Reference-based checklist of gilled Agaricales (Basidiomycota, Fungi) from Ukraine

Study Extent

Data for this checklist comprise references from 345 published sources, dating from 1900 to 2021 y. We also incorporated information on digitized collection specimens from three mycological collections – The mycological part of the Herbarium of M.G. Kholodny Institute of Botany of National Academy of Sciences of Ukraine, Kyiv (KW-M), and the mycological part of the Herbarium of V.N. Karazin Kharkiv National University, Kharkiv (CWU(MYC)), and mycological collection of Halych National Nature Park, Halych (VM) – totally 5371 specimens. Specimens and references were included based on the following criteria: 1. Taxon belongs to the Order Agaricales (excluding families Clavariaceae, Cyphellaceae, Fistulinaceae, Niaceae, Phelloriniaceae, Pterulaceae, Schizophyllaceae, Stephanosporaceae, Typhulaceae, as well as genera Lycoperdon, Calvatia, Disciseda, and other genera comprising taxa with gasteroids, secotioids, and cyphelloids types of fruit bodies), and identified to either species or infraspecific level. 2. Occurrences lie within the official state boundary of Ukraine. 3. Literature source is credible, i.e. authored by recognized mycologists, and published in the peer-review scientific literature (journal articles, monographs, conference proceedings).

Sampling

The largest source of the data was the specimens and literature references available through the online database “Fungi of Ukraine” (Andrianova et al., 2006). The whole database comprises data on more than 52,400 records of fungi and fungus-like protists, covering the vast majority of specimens for KW collection, as well as the records from the sources published by 2000 y. Since data are unable to download and no longer accessible in a raw format, they were mined semi-automatically, using a custom Python parser written by Valeria Yakunina, for occurrences and literature references separately. 5078 occurrences of gilled Agaricales were then filtered based on family and genus names (see Taxonomic coverage for the full list of taxa). Literature sources published after 2000 y., as well as the sources not covered by “Fungi of Ukraine”, such as “Identification key for Ukrainian fungi” (Zerova et al., 1979), were digitized manually by the authors of the dataset. Newer collection specimens from the CWU and VM collections were digitized manually. Specimens from CWU collections have been also uploaded into the PlutoF biodiversity data management system (Abarenkov et al., 2010), where they are alongside extended information. If the specimen has been mentioned in one of the digitized literature sources, we treated such cases as a single record, to avoid duplications. For georeferenced records from the “Fungi of Ukraine” database, we converted geographic coordinates provided by the source into a decimal format using the formula “degree + minutes/60 + seconds/3600”. Since we have no information about georeferencing protocol which has been used during the data preparation, we left terms describing georeference and coordinate uncertainty empty. Records derived from the recent sources were georeferenced by the authors of the dataset either manually from maps or obtained from GPS coordinates when available. Coordinate uncertainty values were calculated following DarwinCore recommendations (https://dwc.tdwg.org/terms/#dwc:coordinateUncertaintyInMeters ), as well as Georeference best practices (Chapman and Wieczorek, 2020). For the records for which the source provides location information at a level coarser than a particular protected area (e.g. administrative or natural region of Ukraine, or accompanied with the remark “Throughout the territory of Ukraine”), we left all georeferencing terms empty. To make a list of taxa we harmonized scientific names, provided by the authors of corresponding publications and/or specimens. In the first step, we match our list of names with the GBIF Backbone Taxonomy (GBIF Secretariat, 2022) using GBIF species matching tool (https://www.gbif.org/tools/species-lookup), then manually check mismatching records against Index Fungorum nomenclatural database (Kirk and Cooper, 2022). For the names treated as accepted by both sources, we used the name provided by GBIF Backbone Taxonomy. For the mismatched names, we followed the Index Fungorum view. We also kept all the names for infraspecific taxa, represented non-type varietas/forma, and followed Index Fungorum in nomenclature for such cases. For some taxa which both GBIF Backbone taxonomy and Index Fungorum treat as synonyms, we kept names provided by the authors of records, for example, Agaricus tabularis Peck. For each name in the resulted list of scientific names (species, varietas, and formas) we then assigned a unique identifier (taxonID), through which taxa linked to the records in the occurrence part of the data. Full scientific names as they were written by the authors were kept in “verbatimIdentification” column of “occurrence” data sheet.

Quality Control

Since the main purpose of this checklist is to provide researchers with the most comprehensive list of the scientific names of gilled Agaricales reported from the territory of Ukraine, we did not make a deep taxonomical revision of the data. That is why synonyms or even ambiguous scientific names might be present. For each taxon mentioned in the checklist, we provide references to either known collection specimens or published sources, where researchers can find more information about the records. We used GBIF species matching tool (https://www.gbif.org/tools/species-lookup) to find possible typos in scientific names. We also used Index Fungorum nomenclatural database (Kirk and Cooper, 2022) to check the current status of names. For data cleaning and final adjustment, we used OpenRefine (https://openrefine.org/) and R (R Core Team, 2020).

Method steps

1. Parsing the “Fungi of Ukraine” database, coordinate conversion into decimal degrees when available.
2. Manual digitization of the sources either published after 2000 y. or not covered by the “Fungi of Ukraine” database.
3. Extraction of available collection data from CWU, VM, and KW custom collection management systems.
4. Georeferencing of the records accompanied with annotations described location at the level of the particular protected areas or finer.
5. Adaptation of the data to the DarwinCore standard.
6. Nomenclatural revision, preparing the list of scientific names.

Order Agaricales (Basidiomycota, Agaricomycetes, Fungi), excluding families Clavariaceae, Cyphellaceae, Fistulinaceae, Niaceae, Phelloriniaceae, Pterulaceae, Schizophyllaceae, Stephanosporaceae, Typhulaceae, as well as genera Lycoperdon, Calvatia, Disciseda, and other genera comprising taxa with gasteroids, secotioids, and cyphelloids types of fruit bodies.

1. Fungi
   rank: kingdom
2. Basidiomycota
   rank: phylum
3. Agaricomycetes
   rank: class
4. Agaricales
   rank: family

Data cover all the territory of Ukraine. It was possible to georeference 5904 records (67 per cent of the records).