Corresponding author: M. Teresa Vizoso (
Academic editor: Andreas Beck
A catalogue of types from the Herbarium of the University of Granada has not previously been compiled. As a result, a search of these collections in order to compile digital images for preservation and publication yielded a large number of formerly unrecognized types.
This dataset contains the specimen records from the catalogue of the nomenclature types of fungi and lichens in the Herbarium of the University of Granada, Spain. These herbarium specimens are included in the GDA and GDAC collections, acronyms from Index Herbariorum (
For each specimen, the locality indication, species name, observation date, collector, type status, related information, associated sequences, other catalogue numbers related to each type, and image URL are recorded. The dataset is associated with an image collection named “Colección de imágenes de los tipos nomenclaturales de hongos, líquenes, musgos y algas incluidos en el Herbario de la Universidad de Granada (GDA y GDAC)” (
The Herbarium of the University of Granada combines two general collections: GDA and GDAC (
Since the unification of the GDA and GDAC collections, many tasks have been accomplished. These include a complete review of all materials, recovery and incorporation of unregistered materials, updating curatorial methods and, even more important, the computerization of the entire collection. More recently, the Herbarium of the University of Granada has developed several projects to digitalize images of high-priority specimens in order to preserve them and make them available on Internet. As a result of the reviewing process, many types that had not previously been compiled were detected. In addition, the catalogues of type specimens of different groups of the Herbarium of the University of Granada have been compiled, published, and made accessible on Internet through the “Biodiversity Image Portal of Spanish collections” at the Global Biodiversity Information Facility in Spain (GBIF.ES) Hosting and Publishing Service and at the Herbarium of the University of Granada institutional web. The catalogue of type specimens of fungi and lichens has been one of the first published on the GBIF.ES Integrated Publishing Toolkit (IPT) (
Towards a digital image collection of the Herbarium of the University of Granada
M.Teresa Vizoso
The application of new technologies in the field of natural-history collections is enabling herbaria not only to manage their collections more effectively but also to provide access to a large volume of biodiversity information through computerization and the creation of a specimen database. After this step, databases can enrich their contents by digitizing images associated with high-priority specimens such as nomenclatural types. This represents a major advance in the preservation of sensitive materials. For example, the risk of damage involved in consulting and sending sensitive material is minimized. It is also vital in terms of enhancing information and reaching out to wider audiences at multiple levels, since, at the database level, database records can have links to the associated image (
The main objective was to ensure the preservation of sensitive material of the University of Granada Herbarium by implementing high-quality curatorial standards as well as to generate, manage, and disseminate the associated data in digital formats. This was achieved by:
Creating and making available on Internet an image collection of singular taxa from Andalusia that meets the needs of researchers, managers, and the general public.
Obtaining a detailed report on the number, location, and treatment of nomenclatural types in the University of Granada Herbarium in order to perform a database-cleaning process and to complete the curatorial management of this sensitive material.
Compiling a collection of electronic publications (protologues) that support the study of nomenclatural types and improves accessibility and service that the University of Granada Herbarium offers to researchers.
Ensuring the preservation of the historic collection of Amo y Mora (the oldest collection of this herbarium, started in 1852 by M. Amo y Mora) by fully digitizing it and publishing it online.
The Herbarium of the University of Granada is part of the research group called “The Herbarium of the University of Granada as a Source for Taxonomic, Environmental and Biodiversity Studies” (group code: 288RNM) which is one the Research and Technological Development groups from Regional Government of Andalusia (Junta de Andalucía), Spain. The funds were provided by the Technical Support Program, under the Scientific-Technological Infrastructure modality of the Ministry of Science and Innovation of Spanish Goverment and the University of Granada. The project was undertaken from February 2010 to July 2013.
