Czech Republic

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The DiSSCo consortium in

Czech Republic

The natural history collections in the Czech Republic encompassing more than 25 million specimens from all over the world are housed by more than 150 public institutions (botanical gardens and zoos, museums, universities, and various research institutions). Despite their scientific importance, these unique biodiversity and earth science archives are largely digitally inaccessible because of the lack of appropriate funding resulting in deficient and fragmented digitization effort.

National consortium DiSSCo CZ currently includes six research institutions holding large natural history collections considerable amount of DNA and tissue samples and observational, ecosystems and biotope records.

The DiSSCo CZ Consortium officially operates since 2016 and recently contains six formal partners. We are in discussion with a wider portfolio of collection and research institutions.

participating institutions

Jiří Frank

National Museum

Director of Science

jiri.frank@nm.cz

Pavla Růžková

Institute of Botany of the Czech Academy of Science

Head of Project Department

pavla.ruzkova@ibot.cas.cz

Charles University, Faculty of Science

Charles University, which Faculty of Science belongs to, is a leading educational and research institution not only in the Czech Republic but also in Europe, being repeatedly evaluated in the upper 1.5 percent of the world’s best universities. High quality research and education at the Faculty is supported by excellent research infrastructure, rich scientific collections, motivated scholars and experienced scientists with large international collaboration all over the world.

  • Faculty of Science houses the largest and the oldest herbarium in Czechia (international acronyme PRC; ca 2,300,000 specimens of plants, fungi, algae, seeds and fruits). As of June 2022, about 4% of herbarium specimens from PRC are recorded in a publicly available database JACQ (https://www.jacq.org/) from where the records are harvested for the GBIF portal. Type specimens are regularly added to the largest botanical type specimens repository – Global Plants.
  • Other collections include:
    • living cultures of fungi, algae and cyanobacteria (ca 3,800 strains, Department of Botany),
    • living plants (ca 8,000 taxa, Botanical Garden)
    • the zoological collection (ca 6,000 specimens of skeletons, taxidermic and ethanol/formalin preparations, Department of Zoology)
    • and palaeontological (ca 200,000 specimens)
    • and mineralogical collections (ca 25,000 specimens) at the Institute of Geology and Paleontology.
  • The Genetic bank was established at the Department of Zoology in 2014 and it is registered in the international biobank register GRBio under the code ZCU. The bank holds currently a collection of cca 9,000 animal tissue samples available for genomic research. The collection is constantly growing, focusing mainly on central European fauna and domestic animal breeds. Since 2014 the bank is part of the Global Genome Biodiversity Network (GGBN). In 2015 the Genetic bank of the Department of Zoology became a founding institution of the National Animal Genetic Bank of the Czech Republic (NAGB).
Masaryk University, Faculty of Science

Masaryk University in Brno, established in 1919, is the second largest university in the Czech Republic. All University’s scientific collections are found at the Faculty of Science. The Faculty of Science conducts research and provides higher education in the scientific fields of Mathematics, Physics, Chemistry, Biology, and Earth sciences.

  • The Botanical Garden hosts a collection of about 5,000 taxa of vascular plants, cultivated both indoor and outdoor. The Czech Collection of Microorganisms, part of the Department of Experimental Biology, contains about 3,400 bacterial strains covering more than 1,700 species and about 800 fungal strains with more than 550 species.
  • The collection at the Department of Geological Sciences includes 11,000 samples of minerals, 3,000 samples of rocks and 5,000 palaeontological objects.
  • The University’s herbarium, established in 1921 and registered in Index herbariorum under the acronym BRNU, is the largest collection at Masaryk University and the fourth largest herbarium in the Czech Republic. It is part of the Department of Botany and Zoology. As of September 2020, it included about 675,000 specimens, of which about 575,000 specimens were vascular plants, 60,000 mosses, 2,000 algae, 16,000 fungi and 16,000 lichens. About 25% specimens are now recorded in an electronic catalogue (JACQ database; https://www.jacq.org/) and publicly available, including the GBIF database.
National Museum

National Museum (NM) is the largest and oldest museum institution in the Czech Republic containing more than 20 million collections objects. The institutional aims of NM are closely aligned with the key goals of the DiSSCo initiative especially on national level in Czech Republic. National museum has a strong focus on the care of collections representing also national heritage, making those collections and national heritage accessible to both the scientific community and the public, and increase the reuse of the collections data and collections-based scientific research. Due to its aim and scale is NM the most important museum institution in the Czech Republic.

