Geohistorical plants occurrences database

Morgane Claudel1, Emilie Lerigoleur1, Cécile Brun2, Sylvie Guillerme1, Emilie LERIGOLEUR1, GBIF France3

1 UMR 5602 Géographie de l’environnement (CNRS/Université Toulouse 2), 5 Allées Antonio Machado, 31058, TOULOUSE, France; 2 Université de Nantes, 5 Allées Antonio Machado, 31058, TOULOUSE, France; 3 GBIF France, , France

Corresponding author(s): Morgane Claudel (claudelmorgane@orange.fr)Emilie Lerigoleur (emilie.lerigoleur@univ-tlse2.fr)Cécile Brun (cecile.brun@univ-tlse2.fr)Sylvie Guillerme (sylvie.guillerme@univ-tlse2.fr)

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

Claudel M, Lerigoleur E, Brun C, Guillerme S (2022): Geohistorical plants occurrences database. v1.5. UMR 5602 Géographie de l’environnement (CNRS/Université Toulouse 2). Dataset/Occurrence. https://ipt.gbif.fr/resource?r=ei2p_exotic_plants_geohistorical_occurrences_database&v=1.5

Abstract

The data file contains occurrence data based on historical observations and records between 1651 and 2004. Ten plant species have been studied : Alnus incana (L.) Moench, 1794 ; Buddleja davidii Franch., 1887 ; Castanea sativa Mill., 1798 ; Helianthus tuberosus L., 1753 ; Impatiens glandulifera Royle, 1833 ; Prunus cerasifera Ehrh., 1784 ; Prunus laurocerasus L., 1753 ;  Reynoutria japonica Houtt., 1777 ; Robinia pseudoacacia L., 1753 ; and Spiraea japonica L.f., 1782. The data file is the result of a geo-historical study conducted over five months on the invasive plants species's introduction and distribution in Occitania (France), carried out within the framework of the EI2P-VALEEBEE project (Invasive species and pollinators, between constraints and potentials). Historical sources have been consulted during 2020 in order to find the oldest elements about the ten species. Each data corresponds to an historical observation or mention on one of the ten species of the study mainly on Metropolitan French territory since their introduction. Without an historical analysis, it is difficult to understand the current local distribution dynamics of invasive plant species, especially when some of them have been introduced on Metropolitan French territory for several centuries. All the interest of these occurrence data is to bring an historical depth allowing us to apprehend the local distribution of the ten species of the study over time. This can be allowed thanks to the record of several elements on their places of introduction, the comments from authors and observers on their abundance, and elements on the historical context of introduction. More generally, this historical data file is part of a multidisciplinary approach proposed by the members of EI2P project whose objective is to better take into account the ecological socio-cultural and economic issues raised by the issue of invasive alien plants.
This work was endorsed by the CNRS/INEE Zone Atelier Pyrénées Garonne (ZA PYGAR). The Zones Ateliers network (RZA) is recognized by ALLENVI, as an eLTER (European Long-Term Ecological Research).
A data paper explains precisely this dataset:
Claudel M, Lerigoleur E, Brun C, Guillerme S (2022) Geohistorical dataset of ten plant species introduced into Occitania (France). Biodiversity Data Journal 10: e76283. https://doi.org/10.3897/BDJ.10.e76283

Keywords: Occurrence, Observation, invasive species, introduced species, plants, Alnus incana (L.) Moench, 1794, Buddleja davidii Franch., 1887, Castanea sativa Mill., 1798, Helianthus tuberosus L., 1753, Impatiens glandulifera Royle, 1833, Prunus cerasifera Ehrh., 1784, Prunus laurocerasus L., 1753, Reynoutria japonica Houtt., 1777, Robinia pseudoacacia L., 1753, Spiraea japonica L.f., 1782, Europe, 17th century, 18th century, 19th century, 20th century, 21st century, Historical geography, Historical ecology, Botany, Occurrence

