The effects of increasing genetic distance on alignment of, and tree construction from, rDNA internal transcribed spacer sequences

Molecular Phylogenetics and Evolution

Volumn 26, Issue 3, 2003, Pages 444-451

  Simmons, Mark P ^a,b   Freudenstein, John V ^a  

^a OHIO STATE UNIVERSITY   (United States)

^b Department of Environmental and Radiological Health Sciences   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

FUNGI;

EID: 0037355122     PISSN: 10557903     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1055-7903(02)00366-4     Document Type: Article

References (50)

1. Albert, V.A., Chase, M.W., Mishler, B.D., 1993. Character-state weighting for cladistic analysis of protein-coding DNA sequences. Ann. Mo. Bot. Gard. 80, 752-766.
2. Andersson, L., Taylor, C.M., in press. Palicourea Aubl. (Rubiaceae) is polyphyletic.
3. Arup, U., Grube, M., 2000. Is Rhizoplaca (Lecanorales, lichenized Ascomycota) a monophyletic genus? Can. J. Bot. 78, 318-327.
4. Baker, W.J., Hedderson, T.A., Dransfield, J., 2000. Molecular phylogenetics of subfamily Calamoideae (Palmae) based on nrDNA ITS and cpDNA rps16 intron sequence data. Mol. Phylogenet. Evol. 14, 195-217.
5. Baldwin, B.G., Sanderson, M.J., Porter, J.M., Wojciechowski, M.F., Campbell, C.S., Donoghue, M.J., 1995. The ITS region of nuclear ribosomal DNA: a valuable source of evidence on angiosperm phylogeny. Ann. Mo. Bot. Gard. 82, 247-277.
6. Ballard, H.E.J., Sytsma, K.J., Kowal, R.R., 1999. Shrinking the violets: phylogenetic relationships of infrageneric groups in Viola (Violaceae) based on internal transcribed spacer DNA sequences. Syst. Bot. 23, 439-458.
7. Chambers, S.M., Liu, G., Cairney, J.W.G., 2000. ITS rDNA sequence comparison of ericoid mycorrhizal endophytes from Woolsia pungens. Mycol. Res. 104, 168-174.
8. Clevinger, J.A., Panero, J.L., 2000. Phylogenetic analysis of Silphium and subtribe Engelmanniinae (Asteraceae: Heliantheae) based on ITS and ETS sequence data. Am. J. Bot. 87, 565-572.
9. Coleman, A.W., Mai, J.C., 1997. Ribosomal DNA ITS-1 and ITS-2 sequence comparisons as a tool for predicting genetic relatedness. J. Mol. Evol. 45, 168-177.
10. Cooke, D.E.L., Drenth, A., Duncan, J.M., Wagels, G., Brasier, C.M., 2000. A molecular phylogeny of Phytophthora and related oomycetes. Fungal Genet. Biol. 30, 17-32.
11. Doolittle, R.F., 1981. Similar amino acid sequences: Chance or common ancestry? Science 214, 149-159.
12. Downie, S.R., Katz-Downie, D.S., Spalik, K., 2000. A phylogeny of Apiaceae tribe Scandiceae: evidence from nuclear ribosomal DNA internal transcribed spacer sequences. Am. J. Bot. 87, 76-95.
13. Eriksson, T., Donoghue, M.J., Hibbs, M.S., 1998. Phylogenetic analysis of Potentilla using DNA sequences of nuclear ribosomal internal transcribed spacers (ITS), and implications for the classification of the Rosoideae (Rosaceae). Plant Syst. Evol. 211, 155-179.
14. Farris, J.S., Albert, V.A., Källersjö, M., Lipscomb, D., Kluge, A.G., 1996. Parsimony jackknifing outperforms neighbor-joining. Cladistics 12, 99-124.
15. Felsenstein, J., 1978. Cases in which parsimony or compatibility methods will be positively misleading. Syst. Zool. 27, 401-410.
16. Francisco-Ortega, J., Santos-Guerra, A., Hines, A., Jansen, R.K., 1997. Molecular evidence for a Mediterranean origin of the Macronesian endemic genus Argyranthemum (Asteraceae). Am. J. Bot. 84, 1595-1613.
17. Freudenstein, J.V., Chase, M.W., 2001. Analysis of mitochondrial nad1b-c intron sequences in Orchidaceae: utility and coding of length-change characters. Syst. Bot. 26, 643-657.
18. Gardes, M., Bruns, T.D., 1993. ITS primers with enhanced specificity for basidiomycetes: application to the identification of mycorrhizae and rusts. Mol. Ecol. 2, 113-118.
19. Gatesy, J., DeSalle, R., Wheeler, W., 1993. Alignment-ambiguous nucleotide sites and the exclusion of systematic data. Mol. Phylogenet. Evol. 2, 152-157.
20. Goloboff, P.A., 1993. Nona, version 1.6 (computer software and manual). Distributed by the author, Tucuman, Argentina.
21. Graybeal, A., 1998. Is it better to add taxa or characters to a difficult phylogenetic problem? Syst. Biol. 47, 9-17.
