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herbarium_database

Latest version published by Université de Lomé on May 23, 2018 Université de Lomé

Herbarium specimens and their data are, for the most part, verifiable, repeatable, sustainable, and persistent information on plant diversity and biology (Page et al., 2015; Holmes et al., 2016). Digitalization of herbarium data, ouis publication and integration is brining a new era of discovery, synthesis, and prediction (James et al., 2018). For many major international herbaria (e.g., Kew, Paris, Missouri, etc.), the digitization of botanical collections has become a priority for valuing and making available information on plant biodiversity. Databasing and publishing herbarium label information is becoming and essetial resource for systematic research, biogeography, ethnobiology and ecology. In particular, it is established that at least half of the new species described worldwide are from collections already available in Herbaria (Bebber et al., 2010). These botanical collections are also an indispensable tool in the field of biodiversity conservation. Indeed, they constitute the basic data for the evaluation of species conservation status, a task that presents a significant lack in Africa. Indeed, 90% of the species have the status "not evaluated" in Central Africa. (Billand, 2010). In addition, this digitization should be the source of national or regional checklists production, monographs and flora, as well as for the development of digital tools for plant identification. In West as Central Africa, the degree of digitization of floristic collections by Herbaria are still very disparate or available in various formats, so they are difficult to exploit. In order to avoid errors that could skew the analyzes, the information that is recorded in these digital platforms must be standardized, validated and updated. It is also essential to ensure the interoperability of these databases so that they can have a broader scope (Onana & Chevillotte, 2015). Data capture of the University of Lomé herbarium collections started in 2003 as part of the RIHA (West and Central Africa Herbarium Computer Network) initiative led by the IRD (Research Institut for development) team at the MNHN Paris. In 2008, this work underwent considerable growth with the Sud Expert Plantes project (http://www.sud-expert-plantes.ird.fr/), which enabled more than 12,500 specimens to be captured in the "Letouzey" database. Also in 2008, as part of the "African Plants Initiative" (API) project, began the computerization and image capture of specimens. This global initiative has brought together in a digital library 250,000 images of some 60,000 plant species on the African continent including 8,000 specimens from the Herbarium of Togo. Officially constituted with samples assembled according to international standards, the only one of its kind in the whole country, the herbarium of the University of Lome, hosted in the Department of Botany of the Faculty of Sciences, acts as national herbarium. Creation of this national herbarium coincides with that of the University of Benin resulting from the collapse in 1970 of a higher institute called Institut Supérieur du Bénin (ISB) common in Togo and Dahomey (current Republic of Benin). In fact, the lectures of this institute, common to both countries since 1965, had been divided between Dahomey (scientific programs) and Togo (literary, legal and economic programs). On the continent, the tools for managing these herbarium data vary: Togo, Senegal and Guinea Conakry have the same conceptual model, developed through RIHA project (Chevillotte & Florence, 2006). The same applies to herbaria in Cameroon and Congo, while collections in Benin, Ghana and Burkina Faso are managed in partnership with the National Herbarium of the Netherlands (WAG), which uses the BRAHMS software. DRC, Rwanda and Burundi should also be managed with the latter software and in collaboration with the National Botanical Garden of Belgium (BR). Other sources of data (inventories, surveys) are available through SEP project (http://phyto-afri.ird.fr). Primary biodiversity data have a pleiad of applications, providing an information base that is crucial to addressing challenges of knowledge, pedagogy, sustainable development and decision-making about natural resources and environments (Chapman, 2005; Sousa-Baena et al., 2013). Digital Accessible Knowledge (DAK) regarding biodiversity comprises primary data records that are in digital format, accessible globally without cost, and integrated with the broader university of such data (Sousa-Baena et al., 2013). Some exciting examples of uses of DAK exist, including for prioritizing areas for conservation, assessing geographic potential for species invasions, and understanding ecological and evolutionary processes (Mora et al., 2008; Nakamura & Soberón, 2008). In Togo, significant efforts have been made in digitization of and providing access to primary biodiversity data on the plants from herbarium sheets. The National Strategy and Action Plan for the Biodiversity of Togo (SPANB, 2014) indicated that the latest national CBD report in 2009 estimated the spontaneous plant diversity of Togo at 3,428 terrestrial species and 261 aquatic species (MERF, 2009) without taking into account the 621 species of the introduced flora (Radji et al., 2010). So, the number of species of Togolese flora should be revised upwards thanks to the many other works carried out in recent years. As such, can be mentionned: the works carried out in the ecological zone IV (zone of the humid forests of Togo) and surveys of Pteridophytes and algae, which respectively allowed the harvest of 72 new species of Angiosperms (Adjossou, 2009), 17 species of Pteridaceae (Pteridophyta) (Abotsi, 2013) and 240 species of microalgae (SPANB, 2014) newly described. This research improves knowledge on plant diversity, bringing the current flora of Togo to 4002 species, including 3501 terrestrial spontaneous species and 501 aquatic species. The state of the specific diversity of the spontaneous Togolese flora is not exhaustive, due to the lack of in-depth studies on the lower taxonomic groups, which for the most part are of great importance in maintening and developping ecosystems.

