Biodiversity Data Journal :
Data Paper (Biosciences)
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Corresponding author: Nina Filippova (filippova.courlee.nina@gmail.com)
Academic editor: Dmitry Schigel
Received: 06 Apr 2020 | Accepted: 17 Jun 2020 | Published: 09 Jul 2020
© 2020 Nina Filippova, Stanislav Arefyev, Elena Zvyagina, Vladimir Kapitonov, Tatiana Makarova, Victor Mukhin, Nellya Sedelnikova, Iraida Stavishenko, Anton Shiryaev, Tatiana Tolpysheva, Natalia Ryabitseva, Alexander Paukov
This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Citation:
Filippova N, Arefyev S, Zvyagina E, Kapitonov V, Makarova T, Mukhin V, Sedelnikova N, Stavishenko I, Shiryaev A, Tolpysheva T, Ryabitseva N, Paukov A (2020) Fungal literature records database of the Northern West Siberia (Russia). Biodiversity Data Journal 8: e52963. https://doi.org/10.3897/BDJ.8.e52963
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Mycological research in the Northern part of West Siberia has now become sufficient for review and digitisation as over 460 scientific works have been completed mainly since the beginning of the 20th century. The history of research in the region started from isolated studies at the beginning of the 20th century, but regular and systematic research started from the 1970s. Over the following decades, several dozens of researchers have worked in the area, but the reported occurrences were scattered amongst a broad variety of publications, mainly hardly available. The great need in digitisation and accumulation of fungal records reported in published literature in a standardised regional database has now become evident. The «Fungal records database of the Northern West Siberia» (FuNWS) was initiated in 2016 according to contemporary biodiversity data standards (Darwin Core), to be compatible and accessible by the broad research community. The database has been supplemented ever since by the collective effort of specialists working in the area. According to the database summary report, there are 3358 fungal and fungus-like species revealed in the Northern West Siberia at present. The richest in species number classes are Agaricomycetes (60%) and Lecanoromycetes (33%) with a total of 25 classes represented. The FuNWS database was uploaded to Global Biodiversity Information Facility (GBIF) (Ygra State University Biological Collection publisher) on 11 November 2017 (earlier titled «Fungal Records Database of Yugra, FReDY») to provide open access to the data and its reusability (
This publication summarises the results of the digitisation of literature-based occurrence records of fungi and fungus-like organisms initiated in the Northern part of West Siberia for the first time in the history of mycological research. The bibliography of regional mycological publications was created to include about 460 published works (Suppl. material
occurrence, specimen, funga, Mycobiota, digitisation, data mobilisation
The mycological research in the Northern part of West Siberia stems from isolated studies in the beginning of the 20th century, yet regular and systematic research only began in the second half of the century. Over the following decades, several dozen researchers worked in the area and a total of over 460 scientific works were published. The history of mycological research in the southern half of this area was described in two publications (
The database was initiated in 2016 using Google Sheets (a web-based service, https://www.google.com/sheets/about/) as a table formatted in accordance with the Darwin Core standards (
According to the database summary report, there are about 3358 species identified in the region to date. Amongst 25 classes represented in the data, the richest are Agaricomycetes (60%) and Lecanoromycetes (30%).
Below we describe the history of mycological research in the Northern part of West Siberia in each administrative region by traditionally-studied morphological or ecological groups.
Yamalo-Nenets Autonomous Okrug
About 25 researchers participated in the inventory of lichens in the region. The most complete species lists were published in a series of works (
Agaricoid basidiomycetes is a less-studied group in the Yamalo-Nenets Autonomous Okrug compared to the bordering southern region. Sporadic studies were conducted in the Polar Urals by
Clavarioid basidiomycetes are a well-studied group mainly by a single researcher working in different regions: the Polar Urals (
Lignicolous basidiomycetes are a well-studied ecological group in the North of West Siberia. N. T. Stepanova-Kartavenko initiated the inventory of the middle Urals (
A number of works was performed to study fungal pathogens of plants in the region, by
Myxomycetes of the Urals, including its northern territories, are described in the PhD thesis by
Soil microfungi were studied in a few works (
The occurrence records of discomycetes and other ascomycetes appeared in the papers by A. V. Raitvir with co-authors (
Additionally, B. V. Krasutsky was deeply engaged in the ecological study of fungivorous Coleoptera communities (
Khanty-Mansi Autonomous Okrug
Lignicolous basidiomycetes have been studied quite extensively by a number of researchers. S. P. Arefyev initiated regional studies on wood-pathogens (
The inventories of lichens were performed in a number of protected areas in the region, with the highest number of species revealed in the Polar Urals and adjacent areas (
Marcofungi were studied in a number of areas, but the most thoroughly studied area were centred around Khanty-Mansiysk and, in the south-east part, in and near the Yuganskiy Nature Reserve. The Nature Reserve has been inventoried since 2007 in a number of studies (
The study of the diversity of myxomycetes was carried out in two protected areas (
Phytopathological studies are developing in the city of Surgut. The flora of fungal pathogens of the city parks of Surgut was studied for many years by T. A. Marakova and colleagues (
The communities of microfungi and yeasts were sampled in a study of mycobiota of raised bogs (
This is the first example of digitisation of species occurrence data published in literature in the Northern part of West Siberia and its publication as a GBIF dataset. The paper also provides the contemporary analysis of the research state of the funga in the region. The aim of the data paper was to provide the description and the link to the published dataset in the format of a peer-reviewed journal paper and to provide recognition for the effort by means of a scholarly article (based on Data paper definition published at https://www.gbif.org/en/data-papers).