NM is engaged in several EU and global initiatives such as TDWG, GGBD, SPNHC and CETAF, and was involved in the preparation phase for DiSSCo ESFRI proposal. It has also participated in collaborative projects and digitisation initiatives as BHL-Europe, Open-up, 4D4Life, Synthesys 3, Synthesys Plus and DiSSCo Prepare.

The natural history collections, holding approximately 15 million specimens including 140,000 types, are the results of more than 200 years of collecting and research activities. Collections are housed in a newly designed large depository building in Praha-Horní Počernice, associated with offices and well-equipped laboratories.

  • NM collections are diverse, including a large herbarium, zoological and entomological collections, fossils, minerals, wet collections, frozen tissues, DNA samples, and slides. Geographically, collections cover mostly Central Europe, however some collections (botanical, zoological, entomological) also come from tropical regions including South America and Australasia. Each collection contains numerous type specimens and type collections.
  • Particularly significant:
    • the Sternberg Fossil Plant Collection,
    • the T. Haenke’s Herbarium,
    • the Barrande Palaeontological Collection,
    • the Obenberger Collection of Buprestidae beetles.
Institute of Botany, The Czech Academy of Sciences

Institute of Botany (IBOT) conducts scientific research covering all botanical disciplines, including taxonomy and biosystematics of plants, fungi and lichens, karyology, evolutionary biology, phytogeography, vegetation studies, the ecology of species and communities, invasion biology, palynology, population biology and genetics, and the study of mycorrhizal symbioses.. IBOT is also responsible for maintenance and management of the Průhonice Park, Czech National Historic Landmark and UNESCO World Heritage site.

The Department of Taxonomy is a major national research centre dealing with taxonomy, biosystematics and evolution of vascular plants, fungi and lichens. The research staff combines traditional alpha taxonomy with state-of-the-art molecular, cytogenetic and experimental approaches. The main focus includes both research of the key evolutionary processes (hybridization, breeding system variation, adaptation and whole genome duplication) as well as practical approaches  classifying such diversity (phylogeny and taxonomy of critical groups).

  • The team members are involved in preparation of major national monographs, including the multi-volume Flora of the Czech Republic, plant identification guides, and the taxonomic part of the Pladias database that integrates information on the vascular flora and vegetation of the Czech Republic (https://pladias.cz).
  • In addition, the staff members contribute to international projects focused on expert assessment of plant diversity, including Species Plantarum – Flora of the World, Flora of China, Euro+Med PlantBase and Atlas Florae Europaeae.
  • The Herbarium of IBOAT (PRA; more than 600,000 specimens, including type specimens) preserves voucher specimens based on of various taxonomic and biosystematics research projects, especially from regions from which it is difficult to obtain material (Central Asia, the Caucasus, North Africa, India, New Caledonia, Australia, North and South America etc.). It containes also the L. Klimeš’ collection of plants from Ladakh (Western Himalayas, India), unique in its size and comprehensiveness; the comparative herbarium of Central European synanthropic flora; the lichen collection of A. Vězda, a leading lichenologist, consisting of 35 000 sheets; the dendrological collection which is among the world’s most significant collections of material from conifers. A new database system, HERBMAN, is being used for documentation http://vranioko.ibot.cas.cz/
  • Selected collections are being documented with the help of modern photographic technology and made available to the public in digital form (e.g., https://dalib.cz/en/)
  • The Gene Pool Collection in the Botanical garden of IBOT includes globally important collections of genera such as Iris (the second largest in the world), Rhododendron, Paeonia and Hemerocallis.
Institute of Vertebrate Biology, The Czech Academy of Sciences

The research at the Institute of Vertebrate Biology (IVB) predominantly focuses on various aspects of wild vertebrates’ biology, ecology and evolution. The particular topics  include research on biological diversity at molecular, organismal and community level; evolutionary relationship among populations and species, natural hybrid zones and speciation; population dynamics, changes and trends of the community structure in natural and disturbed habitats, including modelling and prognoses; physiological, behavioural, ecological and evolutionary mechanisms of the life histories of vertebrates with respect to their ontogenetic development; reproductive strategies, survival rates, feeding behaviour, and inter- and intraspecific interactions; parasites of higher vertebrates and their role as hosts, vectors and reservoirs of human and animal diseases in natural foci.

