Digital Herbarium Research Articles

Digitization of herbarium collection of Manash Kozybaev North-Kazakhstan university as a result of digital technology integration in herbarology

Nowadays, all areas of human knowledge are firmly interacting with digital technologies. These technologies open up new approaches to study and research methods in most scientific fields.The article shows the integration of digital technologies in herbarium science. The relevance of digitization of herbarium collections is described. An algorithm for creating a digital herbarium is presented and a method for publishing the data is proposed. The limiting factors and advantages of working with electronic herbarium are noted.

Two Million Contributions From Citizen Scientists Accelerate the Digitization of the Berlin Herbarium

In 2016, the Botanic Garden Berlin decided to translate into German, the citizen science platform "Les Herbonautes" (Rouhan et al. 2016, developed at the Natural History Museum in Paris) and to integrate it into the digitization workflows of Herbarium Berolinense. "Die Herbonauten" is a web-based platform on which citizen scientists can contribute to the transcription of digital herbarium specimens and their labels. Using a quiz module, users first learn about the various information elements on herbarium labels and their correct semantic assignment and recording. The actual data entry then takes place in so-called "missions," in which herbarium specimens are compiled, e.g., to support work on specific scientific questions. In addition to data entry, there is a forum in which users can discuss problems and their solutions, for example if there is disagreement about the correct transcription of a text element. The forum is moderated by scientific staff of the Herbarium Berlin, who provide support particularly when the knowledge of the collection curators is needed to solve problems. In the course of numerous missions, the knowledge about transcriptions of herbarium specimens was summarized and structured in an evolving and extensive wiki system in German. This wiki has developed into a unique and valuable knowledge base for which an English translation is planned for use by an international audience. To date, 640 registered Herbonauten have made around two million data contributions. Citizen science has thus become an indispensable component of the herbarium's information management. For the further development of the platform, we are experimenting, among other things, with expanding the scope, e.g., to include the recording of character data, and with combining citizen science approaches with AI-based transcription algorithms. In the context of the EU project, Transforming European Taxonomy through Training, Research and Innovations (TETTRIs), the Herbonauten carry out joint missions with other citizen science platforms, where selected specimens are processed by communities that are particularly qualified, for example because they have the necessary knowledge of languages or local geography.

Diversity of Bambusa Species (Poaceae, Bambusoideae) in Kalimantan, Indonesia

Bamboo is reported to have many benefits, including as handicraft material, fishing, building materials, household appliances, furniture, food containers, medicines, vegetable materials, and firewood. In Indonesia, bamboo species richness is quite high with 175 bamboo species that can be found spread from Java to Papua. Research information on Bambusa species data in the Kalimantan region is relatively scarce and invalid. The research aims to provide data on the diversity of Bambusa species in Kalimantan. The research method was carried out descriptively by observing morphological characters from herbarium specimens and digital herbarium. Data were collected from herbarium specimens of bamboo genus Bambusa collected from Kalimantan and digital specimen data stored in online database portals, such as GBIF and Bioportal. All specimens were re-identified and their names validated. The results showed that there are five species of Bambusa in Kalimantan, namely Bambusa glaucophylla Widjaja, B. multiplex (Lour.) Raeusch. ex Schult.f., B. spinosa Roxb., B. tuldoides Munro, and B. vulgaris Schrad. The presentation is complemented by identification keys and explanations.

Heritage of A.P. Khokhryakov in the digital herbarium of the Central Siberian Botanical Garden SB RAS

The article is dedicated to the memory of A.P. Khokhrjakov, a famous Soviet and Russian botanist, who was tirelessly passionate about collecting scientific herbarium throughout his life. The contribution of A.P. Khokhryakov to the study of biodiversity is shown by the example of the genus Salix L. (Salicaceae) specimens in the Digital Herbarium of the Central Siberian Botanical Garden SB RAS. Collectors of S. magadanensis Nedol. type specimens are clarified.