Data Records

The data in this occurrence resource has been published as a Darwin Core Archive (DwC-A), which is a standardized format for sharing biodiversity data as a set of one or more data tables. The core data table contains 12,572 records.

This IPT archives the data and thus serves as the data repository. The data and resource metadata are available for download in the downloads section. The versions table lists other versions of the resource that have been made publicly available and allows tracking changes made to the resource over time.

Downloads

Download the latest version of this resource data as a Darwin Core Archive (DwC-A) or the resource metadata as EML or RTF:

Data as a DwC-A file download 12,572 records in English (360 KB) - Update frequency: annually
Metadata as an EML file download in French (30 KB)
Metadata as an RTF file download in French (29 KB)

Versions

The table below shows only published versions of the resource that are publicly accessible.

How to cite

Researchers should cite this work as follows:

Radji R (2018): herbarium_database. v1.5. Université de Lomé. Dataset/Occurrence. http://ipt-togo.gbif.fr/resource?r=herbarium_database&v=1.5

Rights

Researchers should respect the following rights statement:

The publisher and rights holder of this work is Université de Lomé. This work is licensed under a Creative Commons Attribution (CC-BY) 4.0 License.

GBIF Registration

This resource has been registered with GBIF, and assigned the following GBIF UUID: 3294d36a-987c-4dcb-8ecf-bd2082796f08.  Université de Lomé publishes this resource, and is itself registered in GBIF as a data publisher endorsed by GBIF Togo.

Keywords

Occurrence; Togo; University of Lome; herbarium sheets; RIHA; Magnoliopsida; Liliopsida; herbarium collection; Plants; West Africa; Specimen

Contacts

Who created the resource:

Raoufou Radji
Node Manager
University of Lomé Department of Botany, University of Lome 06BP 6135 Lomé Maritim TG +22890045114

Who can answer questions about the resource:

Raoufou Radji
Herbarium Curator
University of Lomé Department of Botany, University of Lome 06BP 6135 Lomé Maritim TG +22890045114

Who filled in the metadata:

Koudjo Akpene
IT GBIF TOgo
University of Lomé University of Lome 1BP 1515 Lomé Maritim TG +22890038866

Who else was associated with the resource:

User
Kouami Kokou
Professor
Centre of Forestry Research University of Lome 1BP 1515 Lomé Maritim TG +22890020411

Geographic Coverage

Spatial coverage The description dataset collection comes from all over Togo. Indeed, Togo is a country in West Africa which has an area of 56,600 km². It stretches for 600 km from North to South and East to West between 50 and 150 km wide (Figure 7). According to Ern subdivision (1979), Togo Herbarium specimens were collected through the 5 Togo ecological zones (ZE), from north to south and from east to west (Figure 7 & 12). Indeed, ZE.I refers to the Northern Plains Savannah, with Sudan savanna as the predominant vegetation with few islands of dry forests and gallery forests. ZE.II is covered with a mosaic of dry forests of mountain and forest galleries and climate is Sudano-Guinean. ZE.III corresponds to the Guinean savannas of central area plains enjoying a tropical climate with one rainy season. Semi-deciduous forests are noticed in the southern part and dry forests in the northern part. ZE.IV covers the southern part of the Togo Mountains and has a sub-equatorial transition climate. The vegetation is constituted of rainforests, on deep red lateritic soils. This ZE is the domain of dense semi-deciduous forests. The latest one, ZE.V is a coastal plain of southern Togo with a subequatorial climate marked by a deficit in rainfall. It's characterized by a climate with two rainy seasons and the vegetation is set up by a mosaic of savannah, farmland and dry forests (Kokou and Caballé, 2000). Coordinates Togo is located between 6° and 11° latitude and 1° East longitude. Data in Togo National Herbarium are referenced between 11.05 latitude and 0.2 and 1.85 longitude. They are also from "Mont Agou" that is the highest peak in Togo, at an altitude of 986 m and located between Amoussoukopé and Kpalimé in ecological zone IV.

