The comprehensive checklist and extended occurrence and reference datasets of myxomycetes of Ukraine

Iryna Yatsiuk1, Dmytro Leontyev2, Yuliia Leshchenko3, Vitalii Viunnyk4, Iryna Yatsiuk5

1 Institute of Ecology and Earth Sciences, University of Tartu, Juhan Liivi 2, Oecologicum, 50409, Tartu, Estonia; 2 Department of Botany, H.S. Skovoroda Kharkiv National Pedagogical University, Valentynivska 2, 61168, Kharkiv, Ukraine; 3 Department of Ecology, Charles University, Viničná 7, 128 00, Prague, Czechia; 4 National Nature Park "Slobozhanskyi", Zarichna, 15-A, Krasnokuts'k, Ukraine; 5 Institute of Ecology and Earth Sciences, University of Tartu, Juhan Liivi 2, Oecologicum, 50409, Tartu, Estonia

Corresponding author(s): Iryna Yatsiuk (yatsiuk@ut.ee)Dmytro Leontyev (alwisiamorula@gmail.com)Yuliia Leshchenko (leshchey@natur.cuni.cz)Vitalii Viunnyk (vjnnuk@ukr.net)

Received {date}; Revised {date}; Accepted {date}; Published {date}

Citation: Combination of authors, year of data paper publication (in parentheses), Title, Journal Name, Volume, Issue number (in parentheses), and doi of the data paper.

Resource Citation

Yatsiuk I, Leontyev D, Leshchenko Y, Viunnyk V (2024). The comprehensive checklist and extended occurrence and reference datasets of myxomycetes of Ukraine. Version 1.10. V. N. Karazin Kharkiv National University. Checklist dataset. https://ukraine.ipt.gbif.no/resource?r=myxomycetesukraine&v=1.10

Abstract

The datasets presented here aim to summarize over 150 years of myxomycetes research in Ukraine. The majority of the data has been extracted from published literature sources spanning the years 1842 to 2023, with a minor supplement from unpublished herbarium specimens. The datasets include 5036 georeferenced occurrences, 339 taxa and 91 literature sources. Seventy one of used literature sources are published in open access.

Keywords: Checklist, Inventorythematic?
derivedFromOccurrence?
taxonomicAuthority?
nomenclatorAuthority

General description

Purpose: The purpose of this publication is to serve as a foundational resource for conducting country-wise ecological studies, particularly vital for evaluating the potential impact of the ongoing war on biodiversity in the future.

Project details

Project title: Deciphering Cyrillic: the checklist from invisible sources
Personnel: Yuliia Leshchenko, Iryna Yatsiuk
Funding: BioDATA partners, NLBIF, GBIF Norway, and the UiO Natural History Museum

Data published through GBIF: https://ukraine.ipt.gbif.no/resource?r=myxomycetesukraine

Taxonomic coverage

General taxonomic coverage description: The checklist includes 339 taxa of slime moulds, among them 331 are species, and the rest are identified to the genus level. Nearly all records represent the class Myxomycetes (Eumycotozoa, Amoebozoa). One species belongs to the class Ceratiomyxomycetes (Eumycetozoa, Amoebozoa), and one represents the family Acrasidae (Heterolobosea, Excavata).
Taxonomic ranks
Phylum: Myxomycetes, Ceratiomyxomycetes
Family: Acrasidae
Common names: slime moulds, slime moulds, slime moulds

Spatial coverage

General spatial coverage: The entire territory of Ukraine in 1991 borders
Coordinates: 44°27'54''N and 52°41'45.6''N Latitude; 21°58'22.8''E and 40°25'48''E Longitude 

Temporal coverage: January 1, 1830 - September 22, 2021

Methods

Method step description: The occurrence dataset was produced with the following steps:

