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Testing morphology-based delimitation of Vulpicida juniperinus and V. tubulosus (Parmeliaceae) using three molecular markers

  • Kristiina MARK (a1), Lauri SAAG (a2), Andres SAAG (a1), Arne THELL (a3) and Tiina RANDLANE (a1)...

The delimitation of two morphologically similar and not easily separable Vulpicida species, V. juniperinus and V. tubulosus, is analyzed using nuclear ITS and Mcm7, and mitochondrial SSU DNA sequences. Seventy-nine Vulpicida specimens, most from the two focal taxa, are included in the three-locus gene tree. The results from Bayesian and parsimony analyses are presented. There are strong conflicts between the single locus gene trees. Vulpicida juniperinus and V. tubulosus are divided into two clearly distinguished groups in the ITS and concatenated B/MCMC tree. However, these species are mixed in both clades, appearing polyphyletic. Currently accepted V. juniperinus and V. tubulosus are not distinct according to the loci studied. Vulpicida pinastri appears monophyletic based on the available sequences.

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M. F. Boni , D. Posada & M. W. Feldman (2007) An exact nonparametric method for inferring mosaic structure in sequence triplets. Genetics 176: 10351047.

A. Crespo & S. Pérez-Ortega (2009) Cryptic species and species pairs in lichens: a discussion on the relationship between molecular phylogenies and morphological characters. Anales del Jardín Botánico de Madrid 66: 7181.

A. Crespo , H. T. Lumbsch , J.-E. Mattsson , O. Blanco , P. K. Divakar , K. Articus , E. Wiklund , P. A. Bawingan & M. Wedin (2007) Testing morphology-based hypotheses of phylogenetic relationships in Parmeliaceae (Ascomycota) using three ribosomal markers and the nuclear RPB1 gene. Molecular Phylogenetics and Evolution 44: 812824.

C. J. Douady , F. Delsuc , Y. Boucher , W. F. Doolittle & E. J. P. Douzery (2003) Comparison of Bayesian and maximum likelihood bootstrap measures of phylogenetic reliability. Molecular Biology and Evolution 20: 248254.

J. Felsenstein (1985) Phylogenies and the Comparative Method. American Naturalist 125: 115.

D. J. Funk & K. E. Omland (2003) Species-level paraphyly and polyphyly: frequency, causes, and consequences, with insights from animal mitochondrial DNA. Annual Review of Ecology, Evolution and Systematics 34: 397423.

M. Gardes & T. D. Bruns (1993) ITS primers with enhanced specificity for basidiomycetes – application to the identification of mycorrhizae and rusts. Molecular Ecology 2: 113118.

M. J. Gibbs , J. S. Armstrong & A. J. Gibbs (2000) Sister-Scanning: a Monte Carlo procedure for assessing signals in recombinant sequences. Bioinformatics 16: 573582.

M. Grube & S. Kroken (2000) Molecular approaches and the concept of species and species complexes in lichenized fungi. Mycological Research 104: 12841294.

R. R. Hudson & J. A. Coyne (2002) Mathematical consequences of the genealogical species concept. Evolution 56: 15571565.

J. P. Huelsenbeck , B. Rannala & J. P. Masly (2000) Accommodating phylogenetic uncertainty in evolutionary studies. Science 288: 23492350.

K. Katoh & H. Toh (2008) Recent developments in the MAFFT multiple sequence alignment program. Briefings in Bioinformatics 9: 286298.

L. L. Knowles & B. C. Carstens (2007) Delimiting species without monophyletic gene trees. Systematic Biology 56: 887895.

S. D. Leavitt , J. D. Fankhauser , D. H. Leavitt , L. D. Porter , L. A. Johnson & L. L. St. Clair (2011) Complex patterns of speciation in cosmopolitan “rock posy” lichens – discovering and delimiting cryptic fungal species in the lichen-forming Rhizoplaca melanophthalma species-complex (Lecanoraceae, Ascomycota). Molecular Phylogenetics and Evolution 59: 587602.

H. Lumbsch & S. Leavitt (2011) Goodbye morphology? A paradigm shift in the delimitation of species in lichenized fungi. Fungal Diversity 50: 5972.

D. Martin & E. Rybicki (2000) RDP: detection of recombination amongst aligned sequences. Bioinformatics 16: 562563.

D. P. Martin , D. Posada , K. A. Crandall & C. Williamson (2005 a) A modified bootscan algorithm for automated identification of recombinant sequences and recombination breakpoints. AIDS Research and Human Retroviruses 21: 98102.

D. P. Martin , C. Williamson & D. Posada (2005 b) RDP2: recombination detection and analysis from sequence alignments. Bioinformatics 21: 260262.

J.-E. Mattsson & M. Wedin (1998) Phylogeny of the Parmeliaceae–DNA data versus morphological data. Lichenologist 30: 463472.

K. Müller (2005) SeqState: Primer design and sequence statistics for phylogenetic DNA datasets. Applied Bioinformatics 4: 6569.

K. Müller (2006) Incorporating information from length-mutational events into phylogenetic analysis. Molecular Phylogenetics and Evolution 38: 667676.

M. Padidam , S. Sawyer & C. M. Fauquet (1999) Possible emergence of new geminiviruses by frequent recombination. Virology 265: 218225.

D. Posada & K. A. Crandall (2001) Evaluation of methods for detecting recombination from DNA sequences: computer simulations. Proceedings of the National Academy of Sciences, USA 98: 1375713762.

T. Randlane , A. Saag & A. Thell (1997) A second updated world list of cetrarioid lichens. Bryologist 100: 109122.

F. Ronquist & J. P. Huelsenbeck (2003) MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19: 15721574.

I. Schmitt , A. Crespo , P. K. Divakar , J. D. Fankhauser , E. Herman-Sackett , K. Kalb , M. P. Nelsen , N. A. Nelson , E. Rivas-Plata , A. D. Shimp (2009) New primers for promising single-copy genes in fungal phylogenetics and systematics. Persoonia 23: 3540.

J. W. Taylor , D. J. Jacobson , S. Kroken , T. Kasuga , D. M. Geiser , D. S. Hibbett & M. C. Fisher (2000) Phylogenetic species recognition and species concepts in Fungi. Fungal Genetics and Biology 31: 2132.

A. Thell , S. Stenroos , T. Feuerer , I. Kärnefelt , L. Myllys & J. Hyvönen (2002) Phylogeny of cetrarioid lichens (Parmeliaceae) inferred from ITS and b-tubulin sequences, morphology, anatomy and secondary chemistry. Mycological Progress 1: 335354.

M. Wedin , H. Döring & J.-E. Mattsson (1999) A multi-gene study of the phylogenetic relationships of the Parmeliaceae. Mycological Research 103: 11851192.

M. Wedin , M. Westberg , A. T. Crewe , A. Tehler & O. W. Purvis (2009) Species delimitation and evolution of metal bioaccumulation in the lichenized Acarospora smaragdula (Ascomycota, Fungi) complex. Cladistics 25: 161172.

G. F. Weiller (1998) Phylogenetic profiles: a graphical method for detecting genetic recombinations in homologous sequences. Molecular Biology and Evolution 15: 326335.

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The Lichenologist
  • ISSN: 0024-2829
  • EISSN: 1096-1135
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