Invalidation of Hyperamoeba by Transferring its Species to Other Genera of Myxogastria

Abstract

The genus Hyperamoeba Alexeieff, 1923 was established to accommodate an aerobic amoeba exhibiting three life stages-amoeba, flagellate, and cyst. As more species/strains were isolated, it became increasingly evident from small subunit (SSU) gene phylogenies and ultrastructure that Hyperamoeba is polyphyletic and its species occupy different positions within the class Myxogastria. To pinpoint Hyperamoeba strains within other myxogastrid genera we aligned numerous myxogastrid sequences: whole small subunit ribosomal (SSU or 18S rRNA) gene for 50 dark-spored (i.e. Stemonitida and Physarida) Myxogastria (including a new "Hyperamoeba"/Didymium sequence) and a approximately 400-bp SSU fragment for 147 isolates assigned to 10 genera of the order Physarida. Phylogenetic analyses show unambiguously that the type species Hyperamoeba flagellata is a Physarum (Physarum flagellatum comb. nov.) as it nests among other Physarum species as robust sister to Physarum didermoides. Our trees also allow the following allocations: five Hyperamoeba strains to the genus Stemonitis; Hyperamoeba dachnaya, Pseudodidymium cryptomastigophorum, and three other Hyperamoeba strains to the genus Didymium; and two further Hyperamoeba strains to the family Physaridae. We therefore abandon the polyphyletic and redundant genus Hyperamoeba. We discuss the implications for the ecology and evolution of Myxogastria, whose amoeboflagellates are more widespread than previous inventories supposed, being now found in freshwater and even marine environments.

Polyphyletic origin of the genus Physarum(Physarales, Myxomycetes) revealed by nuclear rDNA mini-chromosome analysis and group I intron synapomorphy

“…Furthermore, each of the five main myxomycete orders (Physarales, Stemonitales, Trichiales, Liceales and Echinosteliales) represented distinct groups within the plasmodial slime molds. These findings corroborate earlier studies on the phylogeny of slime molds [13-16,30,31]. Finally, Soliformovum irregulare (protostelid) and Acrasis rosea (acrasid) appeared both distantly related from each other and from the dictyostelids and myxomycetes.…”

“…More recently, nuclear DNA sequence markers have contributed in resolving relationships among and within taxonomic groups. The ribosomal DNA (rDNA) spacers [10], obligatory group I introns [11], ribosomal RNA (rRNA) genes [11-16], and the elongation factor-1α (EF-1α) gene [17] and have all been applied.…”

Intra-Genomic Ribosomal RNA Polymorphism and Morphological Variation in Elphidium macellum Suggests Inter-Specific Hybridization in Foraminifera

“…The nuclear ribosomal RNA genes are widely used for inferring protists phylogeny [14]–[16] and species identification [13], [17]. Arranged in tandem arrays and typically repeated several hundred to some thousand times, these genes encode for rRNA molecules that fold into secondary structures, which possess conserved core regions alternating with more variable sequence segments [18] that have been called expansion segments [19], V (variable) regions [20], [21] or D (divergent) regions [22].…”

Genetic Structure of Two Protist Species (Myxogastria, Amoebozoa) Suggests Asexual Reproduction in Sexual Amoebae

“…1). The topology of the “ Stemonitis ” and “ Comatricha ” groups was identical to current phylogenies of Myxogastria [31], [39]. All Lamproderma specimens formed a monophyletic clade (maximum support in all analyses).…”

“…collected in Saxony, we obtained nine nearly complete SSU rRNA gene sequences (1811–1890 bp excluding introns). We assembled them with those of selected representative of Stemonitida according to current phylogenies of Myxogastria [14], [31], [39]. Sequences that were identical (or nearly so) or partial sequences in clades already well represented were not included.…”