Studying the species distribution of rhubarbs (Rheum L.) in Kazakhstan

Critical processing of herbarium materials revealed the distribution in Kazakhstan of 10 species of the genus Rheum, including Rheum compactum L., R. wittrokii Lundstr., which are classified as rare and declining in number. R. altaicum Losinsk. was discovered – relict and endemic of Altai. To clarify the distribution in Kazakhstan and compile a summary of species of the genus Rheum, 143 herbarium sheets (1840 – 2024) from the Altai Botanical Garden (ABG), Institute of Botany (AA), and the digital herbarium of Moscow State University (MW) were reviewed and processed. 253 actual places of growth were identified for 10 species of rhubarb from the flora of Kazakhstan, belonging to 5 sections: Rhapontica A. Los., Deserticola Maxim., Orbicularia A. Los., Spiciformia A. Los., Ribesiformia A. Los. A high species diversity of rhubarb was established in the Dzungarian Alatau, Altai, Tarbagatai and Ile Kungei Alatau. Geographically, the most widespread are R. tataricum, R. nanum and R. wittrockii. The research made it possible to systematize, clarify and supplement information on the species diversity and distribution of the genus Rheum in the flora of Kazakhstan.

Digitization of the herbarium collection of Irkutsk State University

Since 2019, the Herbarium of Irkutsk State University (IRKU), the largest herbarium collection in Eastern Siberia (150,000 samples), including collections of the XIX century, has been digitized. By March 2023 on the MSU Digital Herbarium platform (https://plant.depo.msu.ru/) 42,297 samples of the IRKU collection from various regions of Siberia and the Far East are freely available. Among them there are species included in the regional and federal Red Books. A modular regional portal “Flora of Baikal Siberia” has been created (https://baikal.depo.msu.ru/) containing 64,163 samples from the territory of Baikal Siberia. More than 42,000 records are integrated into the international GBIF platform.

Study of Hedysarum theinum (Fabaceae Lindl.) in the flora of Kazakhstan

Analysis of historical data on the distribution of Hedysarum theinum Krasnob. in Kazakhstan presented in this paper is based on herbarium collections kept at the Institute of Botany and Phytointroduction, Almaty and the Digital Herbarium of Moscow State University, Moscow, as well as a list of species of Hedysarum theinum on the Ivanovsky Ridge, Kazakhstani Altai with specimens collected as a result of expedition trips to the study area. The cenoflora includes 176 species from 120 genera and 41 families. The hierarchical order of the leading families is as follows: Asteraceae Dumort, Poaceae Barnhart, Ranunculaceae Juss., Rosaceae Juss. Comparative analysis of life forms shows that short rhizomatous plants prevail – 33%, as taproot plants constitute 24% and tussock plants – 11%. The basis of communities in relation to the temperature, moisture and substrate structure are made of the following ecological groups of plants: mesophytes – 30%, and, in a smaller proportion, of mesohygrophytes – 19%, mesoxerophytes – 20% and mesopsychrophytes – 18%.

Statistics and Analysis of Digital Information on Vascular Plant Specimens and the History of Plant Collecting in Guangzhou, China.