Bounding Coordinates South West [6.141, -0.11], North East [11.157, 1.824]

Taxonomic Coverage

The Flora of Togo includes 2,508 species of Angiosperms including 722 Monocotyledons and 1,786 Dicotyledons. Among introduced plants, there are 482 species of Angiosperms including 161 Monocotyledons. Several Gymnosperms (99 in native flora), Bryophyta (133 species) and Algae (201 species) were also reported by the authors whose synthesis of all the research work led to the publication of Flora of Togo (Brunel et al., 1984).The national Herbarium contains about 15,000 samples mounted according to international standards and is a fair representation of the national flora as si detailed in the sections below. This dataset represents the collection of plants that can be found throughout the national territory. The colonial period (1884-1960) was very active in the knowledge of the flora and vegetation of Togo, thanks to civil administrators, ethnologists, foresters, agronomists, doctors, etc. However, botanical surveys did not really start until the creation of the University of Benin (current University of Lomé) in 1970. Since that date, several authors, notably Aké Assi (1971), Ern (1979, 1982), Brunel (1975, 1984, 1987); Scholz and Scholz (1983) contributed to the improvement of this knowledge. The synthesis of all these works resulted in the publication of the Flora of Togo (Brunel et al., 1984) with botanical identification keys and illustrations for some selected species. After this work, botanical investigations have continued and expanded the knowlege on the Togolese flora. Botanical works of Akpagana and Guelly (1994) have increased the number of known species in 235. The research work of Batawila (1997), Kokou (1998), Kokou et al. (1999, 2000), Akpagana and Gumedzoe (2001) have further increased the knowledege of the flora of Togo. Complementing the natural flora of Togo, it is noted that 40 species are introduced plants used for ornamental purposes of parks and gardens (Brunel et al., 1984). Radji (1997, 1998, 2010) and recorded as horticultural flora of Togo Although the herbarium contains specimens from all mayor botanical groups Phanerogams (angiosperms-gymnosperms), Pteridophyta (ferns), Bryophyta and Thallophyta (algae-lichens-fungi),the database covers exclusively Angiosperms (Dicotyledonous and Monocotyledonous). The Togo flora contains 3,451 species (including plants in the wild and cultivated). Table 1 and Figure 4 to 6 give an idea on each taxonomic group is prepresented and the distribution between wild and ornamental specimens (Radji et al., 2010).

Kingdom  Plantae

Taxonomic ranks Kingdom: Plantae Division: Magnoliophyta (Cronquist, Takht. & W. Zimm., 1996) Phylum: Spermaphyta Class: Magnoliopsida, Liliopsida Family: Agavaceae, Alismataceae, Amaryllidaceae, Anthericaceae, Araceae, Asparagaceae, Aspidiaceae, Cannaceae, Commelinaceae, Costaceae, Cyperaceae, Dioscoreaceae, Dracaenaceae, Droseraceae, Eriocaulaceae, Erythroxylaceae, Gramineae, Hyacinthaceae, Hydrocharitaceae, Hydrophyllaceae, Hypoxidaceae, Iridaceae, Lemnaceae, Liliaceae, Linaceae, Marantaceae, Musaceae, Najadaceae, Opiliaceae, Orchidaceae, Palmae, Pandanaceae, Pontederiaceae, Smilacaceae, Taccaceae, Typhaceae, Xyridaceae, Zingiberaceae. Acanthaceae, Aizoaceae, Amaranthaceae, Anacardiaceae, Annonaceae, Apocynaceae, Araliaceae, Aristolochiaceae, Asclepiadaceae, Avicenniaceae, Azollaceae, Balanitaceae, Balanophoraceae, Balsaminaceae, Basellaceae, Begoniaceae, Bignoniaceae, Bixaceae, Bombacaceae, Boraginaceae, Burseraceae, Cactaceae, Campanulaceae, Capparaceae, Caricaceae, Caryophyllaceae, Casuarinaceae, Cecropiaceae, Celastraceae, Ceratophyllaceae, Chenopodiaceae, Chrysobalanaceae, Cochlospermaceae, Colchicaceae, Combretaceae, Compositae, Connaraceae, Convolvulaceae, Crassulaceae, Cruciferae, Cucurbitaceae, Dichapetalaceae, Dilleniaceae, Dipterocarpaceae, Ebenaceae, Euphorbiaceae, Flacourtiaceae, Flagellariaceae, Gentianaceae, Gesneriaceae, Goodeniaceae, Guttiferae, Haloragaceae, Hernandiaceae, Hippocrateaceae, Icacinaceae, Irvingiaceae, Labiatae, Lauraceae, Lecythidaceae, Leeaceae, Leguminosae, Leguminosae-Caesalpinioideae, Leguminosae-Mimosoideae, Leguminosae-Papilionoideae, Lentibulariaceae, Loganiaceae, Loranthaceae, Lycopodiaceae, Lythraceae, Malpighiaceae, Malvaceae, Melastomataceae, Meliaceae, Menispermaceae, Molluginaceae, Moraceae, Moringaceae, Myristicaceae, Myrsinaceae, Myrtaceae, Nyctaginaceae, Nymphaeaceae, Ochnaceae, Olacaceae , Oleaceae, Onagraceae, Opiliaceae, Oxalidaceae, Pandaceae, Papaveraceae, Passifloraceae, Pedaliaceae, Phytolaccaceae, Piperaceae, Pittosporaceae, Plumbaginaceae, Podostemaceae, Polygalaceae, Polygonaceae, Portulacaceae, Proteaceae, Punicaceae, Ranunculaceae, Rhamnaceae, Rhizophoraceae, Rosaceae, Rubiaceae, Rutaceae, Salicaceae, Santalaceae, Sapindaceae, Sapotaceae, Saxifragaceae, Scrophulariaceae, Simaroubaceae, Solanaceae, Sphenocleaceae, Sterculiaceae, Thymelaeaceae, Tiliaceae, Turneraceae, Ulmaceae, Umbelliferae, Urticaceae, Verbenaceae, Violaceae, Vitaceae, Zygophyllaceae.

