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

Abstract Background Agaricales is the largest order within the class Agaricomycetes (Basidiomycota, Fungi). Most genera have a gilled (lamellate) basidiomata, though gasteroid, secotioid and cyphelloid fruit bodies also occur in several families and genera. Although gilled Agaricales (usually called "agarics") are the most investigated part of the Fungi, the last summary of their diversity in Ukraine was published back in 1996 and needs to be updated. Only several families have undergone an in-depth review over the last 30 years. Most of the data on species occurrences distributed throughout Ukraine are only partially digitised, under-represented on the Web and published primarily in Ukrainian sources. New information Here, we provide the list of the 1201 scientific names of gilled Agaricales (species and infraspecific taxon ranks) ever reported from the territory of Ukraine, based on the more than 300 sources published from 1900 to 2021, as well as digitised collection specimens from three mycological collections. 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 – 8797 records in total.


Introduction
Agaricales is the largest order within the class Agaricomycetes (Basidiomycota, Fungi). Most genera have a gilled (lamellate) basidiomata, though gasteroid, secotioid and cyphelloid types of fruit bodies also occur in several families and genera.
Gilled Agaricales have attracted the attention of mycologists studying fungal diversity in the current territory of Ukraine since the 19 century. However, the first attempt to compile the checklist for its representatives known from the territory of Ukraine was published back in 1979 in the "Handbook of Fungi of Ukraine" (Zerova et al. 1979). Unfortunately, this source did not provide references to the specimens or at least exact dates and places of records, but only botanical regions from which species were reported.
In the 1980s, "Flora Fungorum Ucrainicae" was launched, aimed to provide critical revisions for the major groups of Ukrainian fungi, with references to particular records. To date, three volumes covering gilled Agaricales have been published, devoted to Agaricaceae (Wasser 1980), Amanitales (currently included into Agaricales as Amanitaceae and Pluteaceae, Wasser (1992)), Bolbitiaceae and Coprinaceae (currently Psathyrellaceae, Prydiuk (2015)). The last summary of the known diversity of gilled Agaricales of Ukraine, amongst other fungi, was published in 1996 (Minter and Dudka 1996). Only a part of the mentioned publication was digitised and only the last one is available online (Andrianova et al. 2006). Only a tiny fraction of the data on Ukrainian gilled Agaricales is open access, both human-and machine-readable and meets modern biodiversity data standards (Wieczorek et al. 2012), such as a digitised part of the Mycological collection of the Herbarium of V.N. Karazin Kharkiv National University (Savchenko et al. 2020).
Here, we provide the list of the 1201 scientific names of gilled Agaricales reported from the territory of Ukraine (species and infraspecific taxa), based on more than 300 sources published from 1900 to 2021, as well as digitised collection specimens from three mycological collections. 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 -8797 records in total. Data were published as a "checklist with occurrences" dataset

Sampling methods
Description: Data for this checklist comprise references from 345 published sources issued from 1900 to 2021. We also incorporated information on digitised 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), the mycological part of the Herbarium of V.N. Karazin Kharkiv National University, Kharkiv (CWU(MYC)) and the mycological collection of Halych National Nature Park, Halych (VM(MYC)) -totalling 5371 specimens. Specimens and references were included based on the following criteria:

2.
Occurrences lie within the official state boundary of Ukraine.

3.
Literature source is credible, i.e. authored by recognised mycologists and published in the peer-review scientific literature (journal articles, monographs, conference proceedings).