This paper presents a comprehensive analysis of digitized specimen data and relevant literature to investigate the vascular plant diversity in Guangzhou City, China. Specimen data were collected from various sources, including the China Digital Herbarium (CVH), the National Specimen Resource Sharing Platform (NSII), Global Plants on JSTOR, and the Global Biodiversity Information Facility (GBIF). Following data standardization, the study identified 41,890 vascular plant specimens, encompassing 248 families, 1563 genera, and 4536 species, including subspecies and cultivated plants. Among them, the native plants of Guangzhou city accounted for 60.6% of the species. The temporal analysis identified three distinct peaks in specimen collection: 1916-1920, 1928-1936, and 1950-1964. Collection activities were primarily concentrated between the months of April and November. The distribution of collected specimens exhibited significant variation among different species, with families such as Fabaceae, Poaceae, and Myrtaceae having the highest number of specimens. Similarly, genera such as Eucalyptus, Ficus, and Citrus were well-represented. The most frequently collected species included Litchi chinensis, Eucalyptus robusta, and Cycas taiwaniana. Remarkably, 21 species had specimen counts exceeding 100. Unfortunately, approximately three-quarters of the species had fewer than 10 recorded specimens. Alarmingly, 1220 species were represented by only one specimen. Geographically, the majority of specimens originated from the former suburbs of Guangzhou, Conghua Delta Mountain, and Liuxi River areas, while other regions had limited representation. In terms of specimen collections, the Herbarium of South China Botanical Garden of the Chinese Academy of Sciences (IBSC) recorded the highest number of specimens (13,828 specimens), followed by the Tree Herbarium of South China Agricultural University (CANT; 3869 specimens) and the Herbarium of Sun Yat-sen University (SYS; 3654 specimens). The collection history in Guangzhou spans nearly 300 years and can be broadly divided into two distinct periods. The first period extends from the late 13th century to 1949, primarily encompassing the collection efforts of foreign visitors in Guangzhou, and represents the pioneering phase of plant taxonomy research in China. The second period, from 1949 to the present, is characterized by extensive investigations and collection activities conducted by local scholars, with a specific emphasis on native plant resources. By meticulously organizing and verifying information derived from historical documents and specimens, the paper effectively summarizes the plant collection and research history of Guangzhou, providing detailed profiles of the key collectors. These findings furnish reliable historical reference materials for the study of plant taxonomy and diversity in Guangzhou.

GEODATA OF THE MOSCOW UNIVERSITY HERBARIUM: DATA STRUCTURE AND GEOREFERENCING METHODICS

Digitisation of the Moscow University Herbarium (MW) was started in the spring of 2015. Since October 2016, we have been publishing the images of specimens on the portal of the Moscow Digital Herbarium (https://plant.depo.msu.ru/) in open access mode. Gradually, we started to publish extended metadata on our portal, like full transcriptions of labels and georeferences, i.e. the coordinates of collection sites for each specimen. As of January, 14, 2023, two thirds of the specimens of the Moscow University Herbarium (693168 specimens, or 66%) are georeferenced, while 359593 specimens are still in work. The article describes the geodata of the Moscow University Herbarium both in the geographical aspect (data coverage for different regions) and in the aspect of georeferencing accuracy. General guidelines for georeferencing herbarium collections are given.

Indian Virtual Herbarium: The country's largest digital herbarium and a new resource for botanists

TAXONVolume 72, Issue 1 p. 221-226 IAPT CONTENT Indian Virtual Herbarium: The country's largest digital herbarium and a new resource for botanists Kumar Avinash Bharati, Kumar Avinash Bharati Central National Herbarium, Botanical Survey of India, Howrah, 711 103 West Bengal, IndiaSearch for more papers by this authorA.A. Mao, A.A. Mao Botanical Survey of India, CGO Complex, Salt Lake City, Kolkata, 700 064 West Bengal, IndiaSearch for more papers by this authorAnand Kumar, Corresponding Author Anand Kumar anand_kum234@rediffmail.com Central National Herbarium, Botanical Survey of India, Howrah, 711 103 West Bengal, India Address for correspondence: Anand Kumar, anand_kum234@rediffmail.comSearch for more papers by this author Kumar Avinash Bharati, Kumar Avinash Bharati Central National Herbarium, Botanical Survey of India, Howrah, 711 103 West Bengal, IndiaSearch for more papers by this authorA.A. Mao, A.A. Mao Botanical Survey of India, CGO Complex, Salt Lake City, Kolkata, 700 064 West Bengal, IndiaSearch for more papers by this authorAnand Kumar, Corresponding Author Anand Kumar anand_kum234@rediffmail.com Central National Herbarium, Botanical Survey of India, Howrah, 711 103 West Bengal, India Address for correspondence: Anand Kumar, anand_kum234@rediffmail.comSearch for more papers by this author First published: 07 February 2023 https://doi.org/10.1002/tax.12873 Plant Systematics World edited by Sandra Knapp & JunWen First published as part of this issue. See online for details. Read the full textAboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onFacebookTwitterLinkedInRedditWechat Volume72, Issue1February 2023Pages 221-226 RelatedInformation