IVB (registered in the Global Registry of Scientific Collections (GRSciColl) under code IVB) houses three different biological collections, all focused on vertebrates.

  • The “classic” collection of vertebrate voucher specimens (containing skulls, skeletons, skins, specimen in formaldehyde or ethanol and mounted specimens) was founded in 1950s and the largest part of the material consists of small terrestrial mammals from countries of the former communist bloc. The estimated size of the collection is several tens of thousands of vouchers, however data on these specimens have yet to be digitized.
  • The collection of live laboratory mouse strains derived from mice captured in the wild (WDS) is, with its more than 70 strains, the largest collection of this kind in the world. In comparison with classical laboratory mouse strains (CLS), WDS show higher genetic variation due to higher variability and number of strain founders and are therefore more suitable for some specific research objectives. The strains at the IVB are derived mainly from wild house mice (Mus musculus), but also from Mediterranean mice (Mus spretus) and Macedonian mice (Mus macedonicus) https://housemice.cz/en
  • The Genetic Bank of the Institute of Vertebrate Biology (IVB GB) is a collection of genetic samples (typically a piece of tissue in 96% ethanol, stored in deep freezers) of wild vertebrates. It consists of sample collections from completed research projects (geographically originating from the whole world) as well as samples collected by external sample providers (such as animal rescue stations or natural history museums) directly for the bank (usually representing the Czech fauna). So far, data on 8,500 genetiic samples from 18 countries and four continents have been published on both, GGBN (http://www.ggbn.org/ggbn_portal/search/index) and NAGB data portals (http://data.ngbz.cz/search/index) (repository code IVB) and thousands more samples are waiting to be processed and published.
  • IVB GB is one of the founding members of the Czech network of genetic collections the National Animal Genetic Bank and IVB also houses NAGB Secretariat.
Nature Conservation Agency of the Czech Republic

Nature Conservation Agency of the Czech Republic (NCA CR) is a governmental institution. The main aim of NCA CR is to protect and conserve nature and landscape on the whole territory of the Czech Republic. NCA CR is not a collection institution but has significant amount of databased observational and biotope data including more than 28 million records.

The NCA CR directly manages 24 Protected Landscape Areas (IUCN Category V) and about 800 other types of protected nature areas (IUCN categories Ia, III, IV). Its scientific activity is based on fulfillment of legal obligations of EU Nature Directives and national Nature Conservation Act and covers especially:

  • Biodiversity data management (running of national biodiversity portal; for species diversity Species Occurrence Database, for habitat diversity Habitat Mapping Database),
  • Species and habitat surveillance (monitoring the status, changes and trends in selected habitats and populations of the species (emphasis on endangered or protected)
  • Species and habitat inventories in protected areas under standard methodologies; interpretation and implementation of results into the management cycle of these sites
  • Assessment of the status of Habitat Directive habitats and species under the standard procedures; Red List assessment of species and habitats under IUCN criteria; both on national level.

Participating institutions in

Czech Republic

Roadmaps

National Funding

DiSSCo CZ activities are presently supported through institutional member contributions. The DiSSCo is not on the national Roadmap of Large Infrastructures for Research, Experimental Development and Innovation of the Czech Republic yet. Our aim is to be on the roadmap since 2029.

