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Shchepin ON, López Villalba Á, Inoue M, Prikhodko IS, Erastova DA, Okun MV, Woyzichovski J, Yajima Y, Gmoshinskiy VI, Moreno G, Novozhilov YK, Schnittler M. DNA barcodes reliably differentiate between nivicolous species of Diderma (Myxomycetes, Amoebozoa) and reveal regional differences within Eurasia. Protist 2024; 175:126023. [PMID: 38368650 DOI: 10.1016/j.protis.2024.126023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 01/03/2024] [Accepted: 02/09/2024] [Indexed: 02/20/2024]
Abstract
The nivicolous species of the genus Diderma are challenging to identify, and there are several competing views on their delimitation. We analyzed 102 accessions of nivicolous Diderma spp. that were sequenced for two or three unlinked genes to determine which of the current taxonomic treatments is better supported by molecular species delimitation methods. The results of a haplotype web analysis, Bayesian species delimitation under a multispecies coalescent model, and phylogenetic analyses on concatenated alignments support a splitting approach that distinguishes six taxa: Diderma alpinum, D. europaeum, D. kamchaticum, D. meyerae, D. microcarpum and D. niveum. The first two approaches also support the separation of Diderma alpinum into two species with allopatric distribution. An extended dataset of 800 specimens (mainly from Europe) that were barcoded with 18S rDNA revealed only barcode variants similar to those in the species characterized by the first data set, and showed an uneven distribution of these species in the Northern Hemisphere: Diderma microcarpum and D. alpinum were the only species found in all seven intensively sampled mountain regions. Partial 18S rDNA sequences serving as DNA barcodes provided clear signatures that allowed for unambiguous identification of the nivicolous Diderma spp., including two putative species in D. alpinum.
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Affiliation(s)
- Oleg N Shchepin
- Institute of Botany and Landscape Ecology, University Greifswald, Soldmannstr. 15, 17487 Greifswald, Germany; Komarov Botanical Institute of the Russian Academy of Sciences, Laboratory of Systematics and Geography of Fungi, Prof. Popov Street 2, 197376 St. Petersburg, Russia.
| | - Ángela López Villalba
- Institute of Botany and Landscape Ecology, University Greifswald, Soldmannstr. 15, 17487 Greifswald, Germany
| | - Maho Inoue
- Institute of Botany and Landscape Ecology, University Greifswald, Soldmannstr. 15, 17487 Greifswald, Germany
| | - Ilya S Prikhodko
- Komarov Botanical Institute of the Russian Academy of Sciences, Laboratory of Systematics and Geography of Fungi, Prof. Popov Street 2, 197376 St. Petersburg, Russia
| | - Daria A Erastova
- Komarov Botanical Institute of the Russian Academy of Sciences, Laboratory of Systematics and Geography of Fungi, Prof. Popov Street 2, 197376 St. Petersburg, Russia
| | - Mikhail V Okun
- Komarov Botanical Institute of the Russian Academy of Sciences, Laboratory of Systematics and Geography of Fungi, Prof. Popov Street 2, 197376 St. Petersburg, Russia
| | - Jan Woyzichovski
- Institute of Botany and Landscape Ecology, University Greifswald, Soldmannstr. 15, 17487 Greifswald, Germany
| | - Yuka Yajima
- Department of Science and Informatics, Muroran Institute of Technology, Mizumoto-cho 27-1, 0508585 Muroran, Japan
| | - Vladimir I Gmoshinskiy
- Department of Mycology and Algology, Faculty of Biology, Moscow State University, Leninskie Gory 1/12, Moscow 119992, Russia
| | - Gabriel Moreno
- Departamento Ciencias de la Vida (Botanica), Universidad de Alcala, Alcala de Henares, Madrid 28805, Spain
| | - Yuri K Novozhilov
- Komarov Botanical Institute of the Russian Academy of Sciences, Laboratory of Systematics and Geography of Fungi, Prof. Popov Street 2, 197376 St. Petersburg, Russia
| | - Martin Schnittler
- Institute of Botany and Landscape Ecology, University Greifswald, Soldmannstr. 15, 17487 Greifswald, Germany
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Lloyd SJ, Leontyev DV, Moreno G, Villalba ÁL, Schnittler M. Tasmaniomyxa umbilicata, a new genus and new species of myxomycete from Tasmania. Mycologia 2024; 116:170-183. [PMID: 38032605 DOI: 10.1080/00275514.2023.2274252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 10/19/2023] [Indexed: 12/01/2023]
Abstract
A new genus and species of myxomycete, Tasmaniomyxa umbilicata, is described based on numerous observations in Tasmania and additional records from southeastern Australia and New Zealand. The new taxon is characterized by an unusual combination of characters from two families: Lamprodermataceae and Didymiaceae. With Lamprodermataceae the species shares limeless sporocarps, a shining membranous peridium, an epihypothallic stalk, and a cylindrical columella. Like Didymiaceae, it has a soft, flaccid, sparsely branched capillitium, with rough tubular threads that contain fusiform nodes and are firmly connected to the peridium. Other characters of T. umbilicata that also occur in many Didymiaceae are the peridium dehiscing into petaloid lobes, the yellow, motile plasmodium, and the spores ornamented with larger, grouped and smaller, scattered warts. The transitional position of the new taxon is reflected by a three-gene phylogeny, which places T. umbilicata at the base of the branch of all lime-containing Physarales, thus justifying its description as a monotypic genus.
