Diversity assessment and visualisation of the Tula Oblast flora using modern data technologies

Tatyana Svetasheva (Tula State Lev Tolstoy Pegagogical University) ― general management and supervision of the project, preparation of collections for digitisation, databasing of specimens, georeferencing;

Alexey Seregin (Lomonosov Moscow State University) ― project design, general consulting, management and supervision of imaging and other digitisation activities, online publication of the collections, identification of specimens;

Irina Sheremetyeva (Tula State Lev Tolstoy Pegagogical University) ― identification of specimens and verification of earlier definitions, collection of fresh specimens;

Lyudmila Khoroon (Tula State Lev Tolstoy Pegagogical University) ― identification and verification of specimens, preparation of collections for digitisation;

Alexander Lakomov (Tula Local History Museum) ― georeferencing;

Dina Zatsarinnaya (Tula Local History Museum) ― georeferencing, preparation for digitisation of the collections of Tula Local History Museum (in process);

Elena Volkova (Tula State University) ― preparation for digitisation of the collections of Tula State University and State Museum Reserve "Kulikovo field" (in process);

Oleg Platko (Lomonosov Moscow State University) ― online publication of the collections, data audit, database administration.

Project Background and Aims. Biodiversity conservation is an urgent task for mankind. This environmental challenge is particularly acute in the Tula Oblast characterised by a highly-developed industry, a high proportion of agricultural land, as well as by a low proportion of protected natural areas. The project aimed at the inventory of vascular plant diversity at a new level. For the first time in Tula Oblast, a text database and GIS-module with geolocations have been complemented by the Library of high quality images of herbarium collections. The goal of the project is to assess the actual diversity and spatial structure of the Tula flora by combining various data sources on a single platform, visualising all the available information by digitising data and creating a multifunctional electronic resource with an open access. The main scientific idea is to make the Tula flora visible to the global community.

Project steps.

1. To combine the data on five herbarium collections made in Tula Oblast (stored in Tula State Lev Tolstoy Pedagogical University (TUL), Tula State University, Tula Local History Museum, State Museum Reserve "Kulikovo field" and Moscow State University (MW));
2. to image herbarium specimens;
3. to supplement the materials with photographs of plants in the wild;
4. to outwork a database of label transcriptions;
5. to georeference every specimen;
6. to create a regional information online resource "Digital Herbarium of Tula Oblast" (ca. 20,000 records).

The project is scheduled to run for three years and includes laboratory work with collections and field studies of the Tula Oblast flora. The first year of the project (from May of 2019 to May of 2020) was devoted to the accumulation and structuring of electronic data on the regional diversity of vascular plants. We performed processing (inventory, taxonomic revision and databasing) and digitisation of plant collections from Tula Oblast, preserved in Tula State Lev Tolstoy Pedagogical University (TUL) and Lomonosov Moscow State University (MW). As a result, 13,931 images made at 300 dpi were published via the Moscow Digital Herbarium (https://plant.depo.msu.ru/), including 9,000 specimens from the TUL Herbarium. We also made transcriptions of 12,991 labels and georeferencing of 12,909 specimens. Finally, the dataset of the TUL Herbarium has been published in GBIF and the dataset of MW has been published separately (Seregin 2020).

The obtained data on the Tula Oblast flora have already been used during the preparation of the second edition of the regional "Red Data Book" (Shcherbakov 2020, in press). These data are a solid basis for compiling general floristic reports, assessing the conservation status of species at various levels and developing the strategies for legal protection of rare species and plant communities.

See Acknowledgements section.

Preparation for digitisation

The preparation of the Herbarium collection for imaging included several steps.

