Evidence of Intra-individual SSU Polymorphisms in Dark-spored Myxomycetes (Amoebozoa)

Multigene phylogeny of the order Physarales (Myxomycetes, Amoebozoa): shedding light on the dark-spored clade

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.

Two independent genetic markers support separation of the myxomycete Lycogala epidendrum into numerous biological species

Lycogala epidendrum is one of the most widely known myxomycete species and the first-ever discovered representative of this group. Using 687 original DNA sequences from 330 herbarium specimens from Europe, Asia, North and Central America, and Australia, we constructed the first detailed phylogenies of the genus Lycogala, based on two independently inherited genetic markers, the ribosome small subunit 18S rRNA nuclear gene (18S rDNA) and the mitochondrial cytochrome oxidase subunit I gene (COI). In both phylogenies, L. epidendrum appeared to be a polyphyletic group, represented by numerous clades. The four other recognized species of the genus (L. confusum, L. conicum, L. exiguum, and L. flavofuscum) are scattered between branches corresponding to L. epidendrum. A barcode gap analysis revealed 60 18S rDNA phylogroups of L. epidendrum, which are distant from each other not less than from other species of the genus Lycogala. For 18 of these phylogroups with both 18S rDNA and COI sequences available, recombination patterns were analyzed to test for reproductive isolation. In contrast to the results of a simulation assuming panmixis, no crossing between ribosomal and mitochondrial phylogroups was found, thus allowing the conclusion that all tested phylogroups represent biospecies. More than one third (39.6%) of the studied specimens share a single 18S rDNA phylogroup, which we consider to be L. epidendrum s. str. This group displays the broadest geographic distribution and the highest intraspecific genetic variability. Nearly all (93.3%) of the remaining non-singleton 18S rDNA phylogroups are restricted to certain continents or even regions. At the same time, various reproductively isolated phylogroups occur sympatric at a given location.

Didymium pseudonivicola: A new myxomycete from the austral Andes emerges from broad-scale morphological and molecular analyses of D. nivicola collections

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.