Molecular tools to identify tropical mosses: a case study of the Brazilian species of Schlotheimia Brid. (Bryophyta, Orthotrichaceae)

References

• Atwood, J. J. (2009). A taxonomic revision of Schlotheimia subg. Stegotheca (Orthotrichaceae). The Bryologist, 112, 290–300. doi:10.1639/0007-2745-112.2.290
   Web of Science ®Google Scholar
• Bączkiewicz, A., Szczecińska, M., Sawicki, J., Stebel, A., & Buczkowska, K. (2017). DNA barcoding, ecology and geography of the cryptic species of Aneura pinguis and their relationships with Aneura maxima and Aneura mirabilis (Metzgeriales, Marchantiophyta). Public Library of Science ONE, 12, e0188837. doi:10.1371/journal.pone.0188837
   Google Scholar
• Bell, D., Long, D. G., Forrest, A. D., Hollingsworth, M. L., Blom, H. H., & Hollingsworth, P. M. (2012). DNA barcoding of European Herbertus (Marchantiopsida, Herbertaceae) and the discovery and description of a new species. Molecular Ecology Resources, 12, 36–47. doi:10.1111/j.1755-0998.2011.03053.x
   PubMed Web of Science ®Google Scholar
• Bell, D., Long, D. G., & Hollingsworth, M. L. (2013). The use of DNA barcoding to address major taxonomic problems for rare British bryophytes. Final revised report. Edinburgh: Royal Botanic Garden, 69 pp.
   Google Scholar
• Bergamini, A., & Peintinger, M. (2002). Effects of light and nitrogen on morphological plasticity of the moss Calliergonella cuspidata. Oikos, 96, 355–363. doi:10.1034/j.1600-0706.2002.960217.x
   Web of Science ®Google Scholar
• Biomatters. (2010). Geneious v5.3.6. Retrieved from http://www.geneious.com
   Google Scholar
• Buryová, B., & Shaw, A. J. (2005). Phenotypic plasticity in Philonotis fontana (Bryopsida: Bartramiaceae). Journal of Bryology, 27, 13–22. doi:10.1179/174328205X40545
   Web of Science ®Google Scholar
• Câmara, P. E. A. S. (2010). Métodos de extração de DNA de Briófitas para estudos filogenéticos. Heringeriana, 3, 11–17.
   Google Scholar
• Câmara, P. E. A. S., & Shaw, A. J. (2013). A molecular phylogeny of the moss genus Taxithelium (Pylaisiadelphaceae) based on plastid, mitochondrial and nuclear markers. Systematic Botany, 38, 861–868. doi:10.1600/036364413X674832
   Web of Science ®Google Scholar
• Carter, B. E. (2010). The taxonomic status of the Tasmanian endemic moss Scleropodium australe (Brachytheciaceae). The Bryologist, 113, 775–780. doi:10.1639/0007-2745-113.4.775
   Web of Science ®Google Scholar
• Carter, B. E. (2012). Species delimitation and cryptic diversity in the moss genus Scleropodium (Brachytheciaceae). Molecular Phylogenetics and Evolution, 63, 891–903. doi:10.1016/j.ympev.2012.03.002
   PubMed Web of Science ®Google Scholar
• CBOL Plant Working Group. (2009). A DNA barcode for land plants. Proceedings of the National Academy of Sciences of the USA, 106, 12794∓12797.
   PubMed Web of Science ®Google Scholar
• Costa, D. P., & Peralta, D. F. (2015). Bryophytes diversity in Brazil. Rodriguésia, 66, 1063–1071. doi:10.1590/2175-7860201566409
   Google Scholar
• Cräutlein, M. V., Korpelainen, H., Pietiläinen, M., & Rikkinen, J. (2011). DNA barcoding: A tool for improved taxon identification and detection of species diversity. Biodiversity and Conservation, 20, 373–389. doi:10.1007/s10531-010-9964-0
   Web of Science ®Google Scholar
• Dantas, T. S., Valente, D. V., Carvalho-Silva, M., & Câmara, P. E. A. S. (2018). Bryophyte phylogeny and DNA Barcoding: Tools for assessing Brazilian diversity. Brazilian Journal of Botany, 41, 497–505. doi:10.1007/s40415-018-0473-9
   Web of Science ®Google Scholar
• Doyle, J. J., & Doyle, J. L. (1987). A rapid isolation procedure for small quantities of fresh leaf tissue. Phytochemical Bulletin, 19, 11–15.
