Geohistorical plants occurrences database

Study Extent

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

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

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.

Method steps

1. 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.)
2. 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, ...).
3. 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.
4. 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.
5. 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.

1. Alnus incana (L.) Moench, 1794
   rank: species
2. Buddleja davidii Franch., 1887
   rank: species
3. Castanea sativa Mill., 1798
   rank: species
4. Helianthus tuberosus L., 1753
   rank: species
5. Impatiens glandulifera Royle, 1833
   rank: species
6. Prunus cerasifera Ehrh., 1784
   rank: species
7. Prunus laurocerasus L., 1753
   rank: species
8. Reynoutria japonica Houtt., 1777
   rank: species
9. Robinia pseudoacacia L., 1753
   rank: species
10. Spiraea japonica L.f., 1782
    rank: species

Occurrences are mainly observed in Metropolitan France, particularly in the South-West part (Occitanie). Few occurrences were observed in Belgium and UK.