:Using mitochondrial cox3 and chloroplast rbcL-rbcS DNA sequences, molecular phylogeny of Papenfussiella species that were collected from various localities in Japan revealed considerable species diversity in the genus. Although only P. kuromo has been recognized in Japan, in the molecular phylogeny Japanese Papenfussiella formed four distinct clades (clades 1, 2, 3 and 4) with high statistical supports. Specimens of clade 1 corresponded to P. kuromo because the morphology agreed well with the reported descriptions of the species, and the DNA sequences agreed with the lectotype specimen. Clade 2 comprised the syntype specimens of P. kuromo f. densa Inagaki, having distinctively narrow and well-branched thalli. Papenfussiella kuromo f. gracilis was not distinguishable from P. kuromo f. densa in morphology, nor in the DNA sequences. Specimens of clade 3 were collected from Shikoku and were similar to P. kuromo in gross morphology but were anatomically different from P. kuromo in having a subcortical layer. Specimens comprising clade 4 were collected from Akkeshi, eastern Hokkaido, and resembled P. callitricha in gross morphology but were distinct in having longer assimilatory filaments and isodiametric medullary cells. In summary, we propose the establishment of two new species, P. shikokuensis sp. nov. for clade 3 and P. iemasae sp. nov. for clade 4, and to reappraise P. kuromo f. densa and f. gracilis as an independent species, P. densa stat. nov. In addition, preliminary genetic study of the Southern Hemisphere Papenfussiella species suggested the occurrence of several cryptic species in the genus.
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