   Google Scholar
• Felsenstein, J. (1985). Confidence limits on phylogenies: an approach using the bootstrap. Evolution, 39, 783–783. doi:10.1111/j.1558-5646.1985.tb00420.x
   PubMed Web of Science ®Google Scholar
• Fernandez, C. C., Shevock, J. R., Glazer, A. N., & Thompson, J. N. (2006). Cryptic species within the cosmopolitan desiccation-tolerant moss Grimmia laevigata. Proceedings of the National Academy of Sciences of Sciences of the USA, 103, 637–642. doi:10.1073/pnas.0510267103
   PubMed Web of Science ®Google Scholar
• Frey, W., Stech, M., & Meissner, K. (1999). Chloroplast DNA-relationship in palaeoaustral Lopidium concinnum (Hypopterygiaceae, Musci). An example of steno-evolution in mosses. Studies in austral temperate rain forest bryophytes 2. Plant Systematics and Evolution, 218, 67–75. doi:10.1007/BF01087035
   Web of Science ®Google Scholar
• Frey, W., Stech, M., (2009). Marchantiophyta, bryophyta, anthocerotophyta. In W. Frey, (Ed.), Syllabus of plant families. A. Engler´s Syllabus der Pflanzenfamilien, 13th ed., Part 3, Bryophytes and seedless vascular plants (pp. 13–263). Stuttgart: Gebr. Borntraeger.
   Google Scholar
• Geiger, M. F., Astrin, J. J., Borsch, T., Burkhardt, U., Grobe, P., Hand, R., … Wägele, W. (2016). How to tackle the molecular species inventory for an industrialized nation—Lessons from the first phase of the German Barcode of Life initiative GBOL (2012–2015). Genome, 59, 661–670. doi:10.1139/gen-2015-0185
   PubMed Web of Science ®Google Scholar
• Goffinet, B., Bayer, R. J., & Vitt, D. H. (1998). Circumscription and phylogeny of the Orthotrichales (Bryopsida) inferred from rbcL sequence analyses. American Journal of Botany, 85, 1324–1337. doi:10.2307/2446642
   PubMed Web of Science ®Google Scholar
• Gradstein, S. R., Churchill, S. P., & Salazar-Allen, N. (2001). Guide to the bryophytes of Tropical America. Memoirs of the New York Botanical Garden, 86, 1–577.
   Google Scholar
• Hassel, K., Pedersen, B., & Söderström, L. (2005). Changes in life-history traits in an expanding moss species: Phenotypic plasticity or genetic differentiation? A reciprocal transplantation experiment with Pogonatum dentatum. Ecography, 28, 71–80. doi:10.1111/j.0906-7590.2005.03910.x
   Web of Science ®Google Scholar
• Hassel, K., Segreto, R., & Ekrem, T. (2013). Restricted variation in plant barcoding markers limits identification in closely related bryophyte species. Molecular Ecology Resources, 13, 1047–1057. doi:10.1111/1755-0998.12074
   PubMed Web of Science ®Google Scholar
• Hebert, P. D. N., Cywinska, A., Ball, S. L., & Dewaard, J. R. (2003). Biological identifications through DNA barcodes. Proceedings of the Royal Society of London. Series B: Biological Sciences, 270, 313–321. doi:10.1098/rspb.2002.2218
   PubMed Web of Science ®Google Scholar
• Hedenäs, L., & Eldenäs, P. (2007). Cryptic speciation, habitat differentiation, and geography in Hamatocaulis vernicosus (Calliergonaceae, Bryophyta). Plant Systematics and Evolution, 268, 131–145. doi:10.1007/s00606-007-0529-y
   Web of Science ®Google Scholar
• Higgins, D. G., & Sharp, P. M. (1988). CLUSTAL: A package for performing multiple sequence alignment on a microcomputer. Gene, 73, 237–244. doi:10.1016/0378-1119(88)90330-7
   PubMed Web of Science ®Google Scholar
• Hofbauer, W. K., Forrest, L. L., Hollingsworth, P. M., & Hart, M. L. (2016). Preliminary insights from DNA barcoding into the diversity of mosses colonizing modern building surfaces. Bryophyte Diversity and Evolution, 38, 1–22. doi:10.11646/bde.38.1.1
   Google Scholar
• Hollingsworth, P. M., Graham, S. W., & Little, D. P. (2011). Choosing and using a plant DNA barcode. Public Library of Science ONE, 6, e19254. doi:10.1371/journal.pone.0019254
   Google Scholar
• Kimura, M. (1980). A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences. Journal of Molecular Evolution, 16, 111–120. doi:10.1007/BF01731581