Our achievements

Success Stories

Atlas of Czech lichens. (Malíček J., Palice Z., Bouda F., Knudsen K., Šoun J., Vondrák J. & Novotný P. (2022): Atlas českých lišejníků. – dalib.cz) https://dalib.cz/en/

This e-Atlas, comprising all the about 1750 species known from the Czech Republic, was created for a better accessibility and comprehensibility of data on lichen occurrence and ecology. Information about ecological preferences, distribution and abundances of each taxon are listed. Photos and maps of distribution are included. The Atlas will serve well for scientific and educational purposes, to professional and amateur lichenologists from the Czech Republic and abroad. The data compiled here should also help to improve the protection of the environment. Gradually, new information, records and pictures are being added. Distributional data for the maps is obtained from the Dalibor database. The total amount of data in the database: 151 752. The e-atlas and database were created by support of the Technological Agency of the Czech Republic.

 

Pladias (Plant Diversity Analysis and Synthesis Centre) is an extensive database of critically revised data on Czech flora and vegetation, available at this web portal, was created as an infrastructure to support research and it is continuously updated.

The data from the database are available online on a public portal www.pladias.cz, which also provides download options for various datasets and online identification keys to the species and vegetation types of the Czech Republic.

The flora section of the database contains critically revised information on the Czech vascular flora, including 13.6 million plant occurrence records, which are dynamically displayed in maps, and data on 120 plant characteristics (traits, environmental associations and other information), divided into the sections: (1) Habitus and growth type, (2) Leaf, (3) Flower, (4) Fruit, seed and dispersal, (5) Belowground organs and clonality, (6) Trophic mode, (7) Karyology, (8) Taxon origin, (9) Ecological indicator values, (10) Habitat and sociology, (11) Distribution and frequency, and (12) Threats and protection. The vegetation section of the database contains information on Czech vegetation types extracted from the monograph Vegetation of the Czech Republic. The data are supplemented by national botanical bibliographies, electronic versions of the standard national flora and vegetation monographs, a database of more than 19,000 pictures of plant taxa and vegetation types, and digital maps (shapefiles) with botanical information.

Pladias database was created during a project funded by the Czech Science Foundation in 2014–2018. It integrates research capacities dealing with the diversity of temperate flora and vegetation from Masaryk University (Brno), Institute of Botany of The Czech Academy of Sciences and the University of South Bohemia in České Budějovice, in cooperation with many external specialists.

References

  • Kaplan Z., Danihelka J., Chrtek J., Kirschner J., Kubát K., Štech M. & Štěpánek J. (eds) (2019) Klíč ke květeně České republiky [Key to the flora of the Czech Republic]. Ed. 2. – Academia, Praha.
  • Chytrý M., Danihelka J., Kaplan Z., Wild J., Holubová D., Novotný P., Řezníčková M., Rohn M., Dřevojan P., Grulich V., Klimešová J., Lepš J., Lososová Z., Pergl J., Sádlo J., Šmarda P., Štěpánková P., Tichý L., Axmanová I., Bartušková A., Blažek P., Chrtek J. Jr., Fischer F. M., Guo W.-Y., Herben T., Janovský Z., Konečná M., Kühn I., Moravcová L., Petřík P., Pierce S., Prach K., Prokešová H., Štech M., Těšitel J., Těšitelová T., Večeřa M., Zelený D. & Pyšek P. (2021) Pladias Database of the Czech Flora and Vegetation. – Preslia 93: 1–87.
  • Wild J., Kaplan Z., Danihelka J., Petřík P., Chytrý M., Novotný P., Rohn M., Šulc V., Brůna J., Chobot K., Ekrt L., Holubová D., Knollová I., Kocián P., Štech M., Štěpánek J. & Zouhar V. (2019) Plant distribution data for the Czech Republic integrated in the Pladias database. – Preslia 91: 1–24

Everything on one screen

Collection Dashboard

The dashboard you can see below contains data on the collections of natural science institutions across Europe. Page one shows the approximate number of collections per category for all of the 89 institutes who participated in an initial DiSSCo survey and page two the national contributions to the European collection. The selection boxes allow filtering for country and institutions. The data in this dashboard is populated with information as sent by the DiSSCo partners through an initial survey in November 2017 and should therefore be considered as preliminary Following that survey, we went through a rigorous process of identifying obvious errors and contacting individuals to correct those. Nevertheless it will probably still contain some errors and information might be outdated. Please contact Niels Raes if you detect any issues so the data can be updated.

If you would like to see a full screen version of the dashboard, please click here.