1. A set of traditional methods and techniques for processing of herbarium specimens (Skvortsov 1977, Geltman 1995), checking the current state of previously-collected specimens, mounting; collecting and complete processing of new accessions.
2. A critical revision of identifications with the involvement of highly-qualified botanists specialising in certain taxonomic groups of plants: S.R. Mayorov — genera Thymus, Oenothera, Physalis, Sisymbrium, Coreopsis; A.V. Shcherbakov — family Potamogetonaceae; A.P. Seregin — genera Carex, Galium, Silene, Dactylorhiza.
3. Full label capturing into the MS Access database. The database consists of a system of interconnected tables and a set of frequently-used queries. The main table contains specimen information (phylum, class, family in Latin and in Russian; genus in Latin; species in Latin; authors of species; infraspecific taxa; authors of the infraspecific taxa; synonym from the original label; species name in Russian; geographical region; administrative region; administrative district; city; toponym (i.e. location, the nearest settlement or its vicinity, natural boundary etc.); habitat; collection date; collector's name; identifier's name; re-identification date; re-identifier's name; notes). The main Table also includes some technical fields for the data processing — sign (any character entered when creating special queries); number of the record (unique number that automatically increases by 1 in each new record); the herbarium number (unique number assigned to a specimen); date of recording; recording person.
4. Quality control. Сlarification and correction of the entered information with the help of specific queries selecting data on a certain collector, date, location etc. Some important information has been found in literature and some unpublished sources of botanists who worked in Tula Oblast. This allowed us to restore some information gaps in the available data and include them in the database.
5. Labelling. Each specimen has two labels, i.e. printed label retrieved from the database and the original one. New labels with the unique specimen number and TUL acronym have been obtained from the database by programming external links between MS Access and MS Word. In addition to the new ones, the original labels made by collectors have been placed on the Herbarium sheets to clarify the historical component of the Herbarium.
6. Barcoding. A barcode contains the name of the TUL Herbarium in Latin (Herbarium Universitatis Pedagogical Tulensis), TUL acronym and a six-digit number (like TUL006192). The barcodes were pre-ordered and printed typographically.

Creation a library of images (scanning and processing)

Imaging was carried out by the commercial partner (https://elar.ru/) on planetary scanners of A2 format with a resolution of 300 dpi in two steps in December 2019 and January 2020. The contribution from the commercial partner included:

1. transportation of 9,000 specimens from Tula to Moscow for imaging;
2. imaging of the front sides in TIFF format (300 dpi) with a scale bar;
3. converting TIFF files to JPEG copies;
4. renaming of the files against barcodes;
5. structuring of graphic images in accordance with their physical storage within the herbarium (directory names equal species names on folders);
6. manual quality control of the final images;
7. recording of images on storage media (HDD).

Electronic data capture

Each image was supplied with minimum metadata, for example, ID against barcode, species name from the folder and area code (Tula Oblast). The records from the MS Access database with full label transcriptions were cross-linked using barcode IDs and integrated into the dataset.

Georeferencing specimen data

Manual georeferencing is carried out using standard e-cartographic libraries (Yandex.Maps, Google Maps etc.). We used the old scanned maps (of the early 20th century) for georeferencing of some historical collections, since the names of some geographic locations have been changed or disappeared over time.

Manual georeferencing was supplemented by automatic georeferencing by the ISTRA system (Intellectual System of Toponymic Reading and Attribution), with several lines of the code being written in JAVA (Seregin and Stepanova 2020). This code is integrated into the Moscow Digital Herbarium and unavailable as a stand-alone product. The first algorithm of the ISTRA system combines the specimens into the groups according to the matching of the captured label text. In this case, there are two options for combining — complete matching mode and letters-only mode. The results do not differ in accuracy from the manual georeferencing. The second algorithm of the ISTRA system forms the specimen groups according to the matching of three fields—collection date, collector’s surname and curatorial area. Within the walking-day route, the standard georeferencing accuracy in most cases does not exceed 5 km. Further data refinement will help us to replace automatic georeferencing with a more accurate manual one. In both cases, the operator inserts the coordinates manually and the system sets the coordinates automatically for all specimens of the group. The first algorithm takes precedence over the second one. We save the log file and note the georeferencing method in the form of the standard disclaimers.

Publication of digitised collections

Digitised collections of the TUL Herbarium were published in the Moscow Digital Herbarium. This means that images and metadata are available on three platforms (Seregin 2018).

1. Moscow Digital Herbarium (https://plant.depo.msu.ru/) is actually an operational version with a number of search tools like label search, geosearch, search on the taxonomic tree, search by Latin and vernacular names etc. Data administrators of Lomonosov Moscow State University are managing the content and editing the data. IT staff are incorporating new large datasets like labels, georeferences, taxonomic treatments etc. The content of the portal is hidden from search robots, but users can download XLSX-files with general metadata. One can see basic statistics of the Moscow Digital Herbarium right on the homepage.
2. Open version (https://plant.depo.msu.ru/open/). – This portal is optimised for computers, tablets and mobile platforms. The content is updated once a day. The open version allows search robots to access the text and JPG images, as well as quick simple searches through all fields of the database. The content is accessible 24/7 even if we are updating the system or content. One can see search results in the form of small icons and search criteria could be saved as a unique URL.
3. Global Biodiversity Information Facility (https://www.gbif.org/). – Our data are fully available in GBIF without any limitations (Svetasheva and Seregin 2020). Since 2 November 2017, Moscow Digital Herbarium is updating the GBIF-mirror once a week, including datasets of the consortium members (Seregin 2020a). Loading the data into GBIF helps us check data consistency and find mistakes, like coordinate swapping, inaccurate georeferencing, errors in dates etc. The GBIF portal is the only place where one can download our geodata. The real advantage of GBIF is that it delivers our information to a wider community.