   PubMed Web of Science ®Google Scholar
• Kress, W. J., Wurdack, K. J., Zimmer, E. A., Weigt, L. A., & Janzen, D. H. (2005). Use of DNA barcodes to identify flowering plants. Proceedings of the National Academy of Sciences of Sciences of the USA, 102, 8369–8374. doi:10.1073/pnas.0503123102
   PubMed Web of Science ®Google Scholar
• Kumar, S., Stecher, G., & Tamura, K. (2016). MEGA7: Molecular evolutionary genetics analysis version 7.0 for bigger datasets. Molecular Biology and Evolution, 33, 1870–1974. doi:10.1093/molbev/msw054
   PubMed Web of Science ®Google Scholar
• Lang, A. S., Kruijer, J. D., & Stech, M. (2014). DNA barcoding of Arctic bryophytes: An example from the moss genus Dicranum (Dicranaceae, Bryophyta). Polar Biology, 37, 1157–1169. doi:10.1007/s00300-014-1509-7
   Web of Science ®Google Scholar
• Leon, B., Rothfels, C. J., Arakaki, M., Young, K. R., & Pryer, K. M. (2013). Revealing a cryptic fern distribution through DNA sequencing: Pityrogramma trifoliata in the Western Andes of Peru. American Fern Journal, 103, 40–48. doi:10.1640/0002-8444-103.1.40
   Web of Science ®Google Scholar
• Li, D.-D., Guo, S.-L., Yu, J., Li, S., & Cao, T. (2013). Feasibility study on the identification of genus Macromitrium based on four chloroplast genes. Plant Science Journal, 31, 23–33. doi:10.3724/SP.J.1142.2013.10023
   Google Scholar
• Liu, Y., Yan, H. F., Cao, T., & Ge, X. J. (2010). Evaluation of ten plant barcodes in Bryophyta (Mosses). Journal of Systematics and Evolution, 48, 36–46. doi:10.1111/j.1759-6831.2009.00063.x
   Web of Science ®Google Scholar
• Liu, Y., Cao, T., & Ge, X.-Y. (2011). A case study of DNA barcoding in Chinese Grimmiaceae and a moss recorded in China for the first time. Taxon, 60, 185–193. doi:10.1002/tax.601016
   Web of Science ®Google Scholar
• Maddison, W. P., & Maddison, D. R. (2015). Mesquite: A modular system for evolutionary analysis. version 3.51. Retrieved from http://mesquiteprojetct.org (accessed 9 March 2019).
   Google Scholar
• McDaniel, S. F., & Shaw, A. J. (2003). Phylogeographic structure and cryptic speciation in the trans-antarctic moss Pyrrhobryum mnioides. Evolution, 57, 205–215.
   PubMed Web of Science ®Google Scholar
• Medina, R., Lara, F., Goffinet, B., Garilleti, R., & Mazimpaka, V. (2013). Unnoticed diversity within the disjunct moss Orthotrichum tenellum s.l. validated by morphological and molecular approaches. Taxon, 62, 1133–1152. doi:10.12705/626.15
   Web of Science ®Google Scholar
• Müller, K. (2005). SeqState–primer design and sequence statistics for phylogenetic DNA data sets. Applied Bioinformatics, 4, 65–69.
   PubMedGoogle Scholar
• Müller, K., Quandt, D., Müller, J., & Neinhuis, C. (2006). PhyDE®: Phylogenetic data editor. Retrieved from www.phyde.de (accessed 20 May 2018).
   Google Scholar
• Mullis, K. B., & Faloona, F. A. (1987). Specific synthesis of DNA in vitro via a polymerase-catalyzed chain reaction. Methods in Enzymology, 155, 335–350.
   PubMed Web of Science ®Google Scholar
• Myszczyński, K., Bączkiewicz, A., Buczkowska, K., Ślipiko, M., Szczecińska, M., & Sawicki, J. (2017). The extraordinary variation of the organellar genomes of the Aneura pinguis revealed advanced cryptic speciation of the early land plants. Scientific Reports, 7, 9804. doi:10.1038/s41598-017-10434-7
   PubMed Web of Science ®Google Scholar
• Nagalingum, N. S., Schneider, H., & Pryer, K. M. (2007). Molecular phylogenetic relationships and morphological evolution in the heterosporous fern genus Marsilea. Systematic Botany, 32, 16–25. doi:10.1600/036364407780360256
   Web of Science ®Google Scholar
• Pacak, A., & Szweykowska-Kulińska, Z. (2000). Molecular data concerning alloploid character and the origin of chloroplast and mitochondrial genomes in the liverwort Pellia borealis. Journal of Plant Biotechnology, 2, 101–108.