This study includes fungus and lichen collections. The fungus collection of the herbarium comes from two herbaria, one of which originated at the Pharmacy Faculty (GDA) and the other at the Science Faculty (GDAC). In the year 2000, the two herbaria were joined. The Herbarium of the University of Granada (GDA) maintains both sections and, although both collections retain their individuality, new materials are added only to the GDA collection. Currently, the overall fungus collection comprises 7244 specimens derived mostly from research conducted by Dr Antonio Ortega. Some 97% of the specimens come from Spain, followed by just under 2% that correspond mostly to exsiccate Uredineen Sydow (1874-1889) of a collection of
The lichen collection has 3300 specimens, which come exclusively from the herbarium of the Pharmacy Faculty (GDA). This collection started in 1980 with materials that came from the research of Dr Manuel Casares and is subsequently enriched with exsiccate exchange with other institutions. Of this collection, 93% comes from Spain, 75% of which were collected in the south-eastern provinces of Granada, Alicante, Almeria, and Jaen. Other well-represented areas include the south-western provinces of Huelva and Cadiz, central provinces of Madrid, Salamanca, and the north-eastern provinces of Tarragona and Zaragoza. We also found a small representation from Morocco (3.3%) and the rest from Austria, Brazil, Georgia, and the Czech Republic.
The fungus collection has been fully computerized and approximately 50% of the lichen collection has also been. Therefore, developing a complete catalogue involved three kinds of type specimens, namely those that: 1) already have a record in the databases; 2) specimens not recorded as a type in the databases but have been identified as such in the collection; and 3) type specimens not recorded in the databases nor identified or treated as such in the collection. For the first kind, quality control was carried out (see next section). For the second kind of type specimens, the literature from the two main researchers and collectors was reviewed. This led to the identification of type specimens that were not included in the databases and were either identified as such in the collection (case 2) or had not been identified as such (case 3). The review of the literature of these authors provided new data to both the collection and the associated databases. All type specimens are now registered in the GDA-GDAC Fungus and Lichen collections and in some cases another number from other herbaria has been included in RelatedInformation or OtherCatalogNumber fields from DarwinCore standard (
The consistency of data on type-specimen records was verified by comparisons with the information in original publications of the corresponding new species. When some information items such as geographical coordinates, altitude, or identifiers of genetic sequence associated data had not been included in the herbarium database and these data were available in the protologue, they were included in this dataset. The consigned data refer to the original identification for which the nomenclatural type from the taxon name was given. When the nomenclatural type was not recorded as such in the herbarium but was found after searching and reviewing the relevant literature, a revision tag was included in the specimen record. This tag specifies the type status, name, and site where it was validly published and the author who documented it. These data have also been computerized. DARWIN TEST (
First of all, a query was made to each of the two herbarium databases on nomenclatural types of the fungus and lichen collections. The first database (fungi) is managed with the BIOMEN software application (
In an effort to fill out the ImageURL field in the step described above, the following steps were taken: after the catalogue of types of fungi and lichens were obtained, all specimens were checked for appropriate physical curation treatment (placed in a type cover, by convention red, to indicate the presence of type specimens and to ensure better protection). Then, digital images of the nomenclatural type and documents included with each specimen were prepared. A Hewlett Packard Scan Jet 5300C model with a resolution of 600 dpi for specimens and 150 dpi for documents was used. After the metadata for each image was included, the corresponding tiled/pyramid TIFF was generated and uploaded at the GBIF.ES “Biodiversity Image Portal of Spanish collections” Hosting and Publishing Service. This collection is available both at “Colección de imágenes de los tipos nomenclaturales de hongos, líquenes, musgos y algas incluidos en el Herbario de la Universidad de Granada (GDA y GDAC)” (
In general, the distribution of the taxa in this catalogue is the western Mediterranean region. Most of the taxa are from the Iberian Peninsula (72 types records from 39 taxa) as shown in Fig.
33°23'60'' and 50°42'0'' Latitude; 6°30'36'' and 15°26'60'' Longitude.
The main taxonomic coverage of this dataset corresponds to
Note: the terms used to complete the type status reference for this dataset are from the International Code of Nomenclature for algae, fungi, and plants (ICN) (
Fig.
