveiro1@gmail.com
Patrícia Pinto
originator
position: BSc Student
Centre for Functional Ecology, Associate Laboratory TERRA, Department of Life Sciences, University of Coimbra
Calçada Martim de Freitas
Coimbra
3000-456
PT
email: pinto.tita@hotmail.com
Matilde Santos
originator
position: BSc Student
Centre for Functional Ecology, Associate Laboratory TERRA, Department of Life Sciences, University of Coimbra
Calçada Martim de Freitas
Coimbra
3000-456
PT
email: matildebsantos@outlook.pt
Bárbara Nunes
originator
position: BSc Student
Centre for Functional Ecology, Associate Laboratory TERRA, Department of Life Sciences, University of Coimbra
Calçada Martim de Freitas
Coimbra
3000-456
PT
email: bnunes1@outlook.pt
Margarida Barreiro
originator
position: BSc Student
Centre for Functional Ecology, Associate Laboratory TERRA, Department of Life Sciences, University of Coimbra
Calçada Martim de Freitas
Coimbra
3000-456
PT
email: margaridaferreirabarreiro@gmail.com
André Dias
originator
position: BSc Student
Centre for Functional Ecology, Associate Laboratory TERRA, Department of Life Sciences, University of Coimbra
Calçada Martim de Freitas
Coimbra
3000-456
PT
email: abacalhaudias@gmail.com
Gabriel Rodrigues
originator
position: BSc Student
Centre for Functional Ecology, Associate Laboratory TERRA, Department of Life Sciences, University of Coimbra
Calçada Martim de Freitas
Coimbra
3000-456
PT
email: gabrielsamora.rodrigues@gmail.com
Leonor Esteves
originator
position: BSc Student
Centre for Functional Ecology, Associate Laboratory TERRA, Department of Life Sciences, University of Coimbra
Calçada Martim de Freitas
Coimbra
3000-456
PT
email: estevesleonor5@gmail.com
Marina Wanderley
originator
position: BSc Student
Centre for Functional Ecology, Associate Laboratory TERRA, Department of Life Sciences, University of Coimbra
Calçada Martim de Freitas
Coimbra
3000-456
PT
email: marinawander1@gmail.com
Inês Santos
originator
position: BSc Student
Centre for Functional Ecology, Associate Laboratory TERRA, Department of Life Sciences, University of Coimbra
Calçada Martim de Freitas
Coimbra
3000-456
PT
email: ines2705santos@gmail.com
José Pedro Artiaga
originator
position: BSc Student
Centre for Functional Ecology, Associate Laboratory TERRA, Department of Life Sciences, University of Coimbra
Calçada Martim de Freitas
Coimbra
3000-456
PT
email: josepedroartiaga@gmail.com
João Veríssimo
originator
position: BSc Student
Centre for Functional Ecology, Associate Laboratory TERRA, Department of Life Sciences, University of Coimbra
Calçada Martim de Freitas
Coimbra
3000-456
PT
email: jfm.verissimo02@gmail.com
Inês Vilhena
originator
position: BSc Student
Centre for Functional Ecology, Associate Laboratory TERRA, Department of Life Sciences, University of Coimbra
Calçada Martim de Freitas
Coimbra
3000-456
PT
email: inesvilhena2002@gmail.com
Lucas Moniz
originator
position: BSc Student
Centre for Functional Ecology, Associate Laboratory TERRA, Department of Life Sciences, University of Coimbra
Calçada Martim de Freitas
Coimbra
3000-456
PT
email: inesvilhena2002@gmail.com
Arthur Leão
originator
position: BSc Student
Centre for Functional Ecology, Associate Laboratory TERRA, Department of Life Sciences, University of Coimbra
Calçada Martim de Freitas
Coimbra
3000-456
PT
email: arthurmmarti@gmail.com
Marta Couras
originator
position: BSc Student
Centre for Functional Ecology, Associate Laboratory TERRA, Department of Life Sciences, University of Coimbra
Calçada Martim de Freitas
Coimbra
3000-456
PT
email: cunha.alexandra2021@gmail.com
Sara Beatriz Mendes
originator
position: PhD Student
Centre for Functional Ecology, Associate Laboratory TERRA, Department of Life Sciences, University of Coimbra
Calçada Martim de Freitas
Coimbra
3000-456
PT
email: sarabmmendes@gmail.com
userId: https://orcid.org/0000-0002-3149-9743
Mauro Nereu
originator
position: PhD Student
Centre for Functional Ecology, Associate Laboratory TERRA, Department of Life Sciences, University of Coimbra
Calçada Martim de Freitas
Coimbra
3000-456
PT
email: maurogpn21@gmail.com
userId: https://orcid.org/0000-0001-7484-1177
Ana Margarida Dias da Silva
originator
position: Technician
