TUL Herbarium: collections of vascular plants of Tula Oblast, Russia

Abstract Background TUL 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 information The 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).


Introduction
TUL is an acronym of the Herbarium of the Tula State Lev Tolstoy Pedagogical University (TSPU), Russia, which is the main custodian of the herbarium collections from Tula Oblast and one of the oldest in Tula institutions with the natural history collections. The acronym was assigned to the Herbarium in 2019 (New York Botanical Garden 2019).

Geography & Nature
Tula Oblast is located in the Central Federal District of Russia, covering an area of 25,700 km . It borders Moscow Oblast in the north, Ryazan Oblast in the east, Lipetsk Oblast in the southeast, Oryol Oblast in the southwest and Kaluga Oblast in the west. The climate is moderate continental, with precipitation declining from 575 mm in the northwest to 470 mm in the southeast, average July temperature is about +19...+20°C and average January temperature is −10...−9°C.
Vegetation of Tula Oblast includes zones of broadleaved forests in the central part, foreststeppe in the south and east and a narrow strip of the ecotone subtaiga zone in the west and north. The combination of three vegetation zones contributes to the significant diversity of the flora, which includes both northern and southern elements.

Historical background
Tula State Lev Tolstoy Pedagogical University was founded on 19 September 1938 as a federal institution of higher education with the name Tula State Pedagogical Institute. On 18 July 1958, it was named after Lev Tolstoy. On 24 December 1994, it was awarded the status of State Pedagogical University.
The collecting of plant specimens began in the 1960s, when the Faculty of Chemistry and Biology was launched at the Tula State Pedagogical Institute (TSPI). The first collections were made by the students during their summer field practices, as well as from individual assignments on the Botany course. The first herbarium specimens have non-standard appearance and size, since the paper for the specimens was chosen by students at random and it was often cut out manually and then covered with tracing paper attached on the left edge to preserve dry plants. There are ca. 100 those non-standard sheets from the 1960s.
In the 1970s, institute students were the main contributors to the herbarium collections. The specimens acquired a bit more standardised appearance and constant size of sheets 25 x 34 cm, but still differed from the 28 x 42 cm size accepted in the major Russian herbaria. The majority of specimens were supplied with a standard pre-printed label, which included the heading of Tula State Lev Tolstoy Pedagogical Institute in Russian (Fig. 1). With 344 specimens, the total number of collections of 1970s has increased in comparison with the 1960s by about 3.5 times. It is noteworthy that, amongst these old sheets, there are specimens collected by students who later became teachers at the Tula State Pedagogical University and some of them are still working there.
The second half of 1980s became a period of important changes in the scientific life of TSPI. By 1986, the herbarium collection of the Botany Department consisted of several hundred sheets and continued to grow quickly. There was no special hall or even a special cupboard for herbarium storage, so huge piles of specimens were kept just in the labs and staff workrooms.
In 1987, the Botany Department was headed by Professor Lyudmila Fedorovna Tararina (Fig. 2). She initiated the organisation of the scientific herbarium, convinced the administration to provide a room for herbarium storage and equipped it with several custom-made cupboards (Sheremetyeva 2005). In addition, she brought a remarkable feature to the general outlook of our herbarium sheets by ordering a supply of pink paper (30 x 45 cm) for mounting the specimens (Fig. 3).
The first curator of the Herbarium in 1987 was Irina Sergeevna Sheremetyeva (Fig. 4), who just at that time started to teach Botany in TSPU and work under her PhD thesis "Flora of Tula Oblast" (Sheremetyeva 1999). The formal foundation of the herbarium gave a powerful impulse to active botanical research. In 1987, 1,368 specimens were collected in a single year, a threefold increase compared to all previous collections. This number includes scientific collections from various districts of Tula Oblast, as well as student's collections made for the scientific herbarium. In 1988, a large plant collection of Alexey Ivanovich Alyushin  consisting of 2,104 specimens was gifted by his relatives to the Herbarium. Alyushin was a school teacher and skilled naturalist, who especially loved Botany. In 1941-1945 he also worked at the Tula Local History Museum (Lakomov and Svetasheva 2005) (Fig. 5). He intensively investigated the flora of Tula Oblast and made an outstanding collection of vascular plants. His collections are shared by three Herbaria at present -TUL (2,104 specimens), Tula Local History Museum (ca. 1,000) and MW (297). Alyushin published two popular books about plants of Tula Oblast (Alyushin 1975, Alyushin 1982.    