Dataset of herbarium specimens of threatened vascular plants in Catalonia.
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ABSTRACT:
SUBMITTER: Nualart N
PROVIDER: S-EPMC5558802 | biostudies-other | 2017
REPOSITORIES: biostudies-other
Similar Datasets
Project description:This paper describes the herbarium (COFC) dataset of vascular plants of the University of Cordoba (SW Spain). This dataset is made up of two collections, the General collection (61,377 specimens) and the Historical collection (1,614 specimens). This study has focused mainly on the General collection, which contains the largest number of vascular plant specimens, predominantly angiosperms, mainly provincial and regional (Andalusia, Spain), but also with a good representation of other areas of the Iberian Peninsula and neighboring countries. The place of collection is specified in 99.7% of the labels, about 35% being georeferenced, and it is estimated that, currently, about 86% of the material housed in the herbarium has been databased using Elysia v1.0. software. With more than 178 families, 1,178 genera, and 3,750 species, this collection not only has educational importance, but is a valuable research tool that has been useful for the development of important works such as "Flora Vascular de Andalucía Occidental" and the "Flora iberica". The dataset described in this paper is registered with GBIF (accessible at https://doi.org/10.15468/fdzzal).
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Project description:BackgroundWorld herbaria with 387.5M specimens (Thiers 2019) are being rapidly digitised. At least 79.9M plant specimens (20.6%) are already databased throughout the globe in the standard form of GBIF-mediated data. The contribution of smaller herbaria has been steadily growing over the last few years due to cost reduction, usage of platforms and solutions developed by the leaders. A web-resource the Moscow Digital Herbarium (Seregin 2020b) was launched by the Lomonosov Moscow State University in October, 2016 for publication of specimens imaged and databased in the Moscow University Herbarium (MW). As of 31 December 2018, the web-portal included 968,031 images of 971,732 specimens digitised in MW. This dataset is available in GBIF (Seregin 2020). The global trend is largely the same in Russia, where a dozen herbaria started to scan their holdings after imaging of the nation's second largest herbarium (Kislov et al. 2017, Kovtonyuk et al. 2019, Seregin 2020a). In 2019, we started to use Moscow Digital Herbarium as a web-repository for digitised herbarium specimens from some Russian collections, starting with the Herbarium of Tsitsin Main Botanical Gaden, Russian Academy of Sciences (MHA). Due to this, a single-university system became a multi-institutional consortium in April 2019 (Seregin 2020a). The dataset of the Moscow collections and partly of the Eastern European collections of the MHA Herbarium is now available in GBIF (Seregin and Stepanova 2020).New informationMHA Herbarium imaged 64,008 specimens from Moscow Region and partly from other regions of Eastern Europe at 600 dpi and provided key metadata. These data are now fully available in the Moscow Digital Herbarium and GBIF. Complete georeferencing of the specimens from the City of Moscow was a key task in 2020. As of May 2020, 50,324 specimens, including 49,732 specimens from Russia, have been georeferenced (78.6%) and 39,448 specimens have fully-captured label transcriptions (61.6%). Based on these data, we give a detailed overview of the collections including spatial, temporal and taxonomic description of the dataset.
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Project description:The HSS herbarium database includes 69,397 records of vascular plant taxa, representing 91.1% of the herbarium's specimens as for December, 2019, which are available through the Global Biodiversity Information Facility (GBIF) website (accessible at https://doi.org/10.15468/siye1z). The database represents 4,343 species and 787 infraspecific taxa (530 subspecies, 130 varieties and 127 notho-species or hybrids) of 196 families and 1,164 genera, and 105 type sheets. So far, 97.7% of the databased records are georeferenced (geographic coordinates or MRGS coordinates) and the geographic area with the largest number of specimens is the southwest quadrant of the Iberian Peninsula (Spain and Portugal).
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Project description:Premise of the studyHerbarium specimens provide a robust record of historical plant phenology (the timing of seasonal events such as flowering or fruiting). However, the difficulty of aggregating phenological data from specimens arises from a lack of standardized scoring methods and definitions for phenological states across the collections community.Methods and resultsTo address this problem, we report on a consensus reached by an iDigBio working group of curators, researchers, and data standards experts regarding an efficient scoring protocol and a data-sharing protocol for reproductive traits available from herbarium specimens of seed plants. The phenological data sets generated can be shared via Darwin Core Archives using the Extended MeasurementOrFact extension.ConclusionsOur hope is that curators and others interested in collecting phenological trait data from specimens will use the recommendations presented here in current and future scoring efforts. New tools for scoring specimens are reviewed.