Project details

Project title: EI2P - Espèces invasives et pollinisateurs, entre contraintes et potentiels | VALEEBEE - VALorisation des Espèces exotiques Envahissantes et Abeilles
Personnel: Guillerme Sylvie
Funding: Région Occitanie - Appel à projets Recherche et Société(s) 2019 | Maison des Sciences de l'Homme et de la Société de Toulouse (MSH-T) APEX 2020
Study area descriptions/descriptor: Geographic coverage: vallée de l’Oussouet (Hautes-Pyrénées) and vallée de la Pique (Haute-Garonne) in the South-West part of metropolitan France.
Temporal coverage: from the 17th century until nowadays
Taxonomic coverage : 10 plant species (Alnus incana, Buddleja davidii, Castanea sativa, Helianthus tuberosus, Impatiens glandulifera, Prunus cerasifera, Prunus laurocerasus, Reynoutria japonica, Robinia pseudoacacia, Spiraea japonica)
Design description: Invasions biologiques et déclin des pollinisateurs sont deux phénomènes qui représentent des enjeux majeurs car ils impactent négativement les activités économiques et agricoles, menacent la sécurité alimentaire et contribuent à la vulnérabilité des populations humaines, notamment dans la région Occitanie mais aussi au niveau mondial. Accentués par les problèmes de changements globaux ils représentent des risques auxquels les territoires doivent faire face. Or beaucoup de ces espèces dites invasives (les EEE « Espèces Exotiques Envahissantes) sont aussi de grandes pourvoyeuses de pollens et nectars recherchés par les abeilles, et sont également considérées, dans leur pays d'origine, comme des plantes utiles (espèces médicinales, engrais vert, etc).
Les conséquences socio-économiques des invasions biologiques sont nombreuses, et leur estimation varie suivant les acteurs. Il reste cependant largement « politiquement incorrect » de considérer les espèces introduites comme une part intégrante et potentiellement valorisable de notre biodiversité, eu égard aux risques qu’elles représentent. Cependant, au-delà de valorisations économiques qui restent délicates, ces EEE sont à considérer sous un angle de potentiel biologique, par exemple comme substitut de biodiversité dans des contextes de dégradation irréversible des ressources initiales. Dans le projet EI2P nous les interrogeons au prisme du phénomène de déclin des pollinisateurs, et en particulier des abeilles domestiques.

Data published through GBIF: https://ipt.gbif.fr/resource?r=ei2p_exotic_plants_geohistorical_occurrences_database

Taxonomic coverage

Taxonomic ranks
Species: Alnus incana (L.) Moench, 1794, Buddleja davidii Franch., 1887, Castanea sativa Mill., 1798, Helianthus tuberosus L., 1753, Impatiens glandulifera Royle, 1833, Prunus cerasifera Ehrh., 1784, Prunus laurocerasus L., 1753, Reynoutria japonica Houtt., 1777, Robinia pseudoacacia L., 1753, Spiraea japonica L.f., 1782

Spatial coverage

General spatial coverage: Occurrences are mainly observed in Metropolitan France, particularly in the South-West part (Occitanie).
Few occurrences were observed in Belgium and UK.
Coordinates: 42°5'52.8''N and 59°15'57.6''N Latitude; 8°36'46.8''W and 8°26'16.8''E Longitude 