Sampling description:
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 from the KW-M collection, as well as the records from literature sources published by the year 2000. Since data are not downloadable and no longer accessible in a raw format, they were mined semiautomatically, using a custom Python parser written by Valeria Yakunina, for occurrences and literature references separately. Five thousand and seventy-eight occurrences of gilled Agaricales were then filtered, based on family and genus names. Literature sources published after 2000, as well as the sources not covered by "Fungi of Ukraine", such as the "Handbook of Fungi of Ukraine" (Zerova et al. 1979), were digitised manually by the authors of the dataset. Newer collection specimens from the CWU(MYC) and VM(MYC) collections were digitised manually. Specimens from CWU(MYC) collections have also been uploaded into the PlutoF biodiversity data management system (Abarenkov et al. 2010), where they are stored alongside extended information. If the specimen had been mentioned in one of the digitised 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 and 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 harmonised scientific names, provided by the authors of corresponding publications and/or specimens. In the first step, we matched our list of names with the GBIF Backbone Taxonomy (GBIF Secretariat 2022) using GBIF species matching tool, then manually checked 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 most of the mismatched names, we followed the Index Fungorum's 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 the records, for example, Agaricus tabularis Peck. For each name in the resulting 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 the authors wrote them were kept in the "verbatimIdentification" column of the "occurrence" data sheet.
Quality control: Since the primary 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 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 and R (R Core Team 2022).
Parsing the "Fungi of Ukraine" database, coordinate conversion into decimal degrees when available.

2.
Manual digitisation of the sources either published after the year 2000 or not covered by the "Fungi of Ukraine" database.

3.
Extraction of available collection data from CWU(MYC), VM(MYC) and KW-M custom collection management systems.

4.
Georeferencing of the records accompanied with annotations of the 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.

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

Usage licence
Usage licence: Creative Commons Public Domain Waiver (CC-Zero)

IP rights notes:
To the extent possible under law, the publisher has waived all rights to these data and has dedicated them to the Public Domain (CC0 1.0). Users may copy, modify, distribute and use the work, including for commercial purposes, without restriction. Concatenated list of hig.her taxa, from kingdom to genus.

kingdom (Darwin Core Taxon)
The full scientific name of the kingdom in which the taxon is classified.

phylum (Darwin Core Taxon)
The full scientific name of the phylum in which the taxon is classified.

class (Darwin Core Taxon)
The full scientific name of the class in which the taxon is classified.

order (Darwin Core Taxon)
The full scientific name of the order in which the taxon is classified.

family (Darwin Core Taxon)
The full scientific name of the family in which the taxon is classified.

genus (Darwin Core Taxon)
The full scientific name of the genus in which the taxon is classified.

specificEpithet (Darwin Core
Taxon) The name of the species epithet of the scientificName.

infraspecificEpithet (Darwin Core
Taxon) The name of the infraspecific epithet of the scientificName for either formas or varietas.
taxonRank (Darwin Core Taxon) The taxonomic rank of the most specific name in the scientificName.

scientificNameAuthorship (Darwin Core Taxon)
Full nomenclatural citation for scientific name. Original scientific names as provided in either publication or specimen label to which an Occurrence referenced.

basisOfRecord (Darwin Core
Occurrence Extension) The method in which data were acquired. Three levels: "PreservedSpecimen" for Occurrences derived from collection specimens, "MaterialCitation" for Occurrences derived from scholarly publications and "HumanObservation" for the Occurrences obtained from field diaries and stored in "Fungi of Ukraine" database.
institutionCode ( The geographic latitude as it was mentioned in the source.

verbatimLongitude (Darwin Core
Occurrence Extension) The geographic longitude as it was mentioned in the source.

verbatimCoordinateSystem (Darwin Core Occurrence
Extension) Coordinate reference system used for verbatim coordinates.

decimalLatitude (Darwin Core
Occurrence Extension) The geographic latitude in decimal degrees.

decimalLongitude (Darwin Core
Occurrence Extension) The geographic longitude in decimal degrees.

coordinateUncertaintyInMeters (Darwin Core Occurrence
Extension) The distance (in metres) from the given decimalLatitude and decimalLongitude describing the smallest circle containing the whole of the Location. Set as 100 m for GPS coordinates obtained before 05-05-2020, 30-50 m for GPS coordinates obtained since 05-05-2020 and from 200 to 6000 m for the coordinates georeferenced based on the description.

geodeticDatum (Darwin Core
Occurrence Extension) The geodetic datum upon which the geographic coordinates were given. References to online resources related to the Occurrences.