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Affiliation(s)
- Sarah J Lloyd
- 206 Denmans Road, Birralee, Tasmania 7303, Australia
| | - Dmytro V Leontyev
- Department of Botany, H.S. Skovoroda Kharkiv National Pedagogical University, Kharkiv 61168, Ukraine
- Institute of Botany and Landscape Ecology, University of Greifswald, Greifswald 17487, Germany
| | - Gabriel Moreno
- Departamento de Biología Vegetal (Botánica), Universidad de Alcalá, Alcalá de Henares 28805, Spain
| | - Ángela López Villalba
- Institute of Botany and Landscape Ecology, University of Greifswald, Greifswald 17487, Germany
| | - Martin Schnittler
- Institute of Botany and Landscape Ecology, University of Greifswald, Greifswald 17487, Germany
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Geisen S, Lara E, Mitchell E. Contemporary issues, current best practice and ways forward in soil protist ecology. Mol Ecol Resour 2023; 23:1477-1487. [PMID: 37259890 DOI: 10.1111/1755-0998.13819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 02/23/2023] [Accepted: 05/17/2023] [Indexed: 06/02/2023]
Abstract
Soil protists are increasingly studied due to a release from previous methodological constraints and the acknowledgement of their immense diversity and functional importance in ecosystems. However, these studies often lack sufficient depth in knowledge, which is visible in the form of falsely used terms and false- or over-interpreted data with conclusions that cannot be drawn from the data obtained. As we welcome that also non-experts include protists in their still mostly bacterial and/or fungal-focused studies, our aim here is to help avoid some common errors. We provide suggestions for current terms to use when working on soil protists, like protist instead of protozoa, predator instead of grazer, microorganisms rather than microflora and other terms to be used to describe the prey spectrum of protists. We then highlight some dos and don'ts in soil protist ecology including challenges related to interpreting 18S rRNA gene amplicon sequencing data. We caution against the use of standard bioinformatic settings optimized for bacteria and the uncritical reliance on incomplete and partly erroneous reference databases. We also show why causal inferences cannot be drawn from sequence-based correlation analyses or any sampling/monitoring, study in the field without thorough experimental confirmation and sound understanding of the biology of taxa. Together, we envision this work to help non-experts to more easily include protists in their soil ecology analyses and obtain more reliable interpretations from their protist data and other biodiversity data that, in the end, will contribute to a better understanding of soil ecology.