Temporal coverage: 1651 - 2004

Methods

Method step description: 
- . 	Step 1 : Species selection
Current field observations were made particularly on the two valleys selected in the South-West of France: the Vallée de la Pique in the Pyrenean Piedmont and the Vallée de l'Oussouet in the Pyrenees.
These two territories present a high rate of plant invasions. Four alien plant species were firstly observed to have a certain spatial coverage  regarding to the two fields of study: Buddleja davidii Franch., 1887 ; Impatiens glandulifera Royle,1883 ; Reynoutria japonica Houtt., 1777 and Spiraea japonica L.f., 1782. The "Reference list on invasive alien plants in Midi-Pyrenees" (Occitania-France) updated by the Conservatoire botanique national des Pyrénées et de Midi-Pyrénées (CBNPMP) in 2018 was also consulted and six plant species were added to the selection on the basis of several relevance criteria: a lack of/ a lot of reference data in the existing literature at the national and/or local level (CBNPMP, GBIF, IUCN, Catalogue of Life, INPN, Tela Botanica BDTFX, Baseflor DB- Ph. Julve, Invasive Species Compendium CABI ISC, Delivering alien invasive species in Europe, DAISIE), the distribution of the species in Occitania (Human observations, GBIF), their current status (Muller S. et al., 2004 ; CBNPMP ; GBIF, IUCN), the most frequent species in the Southwest of France (Planty-Tabacchi, 1997), and the current knowledge on their honey and nectar potentials (FranceAgriMer, the ITSAP, the Ministry of Agriculture and Food, the SNHF, Astredhor and the VAL'HOR interprofession, in partnership with the INRA, the CNPAIM, the Gnis and the SBF). In addition to Buddleja davidii Franch., 1887 ; Impatiens glandulifera Royle,1883 ; Reynoutria japonica Houtt., 1777 and Spiraea japonica L.f., 1782 ; six plant species have been integrated to the selection : Alnus incana (L.) Moench, 1794 ; Castanea sativa Mill., 1798 ; Helianthus tuberosus L., 1753 ;  1833 ; Prunus cerasifera Ehrh., 1784 ; Prunus laurocerasus L., 1753 ; Robinia pseudoacacia L., 1753. (Ten plant species in total.)
- . 	Step 2 : Consultation of historical sources over five months
We first consulted those that contain botanical elements and allow us to have an idea of the presence of the ten species at national and local levels (France, Occitania, Pyrenees) during the different periods of History: herbariums and flores (Bordere Herbariums, 1871-1872 ; Philippe, Herbarium, 1884 ; Ramond Herbariums ,1755-1825 ;  Flore de France, Abbé Coste, 1906 ; Flore de France, Rouy and Foucaud, 1896 ; Flore de France, Grenier and Gordon, 1848; Les quatre Flores de France by Fournier, 1977 ; La Flore des Pyrénées, X. Philippe, 1859 ; ...). To find elements on the introduction and the distribution of the ten plant species, different seed catalogs have been consulted with a special attention to those whose seed merchants are pioneers in the introduction of new seeds during the different periods of history, namely: the seed catalogues of Vilmorin and Andrieux (Andrieux, 1771; P. L. de (1872-1917) Vilmorin, 1906; P.-V. L. de (1746-1804); Vilmorin & Andrieux, 1783); Le catalogue général, Bonamy Frères, 1874; the Catalogue of Perennial and Outdoor Plants, Bonamy Freres, 1874; the Catalogue of Perennial and Outdoor Plants of Van Houtte, 1880; the General Seed Catalogue of Chouvet, 1902; ... In addition, we have collected a lot of information by stripping articles from horticultural, botanical and beekeeping newspapers and magazines (Bibliothèque Numérique de France - Gallica). Most of them appeared in the 19th century: Bulletins de la Société nationale d'acclimatation de France ; Revue des sciences naturelles appliquées ; Journal d'agriculture pratique, de jardinage et d'économie domestique ; Revue horticole ; Bulletins de la Société centrale d'apiculture ; Annales de la Société d’horticulture de la Haute-Garonne ; Bulletins d’exploration de la Société Ramond ; Lavedan et Pays Toy ; Monde des plantes ; Le Cultivateur aveyronnais ; Bulletins de la Société d'histoire naturelle de Toulouse, ... The Departmental Archives of Haute-Garonne and Hautes-Pyrénées, the Municipal Archives of Tarbes and Bagnères de-Luchon and some municipal monographs were also consulted (Barèges, Campan, Bagnères-de-Luchon, Bagnères-de-Bigorre, ...).
- . 	Step 3 : Occurrences record in the data file
Each time a species was mentioned in the historical literature consulted, it was recorded in an occurrence data file created in LibreOffice Calc (spreadsheet program). The file format is OpenDocument Spreadsheet (.ods). To record an occurrence, we paid attention to the vernacular and scientific synonyms used in the historical literature. We recorded the occurrences for which the historical name is currently identified as a synonym in the Catalogue of Life, INPN, and ISSG but also according to the amount of elements in the bibliographic source that allows us to identify the taxon as such: photographic representation, image or a plate of the species, precise description, mention of others known scientific and vernacular names. In the data file, we recorded a maximum of elements mentioned by the author: the synonym cited, the reference code from the French taxonomic referential TAXREF  (https://inpn.mnhn.fr/programme/referentiel-taxonomique-taxref?lg=en), the bibliographic reference in which we found the mention of the species, the date of observation of the species or, failing that, the date of mention of the species, the name of the observers and authors, the type of sources, the description of the location as soon as it was mentioned, its spatial coverage and abundance, its minimum and maximum altitudes, any comments by the author about the species, the location of observation or mention of the species, the city, the latitude and longitude coordinates. In addition, each element concerning the literature source was recorded in the same software (LibreOffice Calc): bibliographic reference number (identifier), name of the author(s), title, year of publication; collection and publisher if they were mentioned as well as the city of publication, the name of the journal (if the source is an article), the URL if accessible, or the reference of the archive document with the location of the archive institution, the call number and the series.
- . 	Step 4 : Darwin Core mapping
The Darwin Core Standard "offers a stable, straightforward and flexible framework for compiling biodiversity data from varied and variable sources. (...) This standardization not only simplifies the process of publishing biodiversity datasets, it also makes it easy for users to discover, search, evaluate and compare datasets as they seek answers to today’s data-intensive research and policy questions." (source: https://www.gbif.org/darwin-core). 
Each column header of the occurrence spreadsheet has been searched for an equivalent term in the Darwin Core quick reference guide (https://dwc.tdwg.org/terms/). We chose also the Identification History extension (https://tools.gbif.org/dwca-validator/extension.do?id=dwc:Identification) to manage synonyms of taxon names as they have been cited in the literature consulted.
- . 	Step 5 : Quality controls
Several quality controls have been implemented. First, data cleaning and corrections were performed with a proofreading by a third party and the use of pivot tables to check data integrity. Harmonization and standardization of content were also necessary to allow and facilitate the mapping with Darwin Core terms. The latter made it possible to identify new additional information such as nomenclatural code, coordinate uncertainty, geodetic datum, georeference source, license, etc. We chose as many standards as possible to describe country codes (ISO 3166-1-alpha-2),  municipality names and their geographic coordinates (geonames.org), taxon scientific names (TAXREF v13.0 - 2019-12-06), and taxon ID from several sources (GBIF, IUCN, Catalogue of Life, IPNI, INPN, Tela Botanica BDTFX). Finally we used a GIS tool (QGIS 3.10 LTR) to check the geographic coordinates of occurrences.
Study extent description: Within the framework of this geohistorical study, we studied archival sources in order to find information on the introductions and distributions of target species in Occitania. However, all historical occurrences outside this area were recorded. This explains the European geographical coverage.
The geohistorical study was realised from July to November 2020.
Sampling description: We have selected ten plant species that all can be observed in our field of study. Some of them are considered as invasive alien species. The objective was to acquire elements on their introduction and distribution over time in the Pyrenean foothills in order to understand their current distribution locally.
Over five months we read and consulted historical and archival sources to find the oldest occurrences of these ten species such as local and national newspapers, magazines, herbariums, monographs. Each time a species was mentioned in the historical literature, it was recorded in an occurrence data file. We recorded all the elements stated about it, the observation date and the mention date, the locality, the observers, a comment, a synonym... We connected all the occurrences with their respective bibliographic reference.
The occurrence data file was checked and we operated to quality controls such as data cleaning and corrections, harmonization and standardization of content, data and metadata enrichment (eg. geolocation refinement, taxa additional information), cross-reference checking for taxa, geolocation municipality names and bibliographic references. 
At the same time a mapping with Darwin Core terms was realized in order to facilitate future deposit of the occurrence data file in the GBIF platform through the Integrated Publishing Toolkit (IPT) tool. Specific work on synonyms of taxon names has also been undertaken in order to record the names of taxa as they have been cited in the literature consulted, using the Darwin Core Identification History (https://tools.gbif.org/dwca-validator/extension.do?id=dwc:Identification).