The period 1987-1999 became the most productive time for the accumulation of plant specimens in the TUL Herbarium (ca. 5,000 specimens). Several scientific research activities, based on intensive collection expeditions across Tula Oblast, were completed at that time, like "Flora of Tula Oblast" (Sheremetyeva 1999), "Adventive flora of Tula Oblast" (Khoroon 1999) and "Register of vegetation cover of Tula Oblast" (unpublished scientific report by L.F. Tararina and I.S. Sheremetyeva). A.V. Shcherbakov from Lomonosov Moscow State University made a large collection of aquatic plants (322 specimens) in line with the preparation of the "Atlas of flora of the Tula Oblast water reservoirs" (Shcherbakov 1999) and habilitation thesis "Hydrophilic flora of vascular plants as a model object for inventory and analysis of flora: the example of the Tula and neighboring regions" (Shcherbakov 2011). Large collections on the flora of Yasnaya Polyana Museum-Estate were made by E.G. Balashova, T.Yu. Svetasheva and I.L. Dorokhina for their master's theses (782 specimens).
In the 2000s, the Herbarium was supplemented with ca. 660 specimens mainly due to a series of works devoted to the study of protected areas of Tula Oblast (1999( -2005 and the preparation of the "Red Data Book: Specially Protected Natural Areas of Tula Oblast" (Tararina et al. 2007) and "Red Data Book of Tula Oblast: Plants and Fungi" (Shcherbakov 2010). Therefore, a significant part of those collections includes specimens of rare and threatened plants. The standard regional checklist, entitled "Synopsis of the flora of vascular plants of Tula Oblast", was published upon thorough study of available collections and vast literature (Sheremetyeva et al. 2008). After 2010, the Herbarium continued to be filled mainly by the collections of students, but their collections were transferred to the educational collection, which is used during lab classes and is not part of the Herbarium. However, in 2018-2019, the TUL Herbarium was replenished with recently-collected specimens due to the preparation of the second edition of the regional "Red Data Book" and monitoring of the protected natural areas . It should be noted that, since the 2000s, the Tula scientists began to form collections of the other groups, for example, fungi, lichens and mosses. Gradually, by 2019, the TUL Herbarium represents a significant base of the Tula Oblast biodiversity, including ca. 10,000 specimens of vascular plants, ca. 1,000 specimens of bryophytes and ca. 2,000 specimens of fungi and lichens.
Today, the Herbarium occupies one room (ca. 25 m ) in the building of the Faculty of Natural Sciences of Tula State Lev Tolstoy Pedagogical University located on 125, Lenina Prospect, in Tula. There is no special regular staff in the TUL Herbarium.
At the end of 2018, Lomonosov Moscow State University, which also houses some plant collections from Tula Oblast, suggested to combine efforts to digitise the entire collection of the Tula flora and place the obtained data on the Internet using a platform of the Moscow Digital Herbarium. The created project "Diversity assessment and visualisation of the Tula Oblast flora using modern data technologies" has been supported by RFBR and Tula Oblast Goverment and this has brought the Herbarium to a higher level. In 2019, the acronym TUL was assigned to the Herbarium of Tula State Lev Tolstoy University after its registration in Index Herbariorum. By 2020, after the first year of project, the larger part of the collections of vascular plants has been digitised, georeferenced and finally published within the Moscow Digital Herbarium and on GBIF.

Project description
Title: Diversity assessment and visualisation of the Tula Oblast flora using modern data technologies Oleg Platko (Lomonosov Moscow State University) -online publication of the collections, data audit, database administration.

Study area description: Tula Oblast
Design description: 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 supplement the materials with photographs of plants in the wild; 4.
to outwork a database of label transcriptions; 5.
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 .
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.
Funding: See Acknowledgements section.

Sampling description: 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: 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 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.

Geographic coverage
Description: 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 gridmapping 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. 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, 1987Svetasheva, -1991; "Spruce plantations of Yasnaya Polyana" by E.G. Balashova, 1987Balashova, -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. Map of the administrative districts of Tula Oblast. Number of digitised specimens is given for every district in Table 1.

Rank First-level administrative unit (districts, cities) Number of digitised specimens Estimated total
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.

Taxonomic coverage
Description: 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.
The most sampled families, genera and species of the TUL Herbarium are given in Table 2, Table 3 and Table 4.     Table 4.
The top species in vascular plant collections of the TUL 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. The temporal distribution of collected specimens over decades is given in Fig. 9.    The top collectors of the TUL Herbarium.