Biodiversity Data Journal :
Data Paper (Biosciences)
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Corresponding author: Dmytro Leontyev (alwisiamorula@gmail.com)
Academic editor: Anne Thessen
Received: 11 Nov 2023 | Accepted: 04 Jan 2024 | Published: 28 Feb 2024
© 2024 Dmytro Leontyev, Iryna Yatsiuk
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:
Leontyev D, Yatsiuk I (2024) Dataset of barcoded Reticulariaceae: ten years of DNA sequencing. Biodiversity Data Journal 12: e115630. https://doi.org/10.3897/BDJ.12.e115630
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As a result of the ten years (2012–2022) work under the critical revision of the genera of Reticulariaceae, a set of papers was published. Collection data of hundreds of specimens, used as a material for these studies, were provided as supplements of corresponding papers, but remained unpublished in biodiversity databases.
Here, we represent an occurrence dataset "Barcoded Reticulariaceae of the World", published in GBIF. It includes data on 523 myxomycete collections (including 36 types) gathered from five continents and spanning 24 countries. The dataset encompasses 43 distinct species and one subspecies of myxomycetes, including rare, endemic, and recently-described taxa. Species included to the database mainly belong to the genera Alwisia, Lycogala, Reticularia, Siphoptychium, Thecotubifera and Tubifera (Reticulariaceae), but as well Lindbladia and Licaethalium (Cribrariaceae). Nearly all of the research material, with the exception of several old collections, underwent molecular barcoding, primarily involving the 18S rDNA gene, but also the elongation factor 1α gene and mitochondrial cytochrome oxidase subunit I gene. For those sequences that are stored in the NCBI GenBank, accession numbers are provided in the dataset. Newly-described species make up a significant part of the studied herbarium collections; many of them can be characterised as common for their region. A particularly high level of taxonomic novelty is observed in Australia, which may be explained by the endemism of the local myxomycete biota.
biodiversity, Cribrariaceae, database, Eumycetozoa, GBIF, geographic coordinates, Lucisporomycetidae, Myxogastrea, Myxomycetes, species distribution
Reticulariaceae is a well-known family of myxomycetes, the first representatives of which were described in the 17th-18th centuries (
The critical re-evaluation of Reticulariaceae involved an integrative approach that combined a comprehensive morphological assessment with molecular barcoding of specimens. The molecular study, aimed primarily at identifying operational taxonomic units, but also at tracing phylogenetic relationships between them, covered almost the entire collection. In this regard, the material of the ten-year critical revision of Reticulariaceae represents the set of data unprecedented in terms of depth of study and accuracy of identification. Until now, these data had only been available as supplementary files in respective publications, making it inaccessible for broader analysis. In this paper, we present a dataset "Barcoded Reticulariaceae of the World" containing all this information, which we have now published on GBIF (
The primary goal of the database is to make data on the global distribution of Reticulariaceae species available for broader studies. Significant changes in the taxonomy of this family due to its critical revision have not yet been incorporated into identification literature. Species described during last several years are not yet represented in the GBIF or they are represented only by data, provided by non-institutional research via iNaturalist and, thus, not supported by molecular data or microscopy. Another problem is that many ‘classical’ species, such as Tubifera ferruginosa, T. casparyi (Rostaf.) T. Macbr., T. microsperma (Berk. & M.A. Curtis) G.W. Martin, Lycogala epidendrum, and L. exiguum Morgan have been redefined more narrowly, based on molecular data. Consequently, their geographical distribution appeared to be more limited than previously believed and available data on the distribution of these taxa should, therefore, be used with caution. Our dataset offers reliable information about the distribution of both recently-described and revised species, providing data, confirmed through molecular barcoding and meticulous morphological studies.
