Genetic diversity among clumps of Acanthorrhynchium papillatum (Harv.) M.Fleisch. as measured by variation in ITS2 sequences

References

• Bilofsky, H. & Burks, C. 1998. The GenBank genetic sequence data bank. Nucleic Acids Research, 16: 1861–4.
   Google Scholar
• Budyakova, A.A., Ignatov, M.S., Yatsentyuk, S.P. & Troitsky, A.V. 2003. Systematic position of Habrodon (Habrodontaceae, Musci) as inferred from nuclear ITS1 and ITS2 and chloroplast trnL intron and trnL–trnF spacer sequence data. Arctoa, 12: 137–50.
   Google Scholar
• Buryová, B. & Shaw, A.J. 2005. Phenotypic plasticity In Philonotis fontana (Bryopsida: Bartramiaceae). Journal of Bryology, 27: 13–22.
   Web of Science ®Google Scholar
• Capesius, I. 1997. Analysis of the ribosomal RNA gene repeat from the moss Funaria hygrometrica. Plant Molecular Biology, 33: 559–64.
   PubMed Web of Science ®Google Scholar
• Chang, Y. 2003. The systematics of Sematophyllaceae (Musci) of Peninsular Malaysia, Philippines and Singapore based on rbcL gene sequences and morphological study. Master’s thesis, National University of Singapore, Singapore.
   Google Scholar
• Chiang, T.-Y. & Schaal, B.A. 1998. Universal primers for amplification and sequencing a noncoding spacer between the atpB and rbcL genes of chloroplast DNA. Botanical Bulletin of Academica Sinica, 39: 245–50.
   Web of Science ®Google Scholar
• Chiang, T.-Y. & Schaal, B.A. 1999. Phylogeography of North American populations of the moss species Hylocomium splendens based on the nucleotide sequence of internal transcribed spacer 2 of nuclear ribosomal DNA. Molecular Ecology, 8: 1037–42.
   Web of Science ®Google Scholar
• Dover, G.A. 1986. Molecular drive in multigene families: how biological novelties arise, spread and are assimilated. Trends in Genetics, 2: 159–65.
   Web of Science ®Google Scholar
• Excoffier, L., Laval, G. & Schneider, S. 2005. Arlequin version 3.0: an integrated software package for population genetics data analysis. Evolutionary Bioinformatics Online, 1: 47–50.
   PubMed Web of Science ®Google Scholar
• Excoffier, L., Smouse, P.E. & Quattro, J.M. 1992. Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics, 131: 479–91.
   PubMed Web of Science ®Google Scholar
• Hallingbäck, T. & Hodgetts, N. eds. 2000. Mosses, liverworts, and hornworts: status survey and conservation action plan for bryophytes. Gland and Cambridge: IUCN, IUCN/SSC Bryophyte Specialist Group.
   Google Scholar
• Hedenäs, L. 2001. Environmental factors potentially affecting character states in pleurocarpous mosses. Bryologist, 104: 72–91.
   Web of Science ®Google Scholar
• Johnson, M.G., Shaw, B., Zhou, P. & Shaw, A.J. 2012. Genetic analysis of the peatmoss Sphagnum cribrosum (Sphagnaceae) indicates independent origins of an extreme infra-specific morphology shift. Biological Journal of Linnean Society, 106: 137–53.
   Web of Science ®Google Scholar
• Leonardía, A.A.P., Kumar, P.P. & Tan, B.C. 2006. Development of microsatellite markers for the tropical moss, Acanthorrhynchium papillatum. Molecular Ecology Notes, 6: 396–8.
   Web of Science ®Google Scholar
• Leonardía, A.A.P., Tan, B.C. & Kumar, P.P. 2013. Population genetic structure of the tropical moss Acanthorrhynchium papillatum as measured by microsatellite markers. Plant Biology, 15: 384–94.
   PubMed Web of Science ®Google Scholar
• Michalakis, Y. & Excoffier, L. 1996. A generic estimation of population subdivision using distances between alleles with special reference for microsatellite loci. Genetics, 142: 1061–4.
   PubMed Web of Science ®Google Scholar
• Mishler, B.D. 2001. The biology of bryophytes — bryophytes aren’t just small tracheophytes. American Journal of Botany, 88: 2129–31.
   Google Scholar
• O’Shea, B. 1997. A revision of Acanthorrhynchium (Sematophyllaceae) in Africa. Tropical Bryology, 13: 125–30.
   Google Scholar
• Page, R.D.M. 1996. TREEVIEW: an application to display phylogenetic trees on personal computers. Computer Applications in the Biosciences, 12: 357–8.
   PubMedGoogle Scholar
• Pearson, W.R. 1990. Rapid and sensitive sequence comparison with FASTP and FASTA. Methods in Enzymology, 183: 63–98.
   PubMed Web of Science ®Google Scholar
• Quandt, D., Tangney, R. S., Frahm J.-P. & Frey, W. 2000. A molecular contribution for understanding the Lembophyllaceae (Bryopsida) based on noncoding chloroplast regions (cpDNA) and ITS2 (nrDNA) sequence data. Journal of Hattori Botanical Laboratory, 89: 71–92.