Biodiversity data digitisation and mobilisation in Northern West Siberia (https://nwsbios.org)
Nina Filippova
The digitisation was aimed at summarising the species occurrences of fungi and fungi-related organisms accumulated in the course of previous mycological studies and published in peer-reviewed scientific literature. The geography extended to the Northern part of West Siberia, in the administrative borders of two regions (Yamalo-Nenets Autonomous Okrug and Khanty-Masi Autonomous Okrug-Yugra). Over 460 publications were reviewed and the species occurrence records were extracted from about 140 selected works. About 80% of species occurrences accumulated in the database were relatively recent, i.e. published in literature since the beginning of 21st century.
Methods of sampling vary in different reviewed publications, but generally follow the protocols of
The original species identifications from the published works were recorded in the database, although no attempt was made for the revision of the species identification accuracy. A single author revised the species list and corrected wrong original identifications: the corrected names were added in identificationRemarks field, totalling 15 records in the database. The incorrect spelling of taxa was verified using the GBIF Species Matching tool at the later stage of the database compilation. Possible georeference errors at the scale of the region were corrected using QGIS software (https://qgis.org/en/site) by eliminating the outliers. Depending on the quality of georeferences provided in publications, the uncertainty was estimated as follows: 1) the coordinate of a fruiting structure or a plot provided in the publication gave the uncertainty about 3-10 m; 2) the coordinates of the fieldwork locality provided in publications gave the uncertainty to about 500 m – 5 km; 3) the report of the species presence in the district or the region gave the central coordinates of the area with the uncertainty radius to include its borders. The occurrences with large uncertainties were not eliminated, as they can still be important in the global context.
The dataset is limited by the administrative borders of two regions (Yamalo-Nenets Autonomous Okrug, Khanty-Masi Autonomous Okrug-Yugra). However, in cases where the digitised work contained records from other regions, they were also entered into the database (totalling about 1300 such records). The region occupies the central to Northern part of the West Siberian Plain. The area extends for about 1300 km from the West to the East, from the Eastern slopes of the Ural mountains to Yenisey river and from North to South – about 1600 km. The total area equals about 1,300,000 km2.
The relief of the region is mainly a plain, but the western part of the area is occupied by the Ural mountains with the highest points reaching up to 2000 m. The three vegetation zones (taiga, forest-tundra and tundra) and well-developed peatland cover represent the plain, while the mountain vegetation of the Urals changes from taiga to alpine zones.
In the southern half of the area (Yugra region), most administrative divisions were covered by mycological research, but the intensity of the research varied. A total of 80% of all records in the database have been made from four districts (Khanty-Mansiyskiy, Surgutskiy, Berezovskiy, Sovetskiy). In total, about 13000 records or 60% come presently from the Yugra region.
The northern part of the region was represented by less numbers of records in the database (about 6000 or 27%). The research is mainly concentrated in two districts (Priuralskiy - 66% of records and Yamalskiy - 22%).
Generally, localities of the studies are situated randomly, with no attempts for regular studies using grid pattern having been made before. The areas under different kinds of nature protection are better studied compared to others: about half of all records in the database come from 13 protected areas (Fig.
58.309 and 73.749 Latitude; 58.887 and 86.353 Longitude.
According to the database summary report, there are about 3358 species revealed in Northern West Siberia to date, representing 1020 genera, 293 families, 94 orders, 25 classes, six phyla and two kingdoms (Fungi, Protozoa). The richest studied classes by number of occurrences are Agaricomycetes (60%) and Lecanoromycetes (30%). The richest ten families by number of species are Parmeliaceae (144 species), Russulaceae (111), Physciaceae (99), Cortinariaceae (96), Tricholomataceae (93), Polyporaceae (84), Lecanoraceae (83), Cladoniaceae (81), Hymenogastraceae (79) and Ramalinaceae (67 species).
Rank | Scientific Name |
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kingdom | Fungi |
kingdom | Protozoa |
1905-01-01 through 2020-01-01
This work is licensed under a Creative Commons Attribution (CC-BY) 4.0 License.
The dataset includes a table in Darwin Core format with 28 fields and about 22000 records.
