Advanced search
Publication Cover
Mycologia Volume 95, 2003 - Issue 6
Submit an article Journal homepage
146
Views
33
CrossRef citations to date
0
Altmetric
Original Articles

New approach to an old problem: Incorporating signal from gap-rich regions of ITS and rDNA large subunit into phylogenetic analyses to resolve the Peltigera canina species complex

Jolanta Miadlikowska Department of Biology, Duke University, Durham, North Carolina 27708-0338 and Department of Plant Taxonomy and Nature Conservation, Gdansk University, Al. Legionow 9, 80-441 Gdansk, Poland
,
François Lutzoni Department of Biology, Duke University, Durham, North Carolina 27708-0338
,
Trevor Goward Herbarium, Department of Botany, University of British Columbia, Vancouver, British Columbia V6T 2B1, Canada
,
Stefan Zoller Department of Biology, Duke University, Durham, North Carolina 27708-0338
&
David Posada Variagenics, 60 Hampshire Street, Cambridge, Massachusettes 02139
Pages 1181-1203 | Accepted 13 Apr 2003, Published online: 31 Jan 2017

  • Alfaro ME, Zoller S, Lutzoni F., 2003 Bayes or bootstrap? A simulation study comparing the performance of Bayesian Markov chain Monte Carlo sampling and bootstrapping in assessing phylogenetic confidence. Mol Biol Evol 20:255-266
  • Darbishire OV., 1926 The structure of Peltigera with especial reference to P. praetextata. Ann Bot 40:727-758
  • Felsenstein J., 1985 Confidence limit on phylogenies: an approach using the bootstrap. Evolution 39:783-791
  • Franc N, Kärnefelt EI., 1998 Phylogeny of Xanthoria calcicola and X. parietina, based on ITS sequences. Graphis Scripta 9:49-54
  • Gardes M, Bruns TD., 1993 ITS primers with enhanced specificity for basidiomycetes—application to the identification of mycorrhizae and rusts. Mol Ecol 2:113-118
  • Goffinet B, Hastings RJ., 1994 The lichen genus Peltigera (lichenized Ascomycetes) in Alberta. Provincial Mus Alberta Nat Hist Occas Papers 21:1-54
  • ———, ———. 1995 Two new sorediate taxa of Peltigera. Lichenologist 27:43-58
  • ———, Miadlikowska J., 1999 Peltigera phyllidiosa (Peltigeraceae, Ascomycotina), a new species from the Southern Appalachians corroborated by ITS sequences. Lichenologist 31:247-255
  • ———, ———, Goward T., 2003 Phylogenetic inferences based on mrDNA sequences support five morphospecies within the Peltigera didactyla complex (lichenized Ascomycota). Bryologist 106:349-364
  • ———, Sérusiaux E, Diederich P., 1994 Le genre Peltigera (lichens) en Belgique et au Grand–Duché de Luxembourg. Belg Journ Bot 127:184-206
  • Goward T, Goffinet B, Vitikainen O., 1995 Synopsis of the genus Peltigera (lichenized Ascomycetes) in British Columbia, with a key to the North American species. Can J Bot 73:91-111
  • Grassly NC, Holmes EC., 1997 A likelihood method for the detection of selection and recombination using nucleotide sequences. Mol Biol Evol 14:239–247. (http://evolve.zoo.ox.ac.uk/Plato/main.html)
  • Groner U, LaGreca S., 1997 The “mediterranean” Ramalina pannizzei north of the Alps: morphological, chemical and nrDNA sequence data. Lichenologist 29:441-454
  • Grube M, Kroken S., 2000 Molecular approaches and the concept of species and species complexes in lichenized fungi. Mycol Res 104:1284-1294
  • Gyelnik V., 1927 Peltigera-tanulmányok. (Peltigera-studien). Botanikai Kozlemények 24:122-140 +(33–38)
  • ———. 1933 Clavis et enumeratio specierum generis Peltigerae. Rev Bryol Lichénol 5:61-73
  • Holtan-Hartwig J., 1993 The lichen genus Peltigera, exclusive of the P. canina group, in Norway. Sommerfeltia 15:1-77
  • Huelsenbeck JP., 2000 “MrBayes 2.01: Bayesian inference of phylogeny”. University of Rochester, U.S.A. (http://morphbank.ebc.uu.se/mrbayes/)
  • ———, Hillis DM., 1993 Success of phylogenetic methods in the four-taxon case. Syst Biol 42:247-264
  • Jakobsen IB, Easteal S., 1996 A program for calculating and displaying compatibility matrices as an aid in determining reticulate evolution in molecular sequences. Comp Appl Biosci 12:291-295. (http://jcsmr.anu.edu.au/dmm/humgen/ingrid/reticulate.htm)
  • Kimura M., 1980 A simple method for estimating evolutionary rate of base substitution through comparative studies of nucleotide sequences. J Mol Evol 16:111-120
  • Kjer KM., 1995 Use of rRNA secondary structure in phylogenetic studies to identify homologous positions: an example of alignment and data presentation from the frogs. Mol Phyl Evol 4:314-330
  • Kroken S, Taylor JW., 2001 A gene genealogical approach to recognize phylogenetic species boundaries in the lichenized fungus Letharia. Mycologia 93:38-53
  • Larget B, Simon DL., 1999 Markov chain Monte Carlo algorithm for the Bayesian analysis of phylogenetic trees. Mol Biol Evol 16:750-759
  • Larsen N, Olsen GJ, Maidak BL, McCaughey MJ, Overbeek R, Macke TJ, Marsh TL, Woese CR., 1993 The ribosomal database project. Nucleic Acids Res 21: (suppl) 3021-3023