   Google Scholar
• Palhares, R. M., Drummond, M. G., Brasil, B. I. A. F., Cosenza, G. P., Brandão, M. G. L., & Oliveira, G. (2015). Medicinal plants recommended by the World Health Organization: DNA barcode identification associated with chemical analyses guarantees their quality. Public Library of Science ONE, 10, e0127866. doi:10.1371/journal.pone.0127866
   Google Scholar
• Peralta, D. F., & Ristow, R. (2017). Schlotheimia spinomitria (Orthotrichaceae, Subg. Schlotheimia), a new species from Brazilian Cerrado. Phytotaxa, 305, 217–221. doi:10.11646/phytotaxa.305.3.9
   Web of Science ®Google Scholar
• Posada, D. (2008). jModeltest: phylogenetic model averaging. Molecular Biology and Evolution, 25, 1253–1256. doi:10.1093/molbev/msn083
   PubMed Web of Science ®Google Scholar
• Pryer, K. M., Schuettpelz, E., Huiet, L., Grusz, A. L., Rothfels, C. J., Avent, T., … Windham, M. D. (2010). DNA barcoding exposes a case of mistaken identity in the fern horticultural trade. Molecular Ecology Resources, 10, 979–985. doi:10.1111/j.1755-0998.2010.02858.x
   PubMed Web of Science ®Google Scholar
• Puillandre, N., Lambert, A., Brouillet, S., & Achaz, G. (2012). ABGD, automatic barcode gap discovery for primary species delimitation. Molecular Ecology, 21, 1864–1877. doi:10.1111/j.1365-294X.2011.05239.x
   PubMed Web of Science ®Google Scholar
• Rambaut, A., & Drummond, A. J. (2013). Tracer v1.4. Retrieved from http://beast.bio.ed.ac.uk/Tracer (accessed 8 August 2019).[
   Google Scholar
• Rivera-Jiménez, H., Rossini, B. C., Tambarussi, E. V., Veasey, E. A., Ibanes, B., & Marino, C. L. (2017). DNA barcode regions for differentiating Cattleya walkeriana and C. loddigesii. Acta Scientiarum, 39, 45–52.
   Google Scholar
• Ronquist, F., Teslenko, M., van der Mark, P., Ayres, D. L., Darling, A., Höhna, S., … Huelsenbeck, J. P. (2012). Mr Bayes 3.2: Efficient Bayesian phylogenetic inference and model choice across a large model space. Systematic Biology, 61, 539–542. doi:10.1093/sysbio/sys029
   PubMed Web of Science ®Google Scholar
• Saitou, N., & Nei, M. (1987). The neighbor-joining method: A new method for reconstructing evolutionary trees. Molecular Biology and Evolution, 4, 406–425. doi:10.1093/oxfordjournals.molbev.a040454
   PubMed Web of Science ®Google Scholar
• Sass, C., Little, D. P., Stevenson, D. W., & Specht, C. D. (2007). DNA barcoding in the Cycadales: Testing the potential of proposed barcoding markers for species identification of cycads. Public Library of Science One, 2, e1154. doi:10.1371/journal.pone.0001154
   Google Scholar
• Shaw, A. J. (2000). Molecular phylogeography and cryptic speciation in the mosses, Mielichhoferia elongata and M. mielichhoferiana (Bryaceae). Molecular Ecology, 9, 595–608. doi:10.1046/j.1365-294x.2000.00907.x
   PubMed Web of Science ®Google Scholar
• Schwarzera, C., & Joshi, J. (2017). Parallel adaptive responses to abiotic but not biotic conditions after cryptic speciation in European peat moss Sphagnum magellanicum Brid. Perspectives in Plant Ecology. Evolution and Systematics, 26, 14–27. doi:10.1016/j.ppees.2017.03.001
   Web of Science ®Google Scholar
• Silvestro, D., & Michalak, I. (2012). raxmlGUI: A graphical front-end for RAxML. Organisms Diversity & Evolution, 12, 335–337. doi:10.1007/s13127-011-0056-0
   Web of Science ®Google Scholar
• Simmons, M. P., & Ochoterena, H. (2000). Gaps as characters in sequence-based phylogenetic analyses. Systematic Biology, 49, 369–381. doi:10.1093/sysbio/49.2.369
   PubMed Web of Science ®Google Scholar
• Stamatakis, A. (2006). RAxML-VI-HPC: Maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics, 22, 2688–2690. doi:10.1093/bioinformatics/btl446
   PubMed Web of Science ®Google Scholar
• Stech, M., & Frahm, J. P. (1999). The status of Platyhypnidium mutatum Ochyra & Vanderpoorten and the systematic value of the Donrichardsiaceae based on molecular data. Journal of Bryology, 21, 191–195. doi:10.1179/jbr.1999.21.3.191
   Web of Science ®Google Scholar
• Stech, M., & Sparrius, L. (2011). The Netherlands about to barcode the entire Dutch bryophyte flora. Bryological Times, 132, 14.
   Google Scholar
• Stech, M., Veldman, S., Larraín, J., Muñoz, J., Quandt, D., Hassel, K., & Kruijer, J. D. (2013). Molecular species delimitation in the Racomitrium canescens complex (Grimmiaceae) and implications for DNA barcoding of species complexes in mosses. Public Library of Science ONE, 8, e53134. doi:10.1371/journal.pone.0053134
   Google Scholar
• Swofford, D. L. (2002). PAUP*. Phylogenetic Analyses using parsimony (*and other methods), version 4.0. Sunderland. Massachussetts: Sinauer Associates.
   Google Scholar