1. Survey and digitization of professional literature resources on myxomycetes occurrences in the territory of Ukraine in its borders as of 1991 (total 91 sources);
2. Preparation of Darwin Core-formatted template;
3. Data extraction from the literature sources into corresponding columns (in total 5036 occurrences);
4. Data extraction from the herbarium labels into corresponding columns;
5. Taxonomic assessment of names;
6. When necessary, automatic georeferencing of occurrences. If the coordinates of the occurrence were missing in the literature or on herbarium labels, the occurrence was georeferenced based on the text description of the occurrence location. Georeferencing was done automatically using the Geocode by Awesome Table extension for Google Sheets (https://workspace.google.com/marketplace/app/geocode_by_awesome_table/904124517349).  Precision was determined according to the accuracy of the distance to the occurrence from the authors' description in the text. The accuracy of the given coordinates is determined as follows: one number in decimal place corresponds to the precision of 11.1 km, two numbers = 1.11 km, with each subsequent digit, the distance is reduced by a factor of 10. In the case of localities indicated by names that have been renamed or no longer exist, georeferencing was carried out by the method of digitizing available maps using QGIS 3.16.3 (https://qgis.org/en/site/), followed by the extraction of coordinates. WGS84 was used as a spatial reference system.
7. Data cleaning using OpenRefine;
8. Matching species names;
9. Plotting of occurrences on the map and visual checkup of coordinates.

The Reference dataset was derived from the occurrence dataset with the following steps:
1. Preparation of Darwin Core-formatted template;
2. Data extraction from the literature sources into corresponding columns;
3. Data cleaning using OpenRefine.

The checklist dataset was derived from the occurrence dataset with the following steps:
1. Preparation of Darwin Core-formatted template;
2. Extraction of unique values from a scientificName column of the occurrence dataset to a scientificName of the checklist dataset.
3. Adding species from recent scientific publications for which datasets have already been published in GBIF
Study extent description: 1830-2021, Ukraine
Sampling description: The literature sources selected for this dataset included only scientific literature, comprising monographs, peer-reviewed journal articles, conference abstracts, annual reports of protected areas, PhD and Master’s thesis. Herbarium specimens incorporated here have either been identified or verified by academic myxomycetes researchers.
Information from the literature was extracted manually into comma-separated spreadsheets containing columns named according to the Darwin Core standard. To avoid duplication, sources, supported by datasets already published in GBIF, were not entered into the occurrence dataset, but added later on the stage of data analysis and checklist generation. 
The checklist dataset was created automatically by extracting unique values from the scientificName column within the occurrence dataset, following the completion of the taxonomic assessment. 
The References dataset was generated through manual extraction of information from literature sources, with the data organized into a comma-separated spreadsheet. The columns in this dataset adhere to the Darwin Core standard.
The literature sources originally lacking a DOI, were published on Zenodo repository (zenodo.org) and assigned one. In total 71 sources were published.
Quality control description: Spreadsheets were checked and cleaned with Openrefine v. 3.2 (https://openrefine.org/). Taxa names were checked for misspelling by matching against the GBIF Species Matching tool. Results of georeferencing were checked visually by plotting occurrences with QGIS software (QGIS Development Team, 2020).
Taxonomic assessment was based upon “An on line nomenclatural information system of Eumycetozoa” (Lado, 2005), except in cases where subspecies or forms were reported. In instances involving subspecies/forms, as these are not recognized as valid taxa in the aforementioned nomenclature database, taxonomic treatments were based on several monographs (Martin and Alexopoulos, 1969; Nannenga-Bremekamp, 1991; Poulain et al., 2011), as well as expert taxonomic opinions.

Datasets

Dataset description
Object name: Darwin Core Archive The comprehensive checklist and extended occurrence and reference datasets of myxomycetes of Ukraine
Character encoding: UTF-8
Format name: Darwin Core Archive format
Format version: 1.0
Distribution: https://ukraine.ipt.gbif.no/archive.do?r=myxomycetesukraine
Publication date of data: 2024-01-23
Language: English
Licences of use: Creative Commons Attribution (CC-BY 4.0) License

Metadata language: English
Date of metadata creation: 2023-09-22
Hierarchy level: Dataset