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Affiliation(s)
- Stefan Geisen
- Laboratory of Nematology, Wageningen University, Wageningen, The Netherlands
| | | | - Edward Mitchell
- Laboratory of Soil Biodiversity, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
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García-Martín J, Zamora J, Lado C. Multigene phylogeny of the order Physarales ( Myxomycetes, Amoebozoa): shedding light on the dark-spored clade. PERSOONIA 2023; 51:89-124. [PMID: 38665983 PMCID: PMC11041899 DOI: 10.3767/persoonia.2023.51.02] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 11/04/2022] [Indexed: 04/28/2024]
Abstract
The class Myxomycetes consists of free-living protists characterised by their complex life cycle, which includes both microscopic (amoebae, flagellates and cists) and macroscopic stages (spore-bearing fruiting bodies, sclerotia, and plasmodia). Within it, the order Physarales, with more than 450 recognised species, constitutes the largest group. Although previous studies have shown the polyphyly of some of the traditionally accepted genera, its internal phylogenetic relationships have remained uncertain so far, and together with the lack of data for some key species, it prevented any taxonomic and nomenclatural revisions. We have compiled a substantially expanded dataset in terms of both taxon sampling and molecular data, including most of the genera described to date and four unlinked DNA regions, for which we provide partial sequences: nSSU, EF-1α, α-Tub, and mtSSU, analysed through maximum likelihood and Bayesian methods. Our results confirm that the family Didymiaceae is paraphyletic to the rest of Physarales. Within Didymiaceae s.lat., the recent reinstatement of the genus Polyschismium for most species traditionally ascribed to Lepidoderma, except for the type (Ronikier et al. 2022), is further supported here, as well as the definite inclusion of the genus Mucilago in Didymium and Lepidoderma s.str. (L. tigrinum) in Diderma (Prikhodko et al. 2023). Additionally, the genus Diachea is redefined to include some species previously treated in Physaraceae (Craterium spp. with true columella). Within the monophyletic family Physaraceae, most genera are recovered as polyphyletic, suggesting that they should be no longer accepted as currently defined. However, the lack of resolution of some relationships within Physaraceae prevents us from resuscitating or creating several new genera to mitigate polyphyly. Among the well-defined groups with clear molecular signatures, we propose two taxonomic and nomenclatural changes at generic level: 1) a new genus, Nannengaella, is proposed for a major clade containing Physarum globuliferum and other species with heavily calcified sporophores and, often, a true calcareous columella; 2) Lignydium is resurrected for the clade containing Fuligo muscorum. Additionally, Trichamphora is suggested as the correct name for the clade containing Physarum pezizoideum. The taxonomy and nomenclature of some provisional genera, currently synonymous with Fuligo and Physarum, are disentangled, and we provide a comprehensive and updated nomenclatural conspectus that can be used when better resolved phylogenies are obtained. In total, 22 new combinations are proposed in different genera. A provisional key to the genera of the order is also provided. Citation: García-Martín JM, Zamora JC, Lado C. 2023. Multigene phylogeny of the order Physarales (Myxomycetes, Amoebozoa): shedding light on the dark-spored clade. Persoonia 51: 89-124. doi: 10.3767/persoonia.2023.51.02.
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Affiliation(s)
- J.M. García-Martín
- Department of Mycology, Real Jardín Botánico, CSIC, Plaza de Murillo 2, 28014 Madrid, Spain
| | - J.C. Zamora
- Museum of Evolution, Uppsala University, Norbyvägen 16, 752 36 Uppsala, Sweden
- Conservatoire et Jardin botaniques de la Ville de Genève, Chem. de l’Impératrice 1, 1292 Pregny-Chambésy, Switzerland
| | - C. Lado
- Department of Mycology, Real Jardín Botánico, CSIC, Plaza de Murillo 2, 28014 Madrid, Spain
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Woyzichovski J, Shchepin ON, Schnittler M. High Environmentally Induced Plasticity in Spore Size and Numbers of Nuclei per Spore in Physarum albescens (Myxomycetes). Protist 2022; 173:125904. [PMID: 36037769 DOI: 10.1016/j.protis.2022.125904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 06/23/2022] [Accepted: 07/28/2022] [Indexed: 12/30/2022]
Abstract
Spore size enables dispersal in plasmodial slime molds (Myxomycetes) and is an important taxonomic character. We recorded size and the number of nuclei per spore for 39 specimens (colonies of 50-1000 sporocarps) of the nivicolous myxomycete Physarum albescens, a morphologically defined taxon with several biological species. For each colony, three sporocarps were analyzed from the same spore mount under brightfield and DAPI-fluorescence, recording ca. 14,000 spores per item. Diagrams for spore size distribution showed narrow peaks of mostly uninucleate spores. Size was highly variable within morphospecies (10.6-13.5 µm, 11-13%), biospecies (3-13%), even within spatially separated colonies of one clone (ca. 8%); but fairly constant for a colony (mean variation 0.4 µm, ca. 1.5%). ANOVA explains most of this variation by the factor locality (within all colonies: 32.7%; within a region: 21.4%), less by biospecies (13.5%), whereas the contribution of intra-colony variation was negligible (<0.1%). Two rare aberrations occur: 1) multinucleate spores and 2) oversized spores with a double or triple volume of normal spores. Both are not related to each other or limited to certain biospecies. Spore size shows high phenotypic plasticity, but the low variation within a colony points to a strong genetic background.