  • Lindahl PO., 1953 The taxonomy and ecology of some Peltigera species, P. canina (L.) Willd., P. rufescens (Weis.) Humb., P. praetextata (Flk.) Vain. Svensk Bot Tidskr 47:94-106
  • ———. 1959 On the occurrence of pycnidia in the lichen genus Peltigera. Svensk Bot Tidskr 53:475-480
  • ———. 1960 The different types of isidia in the lichen genus Peltigera. Svensk Bot Tidskr 54:565-570
  • Linnaeus C., 1753 Species plantarum. Stockholm. 1200 p
  • Lutzoni F, Wagner P, Reeb V, Zoller S., 2000 Integrating ambiguously aligned regions of DNA sequences in phylogenetic analyses without violating positional homology. Syst Biol 49:628-651
  • Martin D, Rybicki E., 2000 RDP: detection of recombination amongst aligned sequences. Bioinformatics 16:562-563. (ftp://ftp.uct.ac.za/pub/data/geminivirus/recomb.htm)
  • Martínez I, Burgaz AR., 1996 Anatomical study of Peltigera canina, P. membranacea and P. praetextata (lichenized Ascomycotina). Ann Bot Fennici 33:223-229
  • ———, ———, Vitikainen O., 1997 Studies on the genus Peltigera in the Iberian Peninsula. II. Nova Hedwigia 64:367-391
  • Martínez Moreno I., 1999 Taxonomía del Género Peltigera Willd. (Ascomycetes Liquenizados) en la Península Ibérica y estudio de sus Hongos Liquenícolas. Ruizia. Madrid: Monografías del Real Jardín Botánico, 15, Real Jardín Botánico, CSIC. 200 p
  • Mason-Gamer R, Kellogg E., 1996 Testing for phylogenetic conflict among molecular datasets in the tribe Triticeae (Gramineae). Syst Biol 45:524-545
  • Miadlikowska J., 1999 Rodzaj Peltigera (Peltigerales, Ascomycota) na tle jego wspolczesnej systematyki. [Doctoral thesis]. Gdansk: Gdansk University. 206 p
  • ———, Lutzoni F., 2000 Phylogenetic revision of the genus Peltigera (lichen-forming Ascomycota) based on morphological, chemical, and large subunit nuclear ribosomal DNA data. Int J Plant Sci 161:925-958
  • ———, McCune B, Lutzoni F., 2002 Pseudocyphellaria perpetua, a new lichen from western North America. Bryologist 105:1-10
  • Niu Y, Wei J., 1993 Variations in ITS sequences of nuclear nrDNA from two Lasallia species and their systematic significance. Mycosystema 6:25-29
  • O'Keefe FR, Wagner PJ., 2001 Deriving and testing hypotheses of correlated character evolution using character compatibility. Syst Biol 50:657-675. (CompCorr 1.0β; http://pjw3.fmnh.org/data.html)
  • Posada D, Crandall KA., 1998 Modeltest: testing the model of DNA substitution. Bioinformatics 14:817-818. (http://bioag.byu.edu/zoology/crandall_lab/modeltest.htm)
  • ———, ———. 2001 Evaluation of methods for detecting recombination from DNA sequences: computer simulations. PNAS 98:13757-13762
  • Sawyer S., 1989 Statistical tests for detecting gene conversion. Mol Biol Evol 6:526-538. (http://www.math.wustl.edu/~sawyer/geneconv/index.html)
  • Stocker-Wörgötter E, Türk R., 1988 Culture of the cyanobacterial lichen Peltigera didactyla from soredia under laboratory conditions. Lichenologist 20:369-375
  • ———, ———. 1990 Thallus formation of the cyanobacterial lichen Peltigera didactyla from soredia under laboratory conditions. Bot Acta 103:315-321
  • ———, ———. 1991 Artificial resynthesis of thalli of the cyanobacterial lichen Peltigera praetextata under laboratory conditions. Lichenologist 23:127-138
  • Strato JW., 1921 Über Wachstum und Regeneration des Thallus von Peltigera canina. Hedwigia 63:11-42
  • Swofford DL., 2001 PAUP*: phylogenetic analysis using parsimony (* and other methods). Version 4. Sunderland, Massachusetts: Sinauer Associates
  • Tamura K, Nei M., 1993 Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol 10:512-526
  • Thomson JW., 1948 Experiments upon the regeneration of certain species of Peltigera, and their relationship to the taxonomy of the genus. Bull Torrey Bot Club 75:486-491
  • Vitikainen O., 1994 Taxonomic revision of Peltigera (lichenized Ascomycotina) in Europe. Acta Bot Fennica 152:1-96
  • Wheeler WC., 1996 Optimization alignment: the end of multiple sequence alignment in phylogenetics?. Cladistics 12:1-9
  • White TJ, Bruns T, Lee S, Taylor JW., 1990 Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: Innis MA, Gelfand DH, Sninsky JJ, White TJ, eds. PCR protocols. New York: Academic Press. p 315–322
  • Yang Z., 1996 Phylogenetic analysis using parsimony and likelihood methods. J Mol Evol 42:294-307.

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Order Reprints Request Corporate Permissions

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

Request Academic Permissions

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.

Related research

People also read lists articles that other readers of this article have read.

Recommended articles lists articles that we recommend and is powered by our AI driven recommendation engine.

Cited by lists all citing articles based on Crossref citations.
Articles with the Crossref icon will open in a new tab.