In our barcoding project, we thoroughly examined all the herbarium specimens available in various collections (these were around 30 herbaria and private collections from Germany, US, Costa Rica, Australia and other counties, listed in publications, cited above). Consequently, the distribution of species, based on the number of specimens, can offer a somewhat biased, yet valuable indication of their global prevalence. The species with the highest abundance (see the Taxonomic coverage secion) are L. epidendrum and T. ferruginosa. This should not come as a surprise since both species were described in the 18th century and are found worldwide. However, these species are followed in the abundance list by Siphoptychium reticulatum Leontyev, Schnittler & S.L. Stephenson, T. vanderheuliae S.J. Lloyd, Leontyev & Dagamac, L. leopardinum Leontyev, Ishchenko, Schnittler & E. Johannesen and T. montana Leontyev, Schnittler & S.L. Stephenson. All of these taxa are relatively recent discoveries, all made within the scope of our ten-year project (
The percentage of newly-discovered species in herbarium material obtained from various continents is an intriguing aspect. Australia stands out as the leader in this regard, with a remarkable 88% of the Reticulariaceae specimens collected in the country turning out to be new species. Nevertheless, Europe and North America also present impressive results, with 52% and 51%, respectively. These values are probably biased, primarily because we did not include a proportionate number of specimens from L. flavofuscum (Ehrenb.) Rostaf., Reticulara jurana Meyl., R. lycoperdon Bull., and R. splendens Morgan in our studies. This omission occurred because these species exhibit clear morphological distinctions and were found to be taxonomically uniform, based on the sequencing of marker genes. Consequently, the abovementioned percentage of novelty within the studied collections is somewhat inflated. However, as a relative assessment, it can still offer valuable insights and this supposition gains support from the independent evidence of a unique myxomycete flora in Australia (
Barcoded Reticulariaceae of the World
Dmytro Leontyev, Iryna Yatsiuk
Worldwide
The project if partially funded by individual research grants to the first author by: (1) German Academic Exchange Foundation (DAAD) programme, Greifswald, Germany, 2012; (2) Fulbright Program, Fayetteville, AR, USA, 2013–2014; (3) RESPONSE programme of the German Foundation for Fundamental Research (DFG), Greifswald, Germany, 2017 and (4) Alexander von Humboldt Foundation programme, Greifswald, Germany, 2019–2023. Local partners of the project were Prof. Martin Schnittler (for the programmes implemented in Germany) and Prof. Steven Stephenson (for the programme implemented in the USA).
The material of the study encompasses collection data about myxomycete specimens, which were identified and barcoded by the authors of the publications within the framework of the project on critical revision of genera of Reticulariaceae in 2012–2022.
Material from the abovementioned studies was obtained by their authors both directly from fieldwork and as loans from numerous herbaria and individuals, with or without institutional affiliation (see acknowledgements in the cited paper and collector data in the dataset). The total number of collections analysed was over 1500, but only 523 were included in published studies and identified to the species level and are included in the present dataset.
Locality information was either obtained by the authors directly during field studies or recorded from herbarium labels. Coordinates, regardless of the original format, are presented as decimal fractions of a degree. Nearly all of the research material, with the exception of several old collections, underwent molecular barcoding, primarily involving the 18S rDNA gene, but also EF1α and COI. For those sequences that are stored in the NCBI GenBank, accession numbers are provided in the dataset. It should be noted that identical sequences obtained from different specimens were not published in GenBank as separate records in the 2014–2019 publications. Therefore, for most of the Alwisia, Siphoptychium and Tubifera occurrences in the dataset, the records with which they share an identical barcode are given, rather than their own GenBank accession numbers. In such cases, the marker “ident.” is added to the accession number, which means “barcode is identical to this accession number”.
Spreadsheets were checked and cleaned with Openrefine v. 3.2 (
The occurrence dataset was produced with the following steps:
Worldwide land area.
Material was gathered from five continents and represents 24 countries (Fig.
Collection sites of myxomycete specimens, included in the dataset "Barcoded Reticulariaceae of the World". The map was created using the on-line service GPSVisualizer (https://www.gpsvisualizer.com/map_input?form=data).
The dataset includes data on 523 myxomycetes occurrences on the genera Alwisia (7), Lycogala (265), Reticularia (19), Siphoptychium (54), Thecotubifera (16) and Tubifera (158), but as well Lindbladia (2) and Licaethalium (2) from Cribrariaceae (Fig.
Rank | Scientific Name |
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class | Myxomycetes |
family | Reticulariaceae |
family | Cribrariaceae |
Data range: 1893–2021
Amongst dated collections, 90% were made after 2000.