   Google Scholar
• Raymond, M. & Rousset, F. 1995. An exact test for population differentiation. Evolution, 49: 1280–3.
   PubMed Web of Science ®Google Scholar
• Rozen, S. & Skaletsky, H. 2000. Primer 3 on the WWW for general users and for biologist programmers. In: S. Krawetz & S. Misener, eds. Bioinformatics methods and protocols: methods in molecular biology. Totowa, NJ: Humana Press, pp. 365–86.
   Google Scholar
• Ruggiero, M.V. & Procaccini, G. 2004. The rDNA ITS region in the Lessepsian marine angiosperm Halophila stipulacea (Forssk.) Ascjers. (Hydrocharitaceae): intragenomic variability and putative pseudogenic sequences. Journal of Molecular Evolution, 58: 115–21.
   PubMed Web of Science ®Google Scholar
• Saar, D.E., Polans, N.O., Sørensen, P.D. & Duvall, M.R. 2001. Angiosperm DNA contamination by endophytic fungi: detection and methods of avoidance. Plant Molecular Biology Reporter, 19: 249–60.
   Web of Science ®Google Scholar
• Sabovljević, M. & Frahm, J.-P. 2011. Genetic diversity of the relict moss Rhytidium rugosum (Hypnales) in Europe inferred from the ITS region (nrDNA). Biologia, 66: 42–9.
   Web of Science ®Google Scholar
• Saitou, N. & Nei, M. 1987. The Neighbor-Joining method: a new method for reconstructing phylogenetic trees. Molecular Biology and Evolution, 44: 406–25.
   Google Scholar
• Såstad, S.M., Pedersen, B. & Digre, K. 1999. Habitat-specific genetic effects on growth rate and morphology across pH and water-level gradients within a population of the moss Sphagnum angustifolium (Sphagnaceae). American Journal of Botany, 86: 1687–98.
   PubMed Web of Science ®Google Scholar
• Shaw, A.J. 2000. Molecular phylogeography and cryptic speciation in the mosses, Mielichhoferia elongata and M. mielichhoferiana (Bryaceae). Molecular Ecolgy, 9: 595–608.
   PubMed Web of Science ®Google Scholar
• Skotnicki, M.L., MacKenzie, A.M., Clements, M.A. & Selkirk, P.M. 2005. DNA sequencing and genetic diversity of the 18S–26S nuclear ribosomal internal transcribed spacers (ITS) in nine Antarctic moss species. Antarctic Science, 17: 377–84.
   Web of Science ®Google Scholar
• Slack, N.G. 2011. The ecological value of bryophytes as indicators of climate change. In: Z. Tuba, N.G. Slack & L.R. Stark, eds. Bryophyte ecology and climate change. Cambridge: Cambridge University Press, pp. 3–12.
   Google Scholar
• Smith, G.P. 1976. Evolution of repeated DNA sequences by unequal crossover. Science. 191: 528–35.
   Google Scholar
• Spagnuolo, V., Terracciano, S., Castaldo Cobianchi, R. & Giordano, S. 2008. Taxonomy of the Hypnum cupressiforme complex in Italy based on ITS and trnL sequences and ISSR markers. Journal of Bryology, 30: 283–9.
   Web of Science ®Google Scholar
• Stech, M. & Quandt, D. 2010. 20,000 species and five key markers: the status of molecular bryophyte phylogenetics. Phytotaxa, 9: 196–228.
   Web of Science ®Google Scholar
• Sun, Y., Skinner, D.Z., Liang, G.H. & Hulbert, S.H. 1994. Phylogenetic analysis of Sorghum and related taxa using internal transcribed spacers of nuclear ribosomal DNA. Theoretical and Applied Genetics, 89: 26–32.
   PubMed Web of Science ®Google Scholar
• Swofford, D.L. 2002. PAUP*. Phylogenetic analysis using parsimony (*and other methods). Version 4. Sunderland, MA: Sinauer Associates.
   Google Scholar
• Taberlet, P., Gielly, L., Pautou, G. & Bouvet, J. 1991. Universal primers for amplification of three non-coding regions of chloroplast DNA. Plant Molecular Biology, 17: 1105–9.
   PubMed Web of Science ®Google Scholar
• Thompson, J.D., Higgins, D.G. & Gibson, T.J. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignments through sequence weighting, position specific gap penalties and weight matrix choice. Nucleic Acids Research, 22: 4673–80.
   PubMed Web of Science ®Google Scholar
• Vanderpoorten, A., Goffinet, B. & Quandt, D. 2006. Utility of the internal transcribed spacers of the 18S-5·8S-26S nuclear ribosomal DNA in land plant systematics, with special emphasis on bryophytes. In: A.K. Sharma & A. Sharma, eds. Plant genome: biodiversity and evolution, Vol. 2, Part B. Enfield, NH: Science Publishers, pp. 385–407.
   Google Scholar
• White, T.J., Bruns, T., Lee, S. & Taylor, J. 1990. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: M. Innis, D.H. Gelfand, J.J. Sninsky & T.J. White, eds. PCR Protocols: a guide to methods and applications. San Diego, CA: Academic Press Inc., pp. 315–22.
   Google Scholar