22. Hendy, M.D., Penny, D., 1989. A framework for the quantitative study of evolutionary trees. Syst. Zool. 38, 297-309.
23. Hickson, R.E., Simon, C., Perrey, S.W., 2000. The performance of several multiple-sequence alignment programs in relation to secondary-structure features for an rRNA sequence. Mol. Biol. Evol. 17, 530-539.
24. Hillis, D.M., 1996. Inferring complex phylogenies. Science 383, 130-131.
25. Huelsenbeck, J.P., 1997. Is the Felsenstein zone a fly trap? Syst. Biol. 46, 69-74.
26. Källersjö, M., Albert, V.A., Farris, J.S., 1999. Homoplasy increases phylogenetic structure. Cladistics 15, 91-93.
27. Katz-Downie, D.S., Valiejo-Roman, C.M., Terentieva, E.I., Troitsky, A.V., Pimenov, M.G., Lee, B., Downie, S.R., 1999. Towards a molecular phylogeny of Apiaceae subfamily Apioideae: additional information from nuclear ribosomal DNA ITS sequences. Plant Syst. Evol. 216, 167-195.
28. Kiers, A.M., Mes, T.H.M., van der Meijden, R., Bachmann, K., 1999. Morphologically defined Cichoriwn (Asteraceae) species reflect lineages based on chloroplast and nuclear (ITS) DNA data. Syst. Bot. 24, 645-659.
29. Kimura, M., 1980. A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol. 16, 111-120.
30. Lohtander, K., Källersjö, M., Moberg, R., Tehler, A., 2000. The family Physciaceae in Fennoscandia: phylogeny inferred from ITS sequences. Mycologia 92, 728-735.
31. 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.
32. McClure, M.A., Vasi, T.K., Fitch, W.M., 1994. Comparative analysis of multiple protein-sequence alignment methods. Mol. Biol. Evol. 11, 571-592.
33. McDade, L.A., Masta, S.E., Moore, M.L., Waters, E., 2000. Phylogenetic relationships among Acanthaceae: evidence from two genomes. Syst. Bot. 25, 106-121.
34. Mindell, D.P., Shultz, J.W., Ewald, P.W., 1995. The AIDS pandemic is new, but is HIV new? Syst. Biol. 44, 77-92.
35. Molvray, M., Kores, P.J., Chase, M.W., 1999. Phylogenetic relationships within Korthalsella (Viscaceae) based on nuclear ITS and plastid trnL-F sequence data. Am. J. Bot. 86, 249-260.
36. Nepokroeff, M., Bremer, B., Sytsma, K.J., 1999. Reorganization of the genus Psychotria and tribe Psychotrieae (Rubiaceae) inferred from ITS and rbcL sequence data. Syst. Bot. 24, 5-27.
37. Nixon, K.C., 1999. Winclada (BETA). Published by the author, Ithaca, New York.
38. Réblová, M., Winka, K., 2000. Phylogeny of Chaetosphaeria and its anamorphs based on morphological and molecular data. Mycologia 92, 939-954.
39. Roalson, E.H., Friar, E.A., 2000. Infrageneric classification of Eleocharis (Cyperaceae) revisited: evidence from the internal transcribed spacer (ITS) region of nuclear ribosomal DNA. Syst. Bot. 25, 323-336.
40. Saenez, G.S., Taylor, J.W., 1999. Phylogeny of the Erysiphales (powdery mildews) inferred from internal transcribed spacer ribosomal DNA sequences. Can. J. Bot. 77, 150-168.
41. Simmons, M.P., Ochoterena, H., 2000. Gaps as characters in sequence-based phylogenetic analyses. Syst. Biol. 49, 369-381.
42. Simmons, M.P., Ochoterena, H., Carr, T., 2001. Relative quality of gap characters in sequence-based phylogenetic analyses. Syst. Biol. 50, 454-462.
43. Sub, Y., Thien, L.B., Reeve, H.E., Zimmer, E.A., 1993. Molecular evolution and phylogenetic implications of internal transcribed spacer sequences of ribosomal DNA in Winteraceae. Am. J. Bot. 80, 1042-1055.
44. Swofford, D.L., 1998. PAUP*: Phylogenetic Analysis Using Parsimony (*and Other Methods), ver. 4.0. Sinauer, Sunderland, MA.
45. Thompson, J.D., Gibson, T.J., Plewniak, F., Jeanmougin, F., Higgins, D.G., 1997. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 25, 4876-4882.
46. Thompson, J.D., Higgins, D.G., Gibson, T.J., 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22, 4673-4680.
47. Thompson, J.D., Plewniak, F., Poch, O., 1999. A comprehensive comparison of multiple sequence alignment programs. Nucleic Acids Res. 27, 2682-2690.
48. Wagstaff, S.J., Dawson, M.I., 2000. Classification, origin, and patterns of diversification of Corynocarpus (Corynocarpaceae) inferred from DNA sequences. Syst. Bot. 25, 134-149.
49. Wenzel, J.W., Siddall, M.E., 1999. Noise. Cladistics 15, 51-64.
50. Wheeler, W.C., Gladstein, D.S., 1994. MALIGN: a multiple sequence alignment program. J. Hered. 85, 417-418.