Family  Plantae

Project Data

The database of National Herbarium of Togo is the result of several digitization programs: SEP, API, JSTor CESP grant and BID program.

Title Modernization of the Togo National Herbarium
Identifier BID-AF2015-0004-NAC
Funding The use of data captured was made through BID program funded by European Union.
Study Area Description The project was done in University Herbarium in Lome (Togo). Specimen in the herbarium was collected along Togo's country in the fifth ecological zone
Design Description Firstly through RIHA project initiated by IRD from 2000 and joined by Togo in 2003 (Chevillotte & Florence, 2006). Thanks to BEST program funding from IRD (https://www.ird.fr/les-partenariats/ renforcement-des-capacites/des-programmes-specifiques/bourses-d-echanges-scientifiques-et-techno logiques-best), two stays of 3 months each in 2005 and 2006, in the IRD team of the Paris Museum (Phanerogamy Laboratory) made it possible for Togo's Herbarium, to learn and become familiar with the RIHA platform. Indeed, the BEST program promotes the acquisition of new skills for researchers, in the South, through their reception in research or higher education institutions located outside their country of residence and guarantees access to the intellectual and logistical resources necessary for the acquisition of knowledge, the mastery of specific techniques or methodologies. In 2008, with project N° 206 funded by IRD (http://www.sud-expert-plantes.ird.fr/projets/dossier_206), it was possible for the University of Lomé to start modernizing its herbarium (assembly of herbarium specimens to international standard, capture of label data into RIHA database) (Radji et al., 2009). Indeed, RIHA project database is based on a data model (Figure 1 & 2) that describes the relationships between two entities: first, the Taxonomic Repository, which is an index of published scientific names of taxa (species, genera, families, etc.). It manages synonymy, making connections between each correct name and its various synonyms. It also takes into account hierarchical classification by creating links between higher and lower rank taxa. The second entity is the Sample or Harvest part. It contains many forms to be filled according to the herbarium labels established from the information collected at the harvesting sites. These forms include: collector number, date of harvest, location and harvesting station, latitude and longitude, biological type and phenology, ecological and edaphic conditions. The interface "Part" makes it possible to inform the taxon specimen including the name of the taxon, its determiner, the date of determination, the type status, the nature and origin on the part, the deposit herbaria and assign it a barcode. The Collector interface is used to inform the collector (s). The "Doubles" interface allows to capture the acronyms of all herbaria where copies of the specimens are supposed to be deposited. The Other Information interface allows to enter vernacular names and usages. Although all the data to be recorded in the Taxonomic Reference System come from the literature, those that feed the Sample or Harvest interface of the RIHA database are exclusively based on the information provided on the sheets labels to be digitized. Kew was instrumental in founding the African Plants Initiative, working closely with the South African National Biodiversity Institute to engage early partners and establish common standards. Kew has continued as one of the lead partners throughout the programme, providing specialist training, technical support and expertise to new herbarium partners joining the network like Togo Herbarium in 2009 following an initiative of IFAN Herbarium and MNHN/Paris. Indeed, African Plants Initiative is a part of the Global Plants Initiative (GPI) initiated by increasing access to nomenclatural type specimens held in herbaria across the world through digitisation. It is capturing high quality images of type specimens collected in Africa along with detailed transcription of all associated label data. So, more than 8.000 specimens were imaged following a standard of excellence for quality and resolution (600ppi), which enables experts to distinguish closely related species through examination of morphological characters (Figure 3). Images are stored and accessible on https://plants.jstor.org/.