Of the 49 taxa, 34 are accepted in their original position (marked by an asterisk* in the taxonomic ranks) and four had already been combined into other genera:
Rank | Scientific Name | Common Name |
---|---|---|
kingdom |
|
|
phylum |
|
|
phylum |
|
|
phylum |
|
|
order |
|
|
order |
|
|
order |
|
|
order |
|
|
order |
|
|
genus |
|
|
genus |
|
|
order |
|
|
genus |
|
|
genus |
|
|
genus |
|
|
genus |
|
|
genus |
|
|
genus |
|
|
genus |
|
|
genus |
|
|
genus |
|
|
genus |
|
|
genus |
|
|
genus |
|
|
genus |
|
|
genus |
|
|
genus |
|
|
genus |
|
|
genus |
|
|
species | ||
species | * |
|
species | * |
|
species | * |
|
species | * |
|
species | * |
|
species | * |
|
species | * |
|
species | * |
|
species | * |
|
species | * |
|
species | * |
|
species | * |
|
species | * |
|
species | * |
|
species | * |
|
species | * |
|
species | * |
|
species | * |
|
species | * |
|
species | * |
|
species | * |
|
species | * |
|
species | * |
|
species | * |
|
species | * |
|
species | ||
species | * |
|
species | * |
|
species | * |
|
species | * |
|
species | * |
|
species | * |
|
species | * |
|
species | ||
species | ||
variety | ||
variety | ||
variety | ||
variety | ||
variety | * |
|
variety | ||
variety | ||
variety | ||
variety | ||
variety | ||
variety | ||
variety | * |
|
form |
Although the temporal coverage started in 1943, this was a gift and another from 1960 was a single type-specimen included in an exsiccate exchange of lichens. In fact, this collection was started in the mid 1970s and most of the type-specimens were described from 1999 to 2011 (57 type-specimens of 88).
9b8b659f-8470-4445-926c-8b3f2bc32415
GDA-GDAC
Dried
Curatorial unit: 88 with an uncertainty of 0 (specimens); curatorial unit: 49 with an uncertainty of 0 (species); curatorial unit: 19 with an uncertainty of 0 (genera); curatorial unit: 6 with an uncertainty of 0 (order)
Оpen Data Commons Open Database License (ODbL)
Darwin Core Archive Catalogue of type specimens of fungi and lichens deposited in the Herbarium of the University of Granada (Spain)
7ac0504d-0230-4029-afbe-04657ae47c48
1
dwca-gda-tipos-fungi
Darwin Core Archive format
38
UTF-8
1.0
This dataset contains the specimen records from the catalogue of the nomenclature types of fungi and lichens in the Herbarium of the University of Granada, Spain (GDA-GDAC). It contains 88 type material of 49 nominal taxa, most from
Column label | Column description |
---|---|
dateModified | Date on which the resource was changed. |
language | A language of the resource. |
institutionCode | The name (or acronym) in use by the institution having custody of the object(s) or information referred to in the record. |
colletionCode | The name, acronym, coden, or initialism identifying the collection or data set from which the record was derived. |
basisOfRecord | The specific nature of the data record. |
occurrenceID | An identifier for the Occurrence (as opposed to a particular digital record of the occurrence). In the absence of a persistent global unique identifier, construct one from a combination of identifiers in the record that will most closely make the occurrenceID globally unique. |
catalogNumber | An identifier (preferably unique) for the record within the data set or collection. |
occurrenceRemarks | Comments or notes about the Occurrence. |
recordedBy | A list (concatenated and separated) of names of people, groups, or organizations responsible for recording the original Occurrence. The primary collector or observer, especially one who applies a personal identifier (recordNumber), should be listed first. |
individualCount | The number of individuals represented present at the time of the Occurrence. |
otherCatalogNumbers | A list (concatenated and separated) of previous or alternate fully qualified catalog numbers or other human-used identifiers for the same Occurrence, whether in the current or any other data set or collection. |
associatedMedia | A list (concatenated and separated) of identifiers (publication, global unique identifier, URI) of media associated with the Occurrence. |
associatedSequences | A list (concatenated and separated) of identifiers (publication, global unique identifier, URI) of genetic sequence information associated with the Occurrence. |
occurrenceDetails | Comments or notes about the specimen description or identification. |
eventDate | The date-time or interval during which an Event occurred. For occurrences, this is the date-time when the event was recorded. Not suitable for a time in a geological context. Recommended best practice is to use an encoding scheme, such as ISO 8601:2004(E). |