Floristic Composition, Diversity, Palatability, and Forage Availability of Forest Rangelands in the Southern Mediterranean Region of Northern Morocco

Forest rangelands are an important component of extensive goat production in the Mediterranean region. The aim of this study was to survey the floristic composition, lifespan, life forms, phytogeographic relationships, palatability degree, and forage availability of forest rangelands in Northern Morocco. To achieve this goal, a plant species inventory was carried out, and a digital herbarium was constructed. Forage availability was estimated using the quadrat method. According to the results, 358 taxa were recorded with 228 genera and 66 families. The flora is mainly dominated by Asteraceae, Fabaceae, Poaceae, and Lamiaceae families. Six principal life forms of plants were recognized with the predominance of therophytes (48.3%). The Mediterranean floristic category was the most dominant in the flora (73.7%) with 264 species. The palatability degree was studied for 95 taxa, known by herders. The palatable plant group was highly represented with 32 species. Of these identified taxa, 93% were evaluated as potential sources of forage for grazing animals. The forage availability depended considerably on the season and the existing plant species (p < 0.01). The spring recorded the higher value with 3143 kg DM/ha. In conclusion, forest rangelands have a high biodiversity, which they need for rigorous protection to preserve their floristic composition and diversity.

On two species of Dracocephalum L. (Lamiaceae)

A composition of taxa included in Dracocephalum imberbe Bunge s. l. is discussed. Species rank of D. laniflorum Rupr. is reinstated based on the following characters: underground part is represented by a system of branching rhizomes, bracts absent, calyx 12–14 mm long, with triangular or narrowly triangular, pointless teeth, the middle tooth of the upper lip up to 1.5 times wider than the lateral ones and plant being nearly scentless. In contrast, in D. imberbeunderground part is represented by the taproot and developed branches of the caudex, bracts present, with well-developed non-rigid points, calyx 15–18 mm long, with lanceolate or narrowly triangular pointed (though not rigid) teeth, the middle tooth of the upper lip 1.5–2 times wider than the lateral ones, the presence of a smell that persists in herbarium specimens. Dracocephalum laniflorum is firstly reported for flora of Kazakhstan (Almaty Region) and China(Xinjiang Uygur Autonomous Region) based on the study of herbarium materials stored in AA and LE, as well as scanned herbarium specimens stored in MW, HNWP and PE, which were available through the Moscow Digital Herbarium and Chinese Virtual Herbarium (CVH) systems.

Conspectus of the genus <i>Juniperus</i> L. growing in Kazakhstan

Background. The genus Juniperus L. is the most numerous in the family Cupressaceae Bartl. and includes about 75 species. There are from 7 to 10 species of this genus in Kazakhstan. All types of juniper are widely used in folk medicine and play an important ecological role. The purpose of our work was to study the current status, systematics and distribution of juniper species. This will help to clarify and expand the information on the current location of Juniperus species in Kazakhstan and will be used in the future to study intra- and interspecific genetic diversity of the genus.Materials and methods. To study the distribution and make a conspectus of the Juniperus spp. growing in Kazakhstan, floristic reports, materials of plant explorations and the herbarium collections for the period from 1890 to 2021 obtained from the herbarium of the Institute of Botany and Phytointroduction (AA), herbarium materials of the Institute of Plant Biology and Biotechnology as well as the digital herbarium of the Lomonosov Moscow State University – Depository of Living Systems “Noah’s Ark” (MW) were analyzed.Results. As a result of the study, 630 herbarium sheets were processed and 70 locations of 7 juniper species growing in Kazakhstan belonging to 2 sections – Juniperus (=Oxycedrus Endl.) and Sabina Endl. – were identified. A conspectus of 7 juniper species identified during the analysis of the three above-mentioned herbarium collections was made. The main division of species is observed in the context of administrative and floristic regions of Kazakhstan. The greatest species concentration occurs in Southern, South-Eastern and Eastern Kazakhstan. The results of the study contribute to the inventory and search for previously forgotten places of growth for the genus Juniperus. Besides, the continuation of comprehensive botanical and molecular genetic studies on junipers will help to examine and preserve the genetic diversity of the species and conserve forest bioresources.