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Project description:BackgroundTUL Herbarium presents collections from Tula Oblast stored at the Tula State Lev Tolstoy Pedagogical University, Russia, which is an educational and scientific institution that supports various types of scientific activities, including research on biodiversity and nature conservation. The university is a holder of some biological collections, such as herbarium of vascular plants, mosses and fungi collected mainly throughout Tula Oblast and from adjacent regions.New informationThe collections of vascular plants (9,000 specimens) were imaged in December 2019 and January 2020. Databasing and georeferencing of the specimens from the TUL Herbarium was performed by the staff members of the Tula State Lev Tolstoy Pedagogical University and Tula Local History Museum. Digital collections of the TUL Herbarium are fully available in the Moscow Digital Herbarium (https://plant.depo.msu.ru/) and GBIF (https://doi.org/10.15468/ca08cm).
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Project description:We provide a quantitative description of the French national herbarium vascular plants collection dataset. Held at the Muséum national d'histoire naturelle, Paris, it currently comprises records for 5,400,000 specimens, representing 90% of the estimated total of specimens. Ninety nine percent of the specimen entries are linked to one or more images and 16% have field-collecting information available. This major botanical collection represents the results of over three centuries of exploration and study. The sources of the collection are global, with a strong representation for France, including overseas territories, and former French colonies. The compilation of this dataset was made possible through numerous national and international projects, the most important of which was linked to the renovation of the herbarium building. The vascular plant collection is actively expanding today, hence the continuous growth exhibited by the dataset, which can be fully accessed through the GBIF portal or the MNHN database portal (available at: https://science.mnhn.fr/institution/mnhn/collection/p/item/search/form). This dataset is a major source of data for systematics, global plants macroecological studies or conservation assessments.
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Project description:BackgroundThe Central Siberian Botanical Garden of the Siberian Branch of the Russian Academy of Sciences (CSBG SB RAS) is the largest botanical institution in the Asian part of Russia. Founded in 1946, CSBG SB RAS is historically a consortium of two herbarium collections with their own acronyms (NS and NSK) and registration in the Index Herbariorum (Thiers 2020).At present the NS+NSK collections contain about 800,000 herbarium specimens comprising vascular plants (680,000), mosses (25,000), lichens (80,000) and fungi (15,000) gathered, not only in Siberia, but also in the European part of Russia and other parts of the Eurasian and American continents. CSBG SB RAS has the third largest collection in Russia after the Komarov Botanical Institute of RAS (LE) and Moscow State University (MW) collections.The dataset consists of 5,384 records of digitised herbarium specimens of vascular plants belonging to 111 families, collected since the 19th century in 54 administrative regions from the European part of Russia and kept in NS+NSK collections. Herbarium specimens were digitised using two special scanners, both ObjectScan 1600, according to international standards, at 600 dpi, with a barcode, 24-colour scale and spatial scale bar and placed into the CSBG SB RAS Digital Herbarium. For each specimen, the species name, locality, collection date, collector, ecology and revision label are recorded. More than 94% of the records have coordinates that fall within the area of European Russia, west of the Ural Mountains.New informationA total of 5,384 records of vascular plant occurrences with 94.8% geolocations in the territory of the European Russia West of the Ural Mountains were entered.