The personnel involved in the project:

Metadata Provider
Komlan Edjèdu Sodjinou
Metadata Provider
Stephane Allassani
Metadata Provider
Watchiou Tchani
Elikplim Abotsi
Metadata Provider
Yawa Dogbé
Metadata Provider
Donko Koda

Sampling Methods

The specimens deposited in the TOGO Herbarium comes from diverse ecofloristic area, which is outcome of several research projects mainly first lecturers in Botany in the university followed by the first PhD students learning in French universities and for who field works was conductied in Togo depositing the specimens. As a result, specimens are not collected using a uniform protocol. Of the materials from donations or purchases (e.g. herbarium of Ern) the protocol followed for the specimens' collection is unknown. The methodology used in collecting plants by researchers from the Botany area may vary depending on the specific objectives pursued in each case. A voucher herbarium specimen is a pressed plant sample deposited for future reference. It supports research work and may be examined to verify the identity of the specific plant used in a study. When possible, duplicates of specimens have been send to recognized herbaria committed to long-term maintenance. These where: P (MNHN, Paris), STR (Institute of Botany, Strasbourg), KEW (England), B (Berlin, Germany), MPU (Montpellier, France), MO (Missouri Botanical Garden , USA), BR (Botanical Garden Meise, Belgium), WAG and K (Royal Botanic Gardens, UK), LMU, MOZ (Mozambique). During the SEP project (2008-2012), 6 students in Master's degree in Plant Biology were recruited to assemble herbarium specimens deposited by collectors in presses and sometimes in Canson papers. Most of specimens have original collectors’ labels. Trained to the use of RIHA database (under Microsoft Access), the data was digitized as and when the specimens were mounted. The result is the extraction of this list exported under Excel.

Study Extent The analysis of this dataset reveals that the eco-floristic zone IV is the most significant and prospected with 31.63% of the herbarium specimens whereas the ecological zone II remains the least prospected with 11.33% of the collected specimens. Although quite rich, Togolese spontaneous flora remains incompletely known (Akpagana 1992b, Radji 1997, Kokou 1998).
Quality Control The present dataset was updated to match the APG III classification for the orders and families of flowering plants (APGIII, 2009) and all species names were checked for validity (spelling, synomyms and authorship) against online databases: http://www.ipni.org/ipni/plantnamesearchpage.do ; http://kiki.huh. harvard.edu/databases/specimen_index.html;http://kiki.huh.harvard.edu/databases/botanist_index.html; http://www.theplantlist.org/ ; http://www.ville-ge.ch/musinfo/bd/cjb/africa/recherche.php.

Method step description:

  1. Specimens are pressed in a plant press, which consists of a wooden frame (for rigidity), corrugated cardboard ventilators (to allow air to flow through the press), blotter paper (to absorb moisture), and folded paper, typically a newspaper (to contain the plant material). The plant press is tightened using straps with buckles or bolts with wing nuts. The objective of pressing plants is to extract moisture in the shortest period of time, while preserving the morphological integrity of the plant, and to yield material that can be readily mounted on herbarium paper (an acid-free cardstock) for long-term storage. In order to fit on a standard herbarium sheet, a plant specimen have been pressed flat to no more than 11 x 16 inches. For the specimen that will not fit those dimensions, it may be folded or cut into sections. Multiples of smaller plants may be pressed together in order to provide ample material for mounting and study. Small loose pieces, such as seeds, may need to be placed in a small paper packet inside of the newspaper. Large fruits or bulbs are often cut in half lengthwise or in slices prior to pressing. In order to insure rapid and thorough drying, extremely succulent materials such as cactus stems may need to be sliced open and some of the fleshy interior scraped out. Knowing that a plant specimen is incomplete without label data, label data must be incorporate with the following important elements: scientific name, determiner of the scientific name; detailed location; habitat, date of collection, collector name and number and plant description as well.

Additional Metadata

Acknowledgements We wish to thank the Government of France for financing the modernization of the National Herbarium of Togo through the project 206 SEP. We also thank European Union for funding through BID Program GBIF Togo (BID-AF2015-0004-NAC) to strenghthen the stakeholder's network that result is an elaboration of this data paper.

Alternative Identifiers 3294d36a-987c-4dcb-8ecf-bd2082796f08
http://ipt-togo.gbif.fr/resource?r=herbarium_database