Comparative analysis of the leaf architectural characters of Saurauia bontocensis Merr. and Saurauia polysperma (Blanco) Merr. with the application of Digital Image Analysis Software

Abstract. Daipan BPO, Buot IE Jr., Daipan HMO. 2022. Comparative analysis of the leaf architectural characters of Saurauia bontocensis Merr. and Saurauia polysperma (Blanco) Merr. with the application of Digital Image Analysis Software. Biodiversitas 23: 3869-3875. Major confusion still exists among several authors concerning the taxonomy of the dagwey plant. This species is economically significant to the Ikalahan tribe of Luzon, Philippines. Several papers claimed that the plant is Saurauia bontocensis, while others stated that it is Saurauia subglabra. Many botanical websites claimed that S. subglabra is synonymous with S. polysperma, while another article distinguished S. subglabra from S. polysperma. Thus, to help resolve the taxonomic ambiguities, this paper performed a comparative analysis of the leaf architectural characters of S. bontocensis and S. polysperma with the aid of digital image analysis software and cluster analysis. Results revealed that the blade characters alone, delineate the two species, particularly, in terms of the laminar size, shape, symmetry, leaf L:W ratio, base and apex angle, and base shape. Additionally, the leaf venation characters delineate the two species, specifically, on the 2º to 5º vein categories, 2º vein angle, 3º vein course, 3º vein angle to 1º, areolation, freely ending ultimate veins, marginal ultimate venation, and leaf rank. Generally, S. bontocensis have larger, longer, and wider leaves compared with the S. polysperma. The leaf architecture analysis performed in this paper produced a very promising result in differentiating the two Saurauia species and could be used to address some of the taxonomic confusion of these species. The study indicated that S. bontocensis and S. polysperma are two distinct species. Moreover, the use of digital image analysis software was very helpful in the computations of the various blade characters, particularly the digital herbarium exsiccate in the absence of actual leaf samples.

Lectotypifications of Three Names in Garcinia, Synonymy of Garcinia pedunculata and Detailed Descriptions of Three Species in Garcinia Section Brindonia (Clusiaceae)

A revision of the genus Garcinia has recently been undertaken by the author as part of the Flora of Thailand. Herbarium specimens deposited in several herbaria, and those included in the digital herbarium databases, were examined by consulting taxonomic literature. In this study, the three names in Garcinia section Brindonia are lectotypified as G. gracilis, G. lanceifolia and G. planchonii. A new synonym for G. pedunculata, namely G. planchonii, is proposed. Detailed descriptions, recognitions and illustrations of three species in Garcinia (G. atroviridis, G. lanceifolia and G. pedunculata) are presented, along with information on distributions, specimens examined, habitats and ecology, IUCN conservation status, phenology, etymology, vernacular names and uses. The fruits, the young shoots and leaves, and the flowers of these three species are edible and have a sour taste. These species are often cultivated for their fruits.

Genotyping NS and NSK herbaria specimens of Hedysarum (Fabaceae) using DNA sequencing

Over 2000 specimens of the genus Hedysarum L., belonging to 48 species and 4 subspecies, were digitised and placed into CSBG SB RAS Digital herbarium whilst making a digital inventory of the herbarium collections of the Central Siberian Botanical Garden (NS, NSK). Totally, 466 nucleotide sequences were determined for 136 voucher specimens using the Sanger sequencing method. DNA sequences were obtained for 25 Hedysarum taxa for the first time.