Column label | Column description |
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occurrenceID | https://dwc.tdwg.org/terms/#dwc:occurrenceID; an identifier of a particular occurrence, unique within this dataset. An abbreviation in the identifier' number (FReDY-xxxxxx) inherited from the previous name of the dataset (Fungal Records Database of Yugra). |
bibliographicCitation | https://dwc.tdwg.org/terms/#dcterms:bibliographicCitation; the bibliographic citation of a publication from which the occurrence was extracted. |
scientificName | https://dwc.tdwg.org/terms/#dwc:scientificName; the original names as provided in publication, but corrected for spelling mistakes using GBIF Species Matching tool. |
verbatimLocality | https://dwc.tdwg.org/terms/#dwc:verbatimLocality; the original locality description of the collection place below county level, in Russian. |
locality | https://dwc.tdwg.org/terms/#dwc:locality; the locality description translation in English. |
habitat | https://dwc.tdwg.org/terms/#dwc:habitat; the description of habitat, including vegetation and substrate, in Russian or English. |
fieldNumber | https://dwc.tdwg.org/terms/#dwc:fieldNumber; the herbarium or field specimen number, when reported in the source. |
basisOfRecord | https://dwc.tdwg.org/terms/#dwc:basisOfRecord |
year | https://dwc.tdwg.org/terms/#dwc:year; the year of observation/collection, if provided in publication. If no particular date were reported, the year of the publication itself was applied as the observation date. |
month | https://dwc.tdwg.org/terms/#dwc:month; the month of observation/collection, if provided in publication. |
day | https://dwc.tdwg.org/terms/#dwc:day; the day of observation/collection, if provided in publication. |
countryCode | https://dwc.tdwg.org/terms/#dwc:countryCode |
stateProvince | https://dwc.tdwg.org/terms/#dwc:stateProvince; the administrative unit below Country level (Okrug, Oblast, Respublica, Kray). |
county | https://dwc.tdwg.org/terms/#dwc:county; the administrative unit below stateProvice level (Rayon). |
decimalLatitude | https://dwc.tdwg.org/terms/#dwc:decimalLatitude |
decimalLongitude | https://dwc.tdwg.org/terms/#dwc:decimalLongitude |
coordinateUncertaintyInMeters | https://dwc.tdwg.org/terms/#dwc:coordinateUncertaintyInMeters; see "Quality control" chapter for the description of the uncertainty calculation algorithm. |
geodeticDatum | https://dwc.tdwg.org/terms/#dwc:geodeticDatum |
georeferenceSources | https://dwc.tdwg.org/terms/#dwc:georeferenceSources; the resource used to georeference the locality (Yandex maps, Google maps or georeferenced in publication). |
taxonRank | https://dwc.tdwg.org/terms/#dwc:taxonRank; extracted from GBIF using Species Matching tool. |
kingdom | https://dwc.tdwg.org/terms/#dwc:kingdom; extracted from GBIF using Species Matching tool. |
eventDate | https://dwc.tdwg.org/terms/#dwc:eventDate; the full date of the observation event if provided in publication or the year of publication itself. |
identificationRemarks | http://rs.tdwg.org/dwc/terms/identificationRemarks; comments or notes about the identification or missing taxa in GBIF backbone. |
identificationQualifier | https://dwc.tdwg.org/terms/#dwc:identificationQualifier; a standard term ("cf.", "aff.") to express the determiner's doubts about the Identification. |
language | https://dwc.tdwg.org/terms/#dcterms:language; languages used to describe the different fields of a record. |
The research was funded by the Russian Fund for Basic Research and Government of the Khanty-Mansiysk Autonomous region according to the research project 18-44-860017 and grant 13-01-20/39 of the Yugra State University. Anton G. Shiryaev was partially funded by the Russian Foundation for Basic Research No 18-05-00398 А. Elena A. Zvyagina was supported by the KhMAO – Ugra government assignment for Surgut State University №20-04-00349. А. S. Arefyev was supported by the Fundemental research programme of the Tyumen Scientific Center SB RAS VI.52.1. project number AAAA-A17-117050400146-1. The authors are grateful to Ilya Filippov for preparation of a graph.
Nina Filippova was the leader of the digitisation initiative and the main author of the paper. All authors participated in compilation of bibliography and revision of the species occurrences included in the database. All authors also participated in revision of the paper. I.V. Stavishenko revised part of the original identifications of the species and made updated identificationRemarks. E.A. Zvyagina verified original georeferences in Yuganskiy Nature Reserve, based on personal knowledge of the area.
To track the digitisation process, a working database was created. Each bibliographic record has a series of fields to describe the digitisation process and its results: the total number of extracted occurrence records, general description of the occurrence quality, presence of observation date, presence of specimen number and details of georeferencing.
The bibliography presents all scientific publications (journal papers, conference proceedings, PhD theseses, monographs and book chapters). The bibliography of publications was formatted according to the rules of Scopus: transliteration and translation of all Russian-language sources was made for the convenience of a foreign reader and standardisation of citations in English-language publications.