fieldNotes | One of a) an indicator of the existence of, b) a reference to (publication, URI), or c) the text of notes taken in the field about the Event. |
country | The full, unabbreviated name of the country or major political unit in which the organism was collected or observed. |
countryCode | Abbreviations on the 2-letters code of the country in which the organism was collected or observed. |
stateProvince | The name of the next smaller administrative region than country (state, province, canton, department, region, etc.) in which the Location occurs. |
locality | The specific description of the place. Less specific geographic information can be provided in other geographic terms (higherGeography, continent, country, stateProvince, county, municipality, waterBody, island, islandGroup). This term may contain information modified from the original to correct perceived errors or standardize the description. |
minimumElevationInMeters | The lower limit of the range of elevation (altitude, usually above sea level), in meters. |
maximumElevationInMeters | The upper limit of the range of elevation (altitude, usually above sea level), in meters. |
verbatimCoordinates | The verbatim original spatial coordinates of the Location. The coordinate ellipsoid, geodeticDatum, or full Spatial Reference System (SRS) for these coordinates should be stored in verbatimSRS and the coordinate system should be stored in verbatimCoordinateSystem. |
verbatimCoordinateSystem | The spatial coordinate system for the verbatimLatitude and verbatimLongitude or the verbatimCoordinates of the Location. Recommended best practice is to use a controlled vocabulary. |
decimalLatitude | The geographic latitude (in decimal degrees, using the spatial reference system given in geodeticDatum) of the geographic center of a Location. Positive values are north of the Equator, negative values are south of it. Legal values lie between -90 and 90, inclusive. |
decimalLongitude | The geographic longitude (in decimal degrees, using the spatial reference system given in geodeticDatum) of the geographic center of a Location. Positive values are east of the Greenwich Meridian, negative values are west of it. Legal values lie between -180 and 180, inclusive. |
coordinateUncertaintyInMeters | The horizontal distance (in meters) from the given decimalLatitude and decimalLongitude describing the smallest circle containing the whole of the Location. Leave the value empty if the uncertainty is unknown, cannot be estimated, or is not applicable (because there are no coordinates). Zero is not a valid value for this term. |
identifiedBy | A list (concatenated and separated) of names of people, groups, or organizations who assigned the Taxon to the subject. |
dateIdentified | The date on which the subject was identified as representing the Taxon. Recommended best practice is to use an encoding scheme, such as ISO 8601:2004(E). |
typeStatus | A list (concatenated and separated) of nomenclatural types (type status, typified scientific name, publication) applied to the subject. |
scientificName | The full scientific name, with authorship and date information if known. When forming part of an Identification, this should be the name in lowest level taxonomic rank that can be determined. This term should not contain identification qualifications, which should instead be supplied in the IdentificationQualifier term. |
kingdom | The full scientific name of the kingdom in which the taxon is classified. |
order | The full scientific name of the order in which the taxon is classified. |
genus | The full scientific name of the genus in which the taxon is classified. |
specificEpithet | The name of the first or species epithet of the scientificName. |
infraspecificEpithet | The name of the lowest or terminal infraspecific epithet of the scientificName, excluding any rank designation. |
taxonRank | The taxonomic rank of the most specific name in the scientificName. Recommended best practice is to use a controlled vocabulary. |
scientificNameAuthorship | The authorship information for the scientificName formatted according to the conventions of the applicable nomenclaturalCode. |
Ballarà J, et al. (2009) Cortinarius ibero-insulares 2.
Ballarà J, Mahiques R (2009)
Bidaud A, Moënne-Loccoz P, Reumaux P (1992) Atlas de Cortinares, Pars IV. Ed. Fédération Mycologique Dauphiné-Savoie, Annecy, France.
Bills GF, Menéndez VG, Platas G (2012)
Bon M (1992)
Cano C, Bago A, Dalpé Y (2009)
Casares-Porcel M, Hafellner J, Gutiérrez-Carretero L (1996) Species of the genus
Chevassut G, Henry R (1982) Cortinaires nouveaux ou rares de la region Languedoc Cevennes. Documents Mycologiques 12: 34-65.