The dataset includes a tabulation-delimited table with 25 fields in Darwin Core terms and 523 records in it (
Column label | Column description |
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occurrenceID | https://dwc.tdwg.org/terms/#dwc:occurrenceID; the identifier for the occurrences, the universal unique identifier (UUID) was used for this purpose |
basisOfRecord | http://rs.tdwg.org/dwc/terms/basisOfRecord; PreservedSpecimen for all occurrences, since all are herbarium specimens |
catalogNumber | http://rs.tdwg.org/dwc/terms/catalogNumber; identifier of the specimen within the herbarium |
otherCatalogNumbers | http://rs.tdwg.org/dwc/terms/otherCatalogNumbers, alternative identifier of the specimen; appears in cases where a part of the specimen was shared with another collection and a duplicate specimen was created |
taxonRank | http://rs.tdwg.org/dwc/terms/taxonRank; the lowest taxonomic rank of the occurrence. |
scientificName | http://rs.tdwg.org/dwc/terms/scientificName; The full name of the currently accepted taxon, name after the taxonomical assessment as described in Methods. |
country | https://dwc.tdwg.org/terms/#dwc:country. |
countryCode | https://dwc.tdwg.org/terms/#dwc:countryCode. |
geodeticDatum | https://dwc.tdwg.org/terms/#dwciri:geodeticDatum; The geodetic datum upon which the geographic coordinates given in dwc:decimalLatitude and dwc:decimalLongitude are based, one value, WGS84. |
decimalLatitude | http://rs.tdwg.org/dwc/terms/decimalLatitude; geographic latitude in decimal degrees. |
decimalLongitude | https://dwc.tdwg.org/terms/#dwc:decimalLongitude; geographic longitude in decimal degrees. |
coordinateUncertaintyInMetres | https://dwc.tdwg.org/terms/#dwc:coordinateUncertaintyInMeters; the distance (in metres) from the given decimalLatitude and decimalLongitude describing the smallest circle containing the whole of the Location. Set as described in Methods. |
georeferencedBy | https://dwc.tdwg.org/terms/#dwc:georeferencedBy; name of the person who georeferenced the occurrence. |
year | http://rs.tdwg.org/dwc/terms/year; year or a range of years in which the occurrence was recorded. |
month | http://rs.tdwg.org/dwc/terms/month; month or a range of months in which the occurrence was recorded. |
day | http://rs.tdwg.org/dwc/terms/day; day or a range of days of the month in which the occurrence was recorded. |
eventDate | https://dwc.tdwg.org/terms/#dwc:eventDate; the full date of the observation as precisely as it could be extracted from the publication. |
stateProvince | https://dwc.tdwg.org/terms/#dwc:stateProvince; the name of the next smaller administrative region than country (province, region etc.) |
county | http://rs.tdwg.org/dwc/terms/county; The full, unabbreviated name of the next smaller administrative region than stateProvince (county, shire, department etc.) |
municipality | https://dwc.tdwg.org/terms/#dwc:municipality; the full, unabbreviated name of the next smaller administrative region than county (city, municipality etc.) |
locality | http://rs.tdwg.org/dwc/terms/locality; more specific description of the locality than municipality, derived from the original. |
habitat | http://rs.tdwg.org/dwc/terms/habitat; description of macrohabitat such as vegetation type and microhabitat, such as a substrate type. |
recordedBy | http://rs.tdwg.org/dwc/iri/recordedBy; the collector/s of the specimen. |
associatedSequences | http://rs.tdwg.org/dwc/terms/associatedSequences; GenBank accession numbers for partial SSU, EF1α and COI genes separated with |. If the sequence has no individual GenBank accession number, the term “ident.” (identical to) is applied after the accession number of an identical sequence of another specimen. |
typeStatus | http://rs.tdwg.org/dwc/terms/typeStatus; indicating whether an occurrence is a nomenclatural type for a corresponding scientificName. |
Authors express their deep gratitude to all colleagues, both with and without institutional affiliation, as well as to the workers of herbaria, who provided us with valuable collections of myxomycetes.