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  • Parnmen, S./ Lücking, R./ Lumbsch, H.T. 2012: Phylogenetic classification at generic level in the absence of distinct phylogenetic patterns of phenotypical variation: A case study in Graphidaceae (Ascomycota). - PLoS ONE 7(12): e51392. [RLL List # 245 / Rec.# 38347]
    Abstract: Molecular phylogenies often reveal that taxa circumscribed by phenotypical characters are not monophyletic. While re-examination of phenotypical characters often identifies the presence of characters characterizing clades, there is a growing number of studies that fail to identify diagnostic characters, especially in organismal groups lacking complex morphologies. Taxonomists then can either merge the groups or split taxa into smaller entities. Due to the nature of binomial nomenclature, this decision is of special importance at the generic level. Here we propose a new approach to choose among classification alternatives using a combination of morphology-based phylogenetic binning and a multiresponse permutation procedure to test for morphological differences among clades. We illustrate the use of this method in the tribe Thelotremateae focusing on the genus Chapsa, a group of lichenized fungi in which our phylogenetic estimate is in conflict with traditional classification and the morphological and chemical characters do not show a clear phylogenetic pattern. We generated 75 new DNA sequences of mitochondrial SSU rDNA, nuclear LSU rDNA and the protein-coding RPB2. This data set was used to infer phylogenetic estimates using maximum likelihood and Bayesian approaches. The genus Chapsa was found to be polyphyletic, forming four well-supported clades, three of which clustering into one unsupported clade, and the other, supported clade forming two supported subclades. While these clades cannot be readily separated morphologically, the combined binning/multiresponse permutation procedure showed that accepting the four clades as different genera each reflects the phenotypical pattern significantly better than accepting two genera (or five genera if splitting the first clade). Another species within the Thelotremateae, Thelotrema petractoides, a unique taxon with carbonized excipulum resembling Schizotrema, was shown to fall outside Thelotrema. Consequently, the new genera Astrochapsa, Crutarndina, Pseudochapsa, and Pseudotopeliopsis are described here and 39 new combinations are proposed.
    – doi:10.1371/journal.pone.0051392

    Notes: New:Astrochapsa alstrupii (Frisch) Parnmen, Lücking & Lumbsch (≡ Chapsa alstrupii Frisch), A. amazonica (Kalb) Parnmen, Lücking & Lumbsch (≡ C. amazonica Kalb), A. astroidea (Berk. & Broome) Parnmen, Lücking & Lumbsch (X≡ Platygrapha astroidea Berk. & Broome), A. calathiformis (Vain.) Parnmen, Lücking & Lumbsch (≡ Thelotrema calathiforme Vain.), A. graphidioides (Kalb) Parnmen, Lücking & Lumbsch (≡ C. graphidioides Kalb), A. lassae (Mangold) Parnmen, Lücking & Lumbsch (≡ C. lassae Mangold), A. magnifica (Berk. & Broome) Parnmen, Lücking & Lumbsch (≡ Platygrapha magnifica Berk. & Broome), A. mastersonii (Rivas Plata, Lumbsch & Lücking) Parnmen, Lücking & Lumbsch (≡ C. mastersonii Rivas Plata, Lumbsch & Lücking), A. megaphylctidioides (Mangold) Parnmen, Lücking & Lumbsch (≡ C. megaphylctidioides Mangold), A. meridensis (Kalb & Frisch) Parnmen, Lücking & Lumbsch (≡ Topeliopsis meridensis Kalb & Frisch), A. platycarpella (Vain.) Parnmen, Lücking & Lumbsch (≡ Thelotrema patycarpellum Vain.), A. pseudophlyctis (Nyl.) Parnmen, Lücking & Lumbsch (≡ Graphis pseudophlyctis Nyl.), A. pulvereodiscus (Hale) Parnmen, Lücking & Lumbsch (≡ Thelotrema pulvereodiscus Hale), A. recurva (G.Salisb.) Parnmen, Lücking & Lumbsch (≡ Thelotrema recurvum G.Salisb.), A. stellata (Hale) Parnmen, Lücking & Lumbsch (≡ Leptotrema stellatum Hale), A. waasii (Hale) Parnmen, Lücking & Lumbsch (≡ Thelotrema waasii Hale), A. wolseleyana (Weerakoon, Lumbsch & Lücking) Parnmen, Lücking & Lumbsch (≡ Weerakoon, Lumbsch & Lücking), A. zahlbruckneri (Redinger) Parnmen, Lücking & Lumbsch (≡ Phaeographina zahlbruckneri Redinger), Crutarndina Parnmen, Lücking & Lumbsch (type: C. petractoides), C. petractoides (P.M.Jørg. & Brodo) Parnmen, Lücking & Lumbsch (≡ Thelotrema petractoides P.M.Jørg. & Brodo), Pseudochapsa Parnmen, Lücking & Lumbsch (type Pseudochapsa dilatata), Pseudochapsa albomaculata (Sipman) Parnmen, Lücking & Lumbsch (≡ Thelotrema albomaculatum Sipman), P. crispata (Müll.Arg.) Parnmen, Lücking & Lumbsch (≡ Ocellularia crispata Müll.Arg.), P. dilatata (Müll.Arg.) Parnmen, Lücking & Lumbsch (≡ O. dilatata Müll.Arg.), P. esslingeri (Hale) Parnmen, Lücking & Lumbsch (≡ O. esslingeri Hale), P. hypoconstictica (Rivas Plata & Lücking) Parnmen, Lücking & Lumbsch nom. inval. [lacking full and direct citation of basionym, and basionym listed as “in press.”] (≡ C. hypoconstictica Rivas Plata & Lücking), P. isidiifera (Frisch & Kalb) Parnmen, Lücking & Lumbsch (≡ C. isidiifera Frisch & Kalb), P. kalbi (Frisch) Parnmen, Lücking & Lumbsch (C. kalbi Frisch), P. lueckingii (Kalb) Parnmen, Lücking & Lumbsch (≡ C. lueckingii Kalb), P. phlyctidea (Nyl.) Parnmen, Lücking & Lumbsch (≡ Thelotrema phlyctideum Nyl.), P. phlyctidioides (Müll.Arg.) Parnmen, Lücking & Lumbsch (≡ O. phlyctidioides Müll.Arg.), P. pseudoexanthismocarpa (Patw. & C.R.Kulk.) Parnmen, Lücking & Lumbsch (≡ O. pseudoexanthismocarpa Patw. & C.R.Kulk.), P. pseudoschizostoma (Hale) Parnmen, Lücking & Lumbsch (≡ O. pseudoschizostoma Hale), P. rhizophorae (Kalb) Parnmen, Lücking & Lumbsch) (≡ C. rhizophorae Hale), P. rivas-platae Kalb) Parnmen, Lücking & Lumbsch (≡ C. rivas-platae Kalb), P. sipmanii Frisch & Kalb) Parnmen, Lücking & Lumbsch (≡ C. sipmanii Frisch & Kalb), P. subpatens (Hale) Parnmen, Lücking & Lumbsch (≡ Thelotrema subpatens Hale), Pseudotopeliopsis Parnmen, Lücking & Lumbsch (type P. laceratula), P aggregata (Hale) Parnmen, Lücking & Lumbsch [epithet listed as “aggregate”] (≡ Phaeotrema aggregatum Hale), P. laceratula (Müll.Arg.) Parnmen, Lücking & Lumbsch (≡ Thelotrema laceratulum Müll.Arg.), P. scabiocarpa (Rivas Plata & Lücking) Parnmen, Lücking & Lumbsch nom. inval. [lacking full and direct citation of basionym, and basionym listed as “in press.”] (≡ C. scabiocarpa Rivas Plata & Lücking), P. scabiomarginata (Hale) Parnmen, Lücking & Lumbsch (≡ Thelotrema scabiomarginatum Hale).
    URL: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0051392
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