Contu M, Bon M (2000) Une nouvelle espèce de
Esteve-Raventós F, Ortega A (1999) Two news agarics found in Andalusia (Peninsular Spain). Mycotaxon 71: 95-103.
Esteve-Raventós F, Ortega A (2003) Dos nuevos Tricholomatales ibéricos:
Esteve-Raventós F, Villareal M, Barrasa JM, Ortega A (2001)
Galán R, Ortega A, Moreno G (1983) Sobre
Gutiérrez C, Ballarà J, Cadiñanos JA, Palazón F, Mahiques R (2005)
Guzmán-Dávalos L, Ortega A, Contu M, Vizzini A, Rodríguez A, Villalobos-Arámbula AR, Santerre A (2009)
Henry R, Contu M (1986) Description d´une nouvelle espece xero-thermophile:
Horak E, Moreno G, Ortega A, Esteve-Raventós F (2002)
Mahiques R (2004)
Mahiques R, Burguete A (2001)
Mahiques R, Ortega A (2002)
Mahiques R, Ortega A, Bidaud A (2001)
Malençon G, Bertault R (1970) Flore des champignons superieurs du Maroc. Tome I, Rabat.
Malençon G, Llimona X (1980) Champignons de la Péninsule Ibérique VI. Est et sud-est. Anales de Biología, Universidad de Murcia 34: 47-135.
Moënne-Loccoz P, Reumaux P (1990) Atlas des Cortinaires, Pars II. Ed. Fédération Mycologique Dauphiné-Savoie, Annecy, France.
Ortega A, Antonín V, Esteve-Raventós F (2003) Three interesting thermophilic taxa of
Ortega A, Bidaud A, Mahiques R (1997) Contribución al estudio del género
Ortega A, Chevassut G (1999)
Ortega A, Contu M (1991) Una nuova specie di
Ortega A, Esteve-Raventós F (1998) Contribution to the study of the mycoflora of Andalusia (Spain) XIII.
Ortega A, Esteve-Raventós F (2003) New and interesting species of
Ortega A, Esteve-Raventós F (2005) A new species of
Ortega A, Mahiques R (2002) Study of some species of the genus
Ortega A, Moënne-Loccoz P (2003)
Ortega A, Suárez-Santiago VN, Reyes JD (2008) Morphological and ITS identification of
Ortega A, Suárez-Santiago VN, Vila J (2009) Two new species of
Ortega A, Vila J, Bidaud A, Llimona X (2000)
Ortega A, Vila J, Bidaud A, Mahiques R, Contu M (2007) Notes on four mediterranean
Ortega A, Zea M (1991)
Palazón F, Mahiques R (2007)
Suárez-Santiago VN, Ortega A, Peintner U, López-Flores I (2009) Study on
Vêzda A (1961) Lichenes novi vel rariores Sudetorum occidentalium. Preslia 33: 365-368.
Vila J, Llimona X (2006) Novesdades sobre el component fúngic de les comunitats de
Vila J, Ortega A, Bidaud A (2007) Deux cortinaires remarquables de la Péninsule Ibérique. Bulleti Société mycologique de France 123: 221-232.
Vila J, Ortega A, Suárez-Santiago VN, Llimona X (2008)
We wish to express our appreciation to Dr A. Ortega (1954-2014) and to Dr M. Casares (Botany Department researchers at the University of Granada) for the assistance provided to gain access to publications of the species described by them and for their help in the interpretation of some type specimens. We also thank Katia Cezón (Users Support at the GBIF Spain) for her help in validating and publishing this resource.
Spanish provinces with the number of taxa with type specimens in the GDA Herbarium. Source: Map was taken from National Geographic Institute (IGN, Instituto Geográfico Nacional, Gobierno de España).
Distribution of the type specimens according to the orders in which they are included. At the right, the genera from the
Distribution of herbarium type-specimens according to type status (Suppl. material
GDA_type specimens_fungi
Data type: tables correspond to figures
Brief description: This file contained a data set of the type-specimens occurrences, and numbers and tables corresponding to the figures in the paper.
File: oo_42773.xlsx