Center for the History of Society and Culture (CHSC-UC)
Calçada Martim de Freitas
Coimbra
3000-456
PT
email: anamargarida.silva@uc.pt
userId: https://orcid.org/0000-0003-1247-8346
Fátima Sales
originator
position: Professor
Centre for Functional Ecology, Associate Laboratory TERRA, Department of Life Sciences, University of Coimbra
Calçada Martim de Freitas
Coimbra
3000-456
PT
email: fsales@bot.uc.pt
userId: https://orcid.org/0000-0003-2876-0610
Maria Teresa Gonçalves
originator
position: Professor
Centre for Functional Ecology, Associate Laboratory TERRA, Department of Life Sciences, University of Coimbra
Calçada Martim de Freitas
Coimbra
3000-456
PT
email: mtgoncal@bot.uc.pt
userId: https://orcid.org/0000-0002-3277-5615
António Coutinho
originator
position: Professor
Centre for Functional Ecology, Associate Laboratory TERRA, Department of Life Sciences, University of Coimbra
Calçada Martim de Freitas
Coimbra
3000-292
PT
email: cafe@bot.uc.pt
userId: https://orcid.org/0000-0002-5371-6411
Helena Freitas
originator
position: Professor
Centre for Functional Ecology, Associate Laboratory TERRA, Department of Life Sciences, University of Coimbra
Calçada Martim de Freitas
Coimbra
3000-292
PT
email: hfreitas@ci.uc.pt
userId: https://orcid.org/0000-0002-1907-9615
Joaquim S. Silva
originator
position: Professor
Escola Superior Agrária, Instituto Politécnico de Coimbra
Bencanta
Coimbra
3045-601
PT
email: jss@esac.pt
userId: https://orcid.org/0000-0001-6604-6878
Jaime Ramos
originator
position: Professor
MARE - Marine and Environmental Sciences Centre / ARNET – Aquatic Research Network, Department of Life Sciences, University of Coimbra
Coimbra
3004-517
PT
email: jramos@uc.pt
userId: https://orcid.org/0000-0002-9533-987X
Elizabete Marchante
originator
position: Researcher
Centre for Functional Ecology, Associate Laboratory TERRA, Department of Life Sciences, University of Coimbra
Calçada Martim de Freitas
Coimbra
3000-456
PT
email: elizabete.marchante@gmail.com
userId: https://orcid.org/0000-0003-1303-7489
José Miguel Costa
originator
position: Technician
Centre for Functional Ecology, Associate Laboratory TERRA, Department of Life Sciences, University of Coimbra
Calçada Martins de Freitas
Coimbra
3000-456
PT
email: jmgncosta@gmail.com
userId: https://orcid.org/0000-0002-4991-7122
Sérgio Timóteo
metadata author
position: Researcher
Centre for Functional Ecology, Associate Laboratory TERRA, Department of Life Sciences, University of Coimbra
Calçada Martim de Freitas
Coimbra
3000-456
PT
email: sergio.timoteo@uc.pt
userId: https://orcid.org/0000-0003-2417-3259
Ruben Heleno
metadata author
position: Professor
Centre for Functional Ecology, Associate Laboratory TERRA, Department of Life Sciences, University of Coimbra
Calçada Martim de Freitas
Coimbra
3000-456
email: rheleno@uc.pt
userId: https://orcid.org/0000-0002-4808-4907
Filipe Covelo
metadata author
position: Collection Manager
Centre for Functional Ecology, Associate Laboratory TERRA, Department of Life Sciences, University of Coimbra
Calçada Martin de Freitas
Coimbra
3000-456
PT
email: fcovelo@uc.pt
userId: https://orcid.org/0000-0003-0432-2843
Joaquim Santos
metadata author
position: Collection Manager
Centre for Functional Ecology, Associate Laboratory TERRA, Department of Life Sciences, University of Coimbra
Calçada Martin de Freitas
Coimbra
3000-456
PT
email: joaquimsantos@gmail.com
userId: https://orcid.org/0000-0002-2160-4968
Sérgio Timóteo
user
position: Researcher
Centre for Functional Ecology, Associate Laboratory TERRA, Department of Life Sciences, University of Coimbra
email: sergio.timoteo@uc.pt
Sérgio Timóteo
administrative point of contact
position: Researcher
Centre for Functional Ecology, Associate Laboratory TERRA, Department of Life Sciences, University of Coimbra
Calçada Martim de Freitas, 3000-456 Coimbra
Coimbra
3000-456
PT
email: sergio.timoteo@uc.pt
userId: https://orcid.org/0000-0003-2417-3259
Ruben Heleno
administrative point of contact
position: Professor
Centre for Functional Ecology, Associate Laboratory TERRA, Department of Life Sciences, University of Coimbra
Calçada Martim de Freitas, 3000-456 Coimbra
Coimbra
3000-456
PT
email: rheleno@uc.pt
userId: https://orcid.org/0000-0002-4808-4907