A multilocus phylogeny and updated classification of the Columellomycetidae (Myxomycetes, Amoebozoa) based on low-pass genome sequencing data
The plasmodial slime molds (Amoebozoa, class Myxomycetes) remain one of the few major eukaryotic groups lacking a classification based on robust multigene phylogenies. Extreme sequence divergence and the scarcity of universal primers have thus far impeded broad taxon sampling and the construction of deeply resolved phylogenies. Herein, we propose an updated system for the subclass Columellomycetidae (dark-spored myxomycetes). We employed a genome skimming approach to assemble a 22-gene matrix for 112 herbarium specimens spanning 101 species and integrated public transcriptomic and genomic data from three additional myxomycete species and two dictyostelid species. Different phylogeny inference methods and sequencing data from different loci (nuclear vs. mitochondrial) produced highly consistent and robust clades, most of which we propose as taxa at the level of families. The 22-gene backbone phylogeny was expanded by adding more than nine hundred accessions of dark-spored myxomycetes sequenced for 1–4 genes. This allowed us to produce a highly resolved and species-rich phylogeny of the Columellomycetidae and to revise the delimitation of several genera and families. We now recognize five orders and 12 families in the subclass Columellomycetidae. A new genus, Argentoderma, is described together with the new family Argentodermataceae and the new order Argentodermatales to accommodate three species forming an early-diverging lineage within the Columellomycetidae. The family Didymiaceae is split into four families that better reflect phylogenetic relationships within the Physarales; for this, three new families (Diacheaceae, Polyschismiaceae, and Didermataceae) are described alongside a more narrowly circumscribed Didymiaceae. Echinostelium australiense is transferred to Clastoderma, and Echinosteliopsis is placed within the Echinosteliaceae rather than in a separate order. Semimorula is synonymized with Echinostelium, Physarella is synonymized with Fuligo, Paradiacheopsis is synonymized with Comatricha, Collaria is restricted to the C. rubens clade within the Meridermataceae, and Stemonaria is synonymized with Stemonitis, herein redefined to include the clade centered on Stemonitis fusca. The genera Aethaliopsis, Angioridium, Carcerina, Claustria, and Scyphium are reinstated. In total, 35 new combinations and one nom. nov. (Stemonitis pinicola) are proposed. Extensive homoplasy in sporophore characters underlines the need to explore more fine-scale morphological characters that reflect the evolutionary history of myxomycetes more precisely. Our study demonstrates the utility of shallow genome sequencing of herbarium collections for resolving systematic problems and provides a phylogenomic foundation for comparative research on this neglected lineage of the Amoebozoa.