The TUL Herbarium was initially launched as a regional one and focused on the flora of Tula Oblast, including native and alien plants. Only a small part of the collections represents plant specimens from other regions of Russia and is not yet digitised. The main goal of plant collecting for years was a thorough investigation of various plant communities in all administrative districts of Tula Oblast according to the grid-mapping scheme (Shcherbakov 1999).

However, there are a number of reasons that did not allow complete sampling throughout the area:

• peculiarities of human transformation of vegetation cover of Tula Oblast, including wide distribution of agricultural land;
• more detailed study of protected nature areas;
• restricted access to certain areas (like museum-reserves);
• intensive studies of some areas during summer field practices of students.

As a result, some districts of Tula Oblast are well-studied and represented by numerous specimens, whereas other districts are poorly sampled. In Table 1, one can see the number of digitised specimens available in GBIF and number of all databased specimens collected in the administrative districts of Tula Oblast (Fig. 7) ranked in descending order.

Figure 7.  

Map of the administrative districts of Tula Oblast. Number of digitised specimens is given for every district in Table 1.

The most sampled area is Shchekinsky District (1,682 digitised specimens), where Leo Tolstoy Museum-Estate "Yasnaya Polyana" is situated. This institution is involved with nature conservation and biodiversity research and periodically supports studies of various groups of organisms. For example, some student master's theses (for instance, "Birch forests of Yasnaya Polyna" by T. Svetasheva, 1987–1991; "Spruce plantations of Yasnaya Polyana" by E.G. Balashova, 1987–1991) were performed due to the on-purpose contracts between the Museum-Estate and TSPI. From the other side, the Museum-Estate is situated not far from the University and is a convenenient place for field practices and botanical excursions.

The City of Tula (1,334) and adjacent Leninsky District (715) are holding the second and the third positions in the ranking. These administrative units are the places of regular excursions and individual assignments, as well as scientific research of the alien flora.

They are superseded by Suvorovsky, Yasnogorsky, Efremovsky, Odoevsky, Kimovsky, and Aleksinsky districts, where local biodiversity hotspots (including localities of rare and threatened plants), as well as some protected areas, are situated. Other districts are either situated on the fringes of the Tula Oblast or have vegetation greatly affected by human activity.

52.9 and 54.9 Latitude; 35.9 and 39 Longitude.

Most of the TUL Herbarium collections are represented by vascular plants from Tula Oblast, of which 95% are currently digitised. The focus of the Herbarium is on native and alien flora, whereas cultivated plants of Tula Oblast are almost missing. The brief taxonomic outline of the collections is based on GBIF dataset with 9,000 specimens.

For many years, we followed the standard "Flora of the middle zone of the European part of Russia" by P.F. Mayevsky (Maevsky 2006, Maevsky 2014) for taxonomy and nomenclature. In recent years, with the emergence of powerful online resources, we used for databasing the taxonomic backbone of the "Plantarium: open on-line atlas and key to plants and lichens of Russia and neighbouring countries" (Oreshkin 2020), based on several modern taxonomic sources. In the Moscow Digital Herbarium, all names accepted in the collection were automatically cross-referenced with the Catalogue of Life (https://www.catalogueoflife.org/).

The digitised TUL collections of vascular plants contain 9,000 specimens which belong to 1,131 species and nothospecies (hybrids), 514 genera, 98 families, 40 orders and five classes. The correlation of represented orders is shown in Fig. 8 retrieved from GBIF webpage of our dataset. There are no type materials in the TUL Herbarium.

Figure 8.  

The leading classes and orders in vascular plant collections of the TUL Herbarium.

The most sampled families, genera and species of the TUL Herbarium are given in Table 2, Table 3 and Table 4.

TUL Herbarium documents hundreds of localities of rare and protected species of the region. Its collections were intensively used during the preparation of the "Red Data Book of Tula Oblast". In the current first edition of the Book (Shcherbakov 2010), there are 165 species of vascular plants. The updated second edition which is in preparation now includes 158 species, of which 129 are represented in the TUL Herbarium (Table 5).

At present, 29 of 158 legally-protected species of Tula Oblast are not represented in the TUL Herbarium. Most of them are kept in the Moscow University Herbarium (Seregin 2020b), as well as in some lesser herbaria of Tula. Some of these species are very rare or their populations are too small to afford collecting of at least a single individual. Nevertheless, one of the important tasks of the Herbarium is to replenish the collections with specimens of the missing species in a professional manner.

This work is licensed under a Creative Commons Attribution (CC-BY) 4.0 License.