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Affiliation(s)
- Jan Woyzichovski
- Institute of Botany and Landscape Ecology, Greifswald University, Soldmannstr. 15, 17487 Greifswald, Germany.
| | - Oleg N Shchepin
- Institute of Botany and Landscape Ecology, Greifswald University, Soldmannstr. 15, 17487 Greifswald, Germany; Komarov Botanical Institute of the Russian Academy of Sciences, Laboratory of Systematics and Geography of Fungi, Prof. Popov Street 2, 197376 St. Petersburg, Russia
| | - Martin Schnittler
- Institute of Botany and Landscape Ecology, Greifswald University, Soldmannstr. 15, 17487 Greifswald, Germany
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Woyzichovski J, Shchepin O, Dagamac NH, Schnittler M. A workflow for low-cost automated image analysis of myxomycete spore numbers, size and shape. PeerJ 2021; 9:e12471. [PMID: 34820196 PMCID: PMC8605758 DOI: 10.7717/peerj.12471] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 10/20/2021] [Indexed: 11/29/2022] Open
Abstract
Measuring spore size is a standard method for the description of fungal taxa, but in manual microscopic analyses the number of spores that can be measured and information on their morphological traits are typically limited. To overcome this weakness we present a method to analyze the size and shape of large numbers of spherical bodies, such as spores or pollen, by using inexpensive equipment. A spore suspension mounted on a slide is treated with a low-cost, high-vibration device to distribute spores uniformly in a single layer without overlap. Subsequently, 10,000 to 50,000 objects per slide are measured by automated image analysis. The workflow involves (1) slide preparation, (2) automated image acquisition by light microscopy, (3) filtering to separate high-density clusters, (4) image segmentation by applying a machine learning software, Waikato Environment for Knowledge Analysis (WEKA), and (5) statistical evaluation of the results. The technique produced consistent results and compared favorably with manual measurements in terms of precision. Moreover, measuring spore size distribution yields information not obtained by manual microscopic analyses, as shown for the myxomycete Physarum albescens. The exact size distribution of spores revealed irregularities in spore formation resulting from the influence of environmental conditions on spore maturation. A comparison of the spore size distribution within and between sporocarp colonies showed large environmental and likely genetic variation. In addition, the comparison identified specimens with spores roughly twice the normal size. The successful implementation of the presented method for analyzing myxomycete spores also suggests potential for other applications.
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Affiliation(s)
- Jan Woyzichovski
- Institute of Botany and Landscape Ecology, Greifswald University, Greifswald, Mecklenburg-Western Pomerania, Germany
| | - Oleg Shchepin
- Institute of Botany and Landscape Ecology, Greifswald University, Greifswald, Mecklenburg-Western Pomerania, Germany.,Laboratory of Systematics and Geography of Fungi, Komarov Botanical Institute of the Russian Academy of Sciences, St. Petersburg, Russia
| | - Nikki Heherson Dagamac
- Institute of Botany and Landscape Ecology, Greifswald University, Greifswald, Mecklenburg-Western Pomerania, Germany.,Department of Biological Sciences and Research Center for the Natural and Applied Sciences, University of Santo Tomas, Manila, Philippines
| | - Martin Schnittler
- Institute of Botany and Landscape Ecology, Greifswald University, Greifswald, Mecklenburg-Western Pomerania, Germany
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Shchepin O, Novozhilov Y, Woyzichovski J, Bog M, Prikhodko I, Fedorova N, Gmoshinskiy V, Borg Dahl M, Dagamac NHA, Yajima Y, Schnittler M. Genetic structure of the protist Physarum albescens (Amoebozoa) revealed by multiple markers and genotyping by sequencing. Mol Ecol 2021; 31:372-390. [PMID: 34676941 DOI: 10.1111/mec.16239] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 09/26/2021] [Accepted: 10/08/2021] [Indexed: 01/05/2023]
Abstract
Myxomycetes are terrestrial protists with many presumably cosmopolitan species dispersing via airborne spores. A truly cosmopolitan species would suffer from outbreeding depression hampering local adaptation, while locally adapted species with limited distribution would be at a higher risk of extinction in changing environments. Here, we investigate intraspecific genetic diversity and phylogeography of Physarum albescens over the entire Northern Hemisphere. We sequenced 324 field collections of fruit bodies for 1-3 genetic markers (SSU, EF1A, COI) and analysed 98 specimens with genotyping by sequencing. The structure of the three-gene phylogeny, SNP-based phylogeny, phylogenetic networks, and the observed recombination pattern of three independently inherited gene markers can be best explained by the presence of at least 18 reproductively isolated groups, which can be seen as cryptic species. In all intensively sampled regions and in many localities, members of several phylogroups coexisted. Some phylogroups were found to be abundant in only one region and completely absent in other well-studied regions, and thus may represent regional endemics. Our results demonstrate that the widely distributed myxomycete species Ph. albescens represents a complex of at least 18 cryptic species, and some of these seem to have a limited geographical distribution. In addition, the presence of groups of presumably clonal specimens suggests that sexual and asexual reproduction coexist in natural populations of myxomycetes.