Glossary:
    ASTREDHOR : Institut Technique de l'Horticulture (France)
    CBNPMP : Conservatoire Botanique National des Pyrénées et de Midi-Pyrénées
    CNPAIM : Conservatoire National des Plantes à Parfum, Médicinales et Aromatiques
    DAISIE : Delivering Alien Invasive Species in Europe
    FranceAgriMer : Établissement national des produits de l'Agriculture et de la Mer
    GNIS : Interprofession des semences et des plants
    INPN : Inventaire National du Patrimoine Naturel
    INRA : Institut National de la Recherche Agronomique
    IPNI : International Plant Names Index
    ISC CABI : Invasive Species Compendium
    ISSG : Invasive Species Specialist Group
    ITSAP : Institut Technique et Scientifique de l'Abeille et de la Pollinisation
    IUCN : International Union for Conservation of Nature
    SBF : Société des Bourses Françaises
    SNHF : Société Nationale d'Horticulture de France
    VAL'HOR : Interprofession française de l'horticulture, de la fleuristerie et du paysage
Quality control description: Several quality controls have been implemented. First, data cleaning and corrections were performed with a proofreading by a third party and the use of pivot tables to check data integrity. Harmonization and standardization of content were also necessary to allow and facilitate the mapping with Darwin Core terms. The latter made it possible to identify new additional information such as nomenclatural code, coordinate uncertainty, geodetic datum, georeference source, license, etc. We chose as many standards as possible to describe country codes (ISO 3166-1-alpha-2),  municipality names and their geographic coordinates (geonames.org), taxon scientific names (TAXREF v13.0 - 2019-12-06), and taxon ID from several sources (GBIF, IUCN, Catalogue of Life, IPNI, INPN, Tela Botanica BDTFX). Finally we used a GIS tool (QGIS 3.10 LTR) to check the geographic coordinates of occurrences.

Datasets

Dataset description
Object name: Darwin Core Archive Geohistorical plants occurrences database
Character encoding: UTF-8
Format name: Darwin Core Archive format
Format version: 1.0
Distribution: https://ipt.gbif.fr/archive.do?r=ei2p_exotic_plants_geohistorical_occurrences_database
Publication date of data: 2022-10-27
Language: English
Licences of use: Creative Commons Attribution (CC-BY) 4.0 License

Metadata language: English
Date of metadata creation: 2021-01-08
Hierarchy level: Dataset

References
Claudel M, Lerigoleur E, Brun C, Guillerme S (2022) Geohistorical dataset of ten plant species introduced into Occitania (France). Biodiversity Data Journal 10: e76283. https://doi.org/10.3897/BDJ.10.e76283 https://doi.org/10.3897/BDJ.10.e76283