Dataset of barcoded Reticulariaceae: ten years of DNA sequencing

Abstract Background 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of specimens, used as a material for these studies, were provided as supplements of corresponding papers, but remained unpublished in biodiversity databases. New information 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.


Introduction
Reticulariaceae is a well-known family of myxomycetes, the first representatives of which were described in the 17 -18 centuries (Leontyev et al. 2022b,Leonytev andSchnittler 2022).In 2012, the family contained three genera and 25 accepted species (Lado 2005), including the trivial Lycogala epidendrum (L.) Fr. and Tubifera ferruginosa (Batsch) J.F. Gmel.In 2012, Dmytro Leontyev (co-author) initiated a critical revision of the family, which was carried out during 2012-2023 through several projects (See Projects section).These studies increased the number of species of the Reticulariaceae to 52 (Lado 2005), the number of genera to six and one more genus, Licaethalium, was re-erected within the Cribrariaceae for species, previously classified within Reticulariaceae (Leontyev et al. 2019b).Fifteen species of the genus Lycogala, nine species and one subspecies of the genus Tubifera, three species of the genus Alwisia and two species of the genus Siphoptychium were described (Leontyev et al. 2014a, Leontyev et al. 2014b,Leontyev et al. 2015, Leontyev et al. 2019a, Lloyd et al. 2019, Leontyev et al. 2022a, Leontyev et al. 2022b, Leontyev and Schnittler 2023b, Leontyev et al. 2023).The classical species L. epidendrum and T. ferruginosa have proven to represent species complexes, which contain at least 13 and 76 biological species, respectively (Leontyev and Schnittler 2023a).
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 (Leontyev and Yatsiuk 2023)  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 18 century and are found worldwide.However, these species are followed in the abundance list by Siphoptychium reticulatum Stephenson.All of these taxa are relatively recent discoveries, all made within the scope of our ten-year project (Leontyev et al. 2015, Leontyev et al. 2019a, Leontyev et al. 2023).It is reasonable to assume that species previously unknown to science before our studies are not necessarily rare.The 'invisibility' of these species to taxonomists before the start of our project can be attributed solely to the limitations of the morphological criteria that were initially used to distinguish taxa within Reticulariaceae.This conjecture is supported by the fact that much rarer species, such as S. casparyi and Licaethalium olivaceum (Ehrenb.)Rostaf., which exhibit distinct morphological characteristics, were described as early as the 19 century (Lado 2005, Leontyev et al. 2019b).By adopting an integrative approach, at the core of which was the quest for morphological features correlated with molecular barcoding data, we were able to delimit species previously unknown to science that are widespread in extensively studied regions like Europe and North America (Leontyev et al. 2014b, Leontyev et al. 2015, Leontyev et al. 2023).
th th 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 (Lloyd 2022).

Sampling description:
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".
Quality control: Spreadsheets were checked and cleaned with Openrefine v. 3.2 (Ham 2013).Results of georeferencing were checked visually by plotting occurrences with GPSVisualizer (https://www.gpsvisualizer.com/map_input?form=data).Taxonomic assessment was based upon our own publications, but also verified with the database "An online nomenclatural information system of Eumycetozoa" (Lado 2005).
Step description: The occurrence dataset was produced with the following steps: 1.
Data extraction from the Excel sheets (mostly Supplementary files of the aforementioned publications) into corresponding columns; 3.
When necessary, manual georeferencing of occurrences.If the coordinates of the occurrence were missing in the literature, the occurrence was georeferenced based on text description of the occurrence location.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 sign, the distance is reduced by a factor of 10.WGS84 was used as a spatial reference system. 5.
Plotting of occurrences on map and visual checkup of coordinates.

Geographic coverage
Description: Worldwide land area.
Material was gathered from five continents and represents 24 countries (Fig. 1).The distribution of occurrences in our dataset reflects, first of all, the invested research effort.Most of records originate from the Europe, US, Central America, Eastern China and Australia, which are known as areas well studied by myxomycetologists.In contrast, molecular signatures of Reticulariaceae remain understudied in Africa, South America, South Asia including the Indian subcontinent, the boreal regions of Asia and North America.Undoubtedly, investigations of specimens collected in these regions will contribute significantly to expanding our understanding of the diversity within this family.

Figure 3 .
Figure 3. Number of occurrences per species of Reticulariaceae and Cribrariaceae, represented in the dataset "Barcoded Reticulariaceae of the World" (logarithmic scale).