| S-EPMC7561608 | biostudies-literature
Project description:BackgroundThe herbarium of the South-Siberian Botanical Garden of Altai State University (ALTB) houses the largest collection of plants from the Altai Mountain Country (AMC), an area that extends across Russia, Kazakhstan, Mongolia and China. The collection of ALTB includes more than 450,00 specimens, making it the seventh largest in Russia and the fourth largest amongst Russian university herbaria. Altai State University (ASU), the home of ALTB, is one of the most important centres of academic education and research in Siberia and the Russian Far East. It is a sociocultural centre that provides a distinguished learning environment for undergraduate and graduate students in many scholarly and professional fields, meeting the needs of today's knowledge-based post-industrial society and contributing to regional development. It actively promotes international cooperation and strategic collaboration amongst countries of the AMC in the fields of science, education and culture. In particular, the activities of the South-Siberian Botanical Garden include: development of measures to protect rare and endangered plant species, research on the flora and vegetation of the AMC, preparation and publication of a multi-volume work "Flora Altaica", monographic study of individual plant groups, conducting laboratory classes, summer practicals and special courses. The main purpose of this article is to attract the attention of the scientific community to the botanical research of transboundary territory of the Altai Mountain Country (Russia, Kazakhstan, China and Mongolia) and to the future development of digital plant collections in partnership with Global Biodiversity Information Facility (GBIF).New informationThe Virtual Herbarium ALTB (Russian interface - altb.asu.ru) is the largest digital collection of plants from the transboundary territory of the Altai Mountain Country and the main source of primary material for the "Flora Altaica" project (http://altaiflora.asu.ru/en/). Since 2017, when Altai State University became a GBIF data publisher, data from the Virtual Herbarium ALTB has been exported to the dataset "Virtual Herbarium ALTB (South-Siberian Botanical Garden)" in GBIF. Currently, it includes images and data from 22,466 vascular plants, of which 67% have geographic coordinates (accessed on 30.03.2021). Most of the specimens have been collected since 1977, with the most intensive collecting years being 1995-2008. In 2019, the label-data table of the Virtual Herbarium ALTB was modified to bring it into conformity with the Darwin Core specification (http://altb.asu.ru/). This effectively solved the major impediment to sharing plant diversity data from the AMC and adjacent regions in a multilingual environment.
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Project description:Premise of the studyMycorrhiza are critical to ecosystem functioning, but a lack of historical baseline data limits our understanding of the long-term belowground effects of global change. Herbarium specimens may provide this needed insight. However, it is unknown whether DNA of arbuscular mycorrhizal fungi (AMF) can be reliably extracted from vascular plant specimen roots.MethodsWe sampled roots from herbarium specimens of four herbaceous forest species collected in western Pennsylvania between 1881-2008. Using molecular methods (terminal restriction fragment length polymorphism and sequence analysis), we quantified AMF communities from specimen roots and tested for contamination.ResultsWe successfully amplified AMF DNA from 44% (21/48) of the root but not leaf samples, indicating specimen contamination was negligible. As expected, there were significant differences in AMF composition between plant species (P < 0.05). However, no differences in AMF communities were detected through time, possibly due to limited sample size and low amplification rates in recent collections.DiscussionHerbaria have potential as sources of valuable belowground microbial data to answer questions across geographic, temporal, and taxonomic scales otherwise not feasible. Ongoing methodological developments will only magnify this potential. Further tests are needed to determine curatorial practices that maximize this innovative use of herbarium specimens.
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Project description:High-throughput sequencing of herbarium specimens' DNA with short-read platforms has helped explore many biological questions. Here, for the first time, we investigate the potential of using herbarium specimens as a resource for long-read DNA sequencing technologies. We use target capture of 48 low-copy nuclear loci in 12 herbarium specimens of Silene as a basis for long-read sequencing using SMRT PacBio Sequel. The samples were collected between 1932 and 2019. A simple optimization of size selection protocol enabled the retrieval of both long DNA fragments (>1 kb) and long on-target reads for nine of them. The limited sampling size does not enable statistical evaluation of the influence of specimen age to the DNA fragmentation, but our results confirm that younger samples, that is, collected after 1990, are less fragmented and have better sequencing success than specimens collected before this date. Specimens collected between 1990 and 2019 yield between 167 and 3403 on-target reads > 1 kb. They enabled recovering between 34 loci and 48 (i.e. all loci recovered). Three samples from specimens collected before 1990 did not yield on-target reads > 1 kb. The four other samples collected before this date yielded up to 144 reads and recovered up to 25 loci. Young herbarium specimens seem promising for long-read sequencing. However, older ones have partly failed. Further exploration would be necessary to statistically test and understand the potential of older material in the quest for long reads. We would encourage greatly expanding the sampling size and comparing different taxonomic groups.
| S-EPMC10735254 | biostudies-literature