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Affiliation(s)
- Oleg Shchepin
- Laboratory of Systematics and Geography of Fungi, Komarov Botanical Institute of the Russian Academy of Sciences, St. Petersburg, Russia.,General Botany and Plant Systematics, Institute of Botany and Landscape Ecology, University of Greifswald, Greifswald, Germany
| | - Yuri Novozhilov
- Laboratory of Systematics and Geography of Fungi, Komarov Botanical Institute of the Russian Academy of Sciences, St. Petersburg, Russia
| | - Jan Woyzichovski
- General Botany and Plant Systematics, Institute of Botany and Landscape Ecology, University of Greifswald, Greifswald, Germany
| | - Manuela Bog
- General Botany and Plant Systematics, Institute of Botany and Landscape Ecology, University of Greifswald, Greifswald, Germany
| | - Ilya Prikhodko
- Laboratory of Systematics and Geography of Fungi, Komarov Botanical Institute of the Russian Academy of Sciences, St. Petersburg, Russia
| | - Nadezhda Fedorova
- Laboratory of Systematics and Geography of Fungi, Komarov Botanical Institute of the Russian Academy of Sciences, St. Petersburg, Russia.,Faculty of Biology, Saint Petersburg State University, Saint Petersburg, Russia
| | - Vladimir Gmoshinskiy
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia.,Polistovsky National Nature Reserve, Pskov Region, Russia
| | - Mathilde Borg Dahl
- General Botany and Plant Systematics, Institute of Botany and Landscape Ecology, University of Greifswald, Greifswald, Germany.,Institute of Microbiology, Center for Functional Genomics of Microbes, University of Greifswald, Greifswald, Germany
| | - Nikki H A Dagamac
- General Botany and Plant Systematics, Institute of Botany and Landscape Ecology, University of Greifswald, Greifswald, Germany.,Department of Biological Sciences and Research Center for the Natural and Applied Sciences, University of Santo Tomas, Manila, Philippines
| | - Yuka Yajima
- Muroran Institute of Technology, Muroran, Japan
| | - Martin Schnittler
- General Botany and Plant Systematics, Institute of Botany and Landscape Ecology, University of Greifswald, Greifswald, Germany
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Dagamac NHA, Bauer B, Woyzichovski J, Shchepin ON, Novozhilov YK, Schnittler M. Where do nivicolous myxomycetes occur? – Modeling the potential worldwide distribution of Physarum albescens. FUNGAL ECOL 2021. [DOI: 10.1016/j.funeco.2021.101079] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Janik P, Szczepaniak M, Lado C, Ronikier A. Didymium pseudonivicola: A new myxomycete from the austral Andes emerges from broad-scale morphological and molecular analyses of D. nivicola collections. Mycologia 2021; 113:1327-1342. [PMID: 34533412 DOI: 10.1080/00275514.2021.1961068] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
A new nivicolous myxomycete is described as a result of a comprehensive study of Didymium nivicola collections from the entire range of its occurrence. Statistical analysis of 12 morphological characters, phylogenetic analyses of nuc 18S rDNA and elongation factor 1-alpha gene (EF1A), and a delimitation method (automatic barcode gap diversity) have been applied to corroborate the identity of the new species. A preliminary morphological analysis of D. nivicola revealed high variability of South American populations where four types of spore ornamentation were noted. However, results of molecular study and statistical analysis of morphological characters did not support recognition of these four forms but the distinction of two morphotypes. Consequently, two species have been recognized: D. nivicola and the newly proposed D. pseudonivicola. The new species can be distinguished from D. nivicola by distinctly larger and mostly plasmodiocarpic sporophores, which are scattered to gregarious, paler spores, and by the paler, more delicate and more elastic capillitium. Spore ornamentation of D. pseudonivicola is uniform and can be described as distinctly spiny (pilate under scanning electron microscope [SEM]), whereas those of D. nivicola is more variable, where spines (pilae under SEM) are delicate, distinct, or conspicuous. Additionally, whereas D. nivicola is a species distributed worldwide, D. pseudonivicola occurs only in the austral Andes of Argentina and Chile.
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Affiliation(s)
- Paulina Janik
- W. Szafer Institute of Botany, Polish Academy of Sciences, Lubicz 46, 31-512 Kraków, Poland
| | - Magdalena Szczepaniak
- W. Szafer Institute of Botany, Polish Academy of Sciences, Lubicz 46, 31-512 Kraków, Poland
| | - Carlos Lado
- Real Jardín Botánico, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, 28014, Spain
| | - Anna Ronikier
- W. Szafer Institute of Botany, Polish Academy of Sciences, Lubicz 46, 31-512 Kraków, Poland
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