Geranium (Geraniaceae) in the digital herbarium of the Central Siberian Botanical Garden SB RAS

During the inventory of the I.M. Krasnoborov (NS) and the M.G. Popov (NSK) herbaria collections, a total of 2793 specimens of the genus Geranium were digitised and placed into CSBG SB RAS Digital herbarium. There were 1500 herbarium sheets in the NS and 1293 specimens in the NSK, 94 taxa in total, containing species, subspecies, variations and forms. The results of digitisation were published as a dataset in the Global Biodiversity Information Facility (GBIF). A short history of the taxonomic study of Geranium collections is given and type specimens of 6 Geranium taxa stored in NS and NSK herbaria are cited.

Vicki Funk's legacy continues – The IAPT Small Collections Grant

Vicki Funk's legacy continues – The IAPT Small Collections Grant

Ferns at the digital herbarium of the Central Siberian Botanical Garden SB RAS.

BackgroundAccording to the data in Index Herbariorum as of 1 December 2020, there are 3426 active herbaria in the world, containing 396,204,891 specimens and 124 herbaria in Russia with more than 16,175,000 specimens. The Central Siberian Botanical Garden of the Siberian Branch of the Russian Academy of Sciences (CSBG SB RAS, Novosibirsk), founded in 1946, historically has two herbarium collections (NS and NSK). Currently these collections contain about 800,000 herbarium specimens comprising vascular plants, mosses, lichens and fungi gathered from all over the world. Digitisation of the NSK type specimens of vascular plants began in 2014 by using the special scanner Herbscan. In 2018, we started digitisation of the NS and NSK collections by using ObjectScan 1600.Pteridophytes (ferns, lycophytes and their extinct free-sporing relatives) are a diverse group of plants that today comprises approximately 12,900 species and plays a major role in terrestrial ecosystems. All herbarium specimens of ferns, collected over 170 years between 1851 and 2021 and stored in the NS and NSK collections, were digitised in 2021, placed at the CSBG SB RAS digital Herbarium (http://herb.csbg.nsc.ru:8081) and published through GBIF. Twenty families of Polypodiopsida, but not Equisetaceae, were included in this dataset. Family Ophioglossaceae was digitised and published in GBIF as a separate dataset.New informationBy August 2021, more than 62,600 specimens with good quality images and fully-captured label transcriptions had been placed at CSBG SB RAS Digital Herbarium. A total of 7,758 records of fern occurrences of 363 taxa in the world with 92% geolocations including 5100 records from Russia with 98.7% geolocations that are new for GBIF.org in 2021 were entered. In the dataset specimens from 43 countries of Europe, Asia, America, Africa and Australia (Oceania), 89% of them from Russia, are presented.

ГИС-анализ распространения охраняемых видов растений на Крымском полуострове

The article presents the results of the analysis of the protected plant species distribution on the Crimean peninsula using GIS technologies. The mapping of protected species is an important scientific and conservation task. The knowledge of the protected species location allows us to effectively select environmental protection measures, to introduce restrictions in the schemes of economic use and territorial planning. As a source of information, we used data from the Global Biodiversity Information Fund (GBIF), which unites such large databases of Russian biodiversity as the Moscow State University Digital Herbarium and the INaturalist portal. The resulting dataset includes 5187 records of 196 taxa of protected Crimean species. The dataset includes 58 plant families. It was determined that the maximum number of observations was noted for trees, especially conifers—high juniper (198) and deltoid juniper (286). Many observations are available for flowering plants—Crimean peony (157), purple orchis (161), dwarf iris (161). It is shown that a high concentration of finds of protected plant species is noted in the southwestern part of Crimea, on the southern coast and in the mountainous part. Separate local areas with protected plant species are noted along the sea coast. It is calculated that the largest number of detected protected plant species falls on the mid-mountain landscape level, the smallest—on the upland level. It was revealed that about 100 species of protected plants of Crimea are not registered in GBIF, which requires special research. The maximum number of species for which there are no data in the databases used are very rare and grow in remote parts of the peninsula. They are partly represented by relics, stenotopic species, single populations, which complicates their search. The obtained results can be used for monitoring protected plant species, territorial planning, environmental studies at the design stage of new residential and infrastructure facilities.