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Comparisons of phylogenetic hypotheses among different data sets in dwarf dandelions (Krigia, Asteraceae): Additional information from internal transcribed spacer sequences of nuclear ribosomal DNA

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Abstract

The internal transcribed spacer (ITS) region of the 18 S–25 S nuclear ribosomal DNA repeat was sequenced from 19 populations of the tribeLactuceae, including all species of dwarf dandelion (Krigia) and five outgroup genera. The incidence of length changes and base substitutions was at least two times higher for ITS 1 than ITS 2. Interspecific sequence divergence withinKrigia averaged 9.62% (1.61%–15.19%) and 4.26% (0%–6.64%) in ITS 1 and ITS 2, respectively. Intergeneric sequence divergence ranged from 15.6% to 44.5% in ITS 1 and from 8.0% to 28.6% in ITS 2. High sequence divergence and homoplasy among genera of tribeLactuceae suggest that the phylogenetic utility of ITS sequence data is limited to interspecific studies or comparisons among closely related genera. Trees generated from ITS sequences are essentially identical to those from restriction site comparisons of the entire nuclear ribosomal (nr) DNA region. The degree of tree resolution differed depending on how gaps were treated in phylogenetic analyses. The ITS trees were congruent with the chloroplast DNA and morphological phylogenies in three major ways: 1) the sister group relationship betweenKrigia andPyrrhopappus; 2) the recognition of two monophyletic sections,Krigia andCymbia, in genusKrigia; and 3) the monophyly of theK. occidentalis-K. cespitosa clade in sect.Cymbia. However, the two nrDNA-based trees are not congruent with morphology/chloroplast DNA-based trees for the interspecific relationships in sect.Krigia. An average of 22.5% incongruence was observed among fourKrigia data sets. The relatively high degree of incongruence among data sets is due primarily to conflict between trees based on nrDNA and morphological/cpDNA data. The incongruence is probably due to the concerted evolution of nrDNA repeating units. The results fromKrigia and theLactuceae suggest that nrDNA data may have limited utility in phylogenetic studies of plants, especially in groups which exhibit high levels of sequence divergence. Our combined phylogenetic analysis as a total evidence shows the least conflict to each of the individual data sets.

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References

  • Appels, R., Dvorak, K., 1982: Relative rates of divergence of species and gene sequences within the rDNA region of species in theTriticeae: implications for the maintenance of homogeneity of a repeated gene family. — Theor. Appl. Genet.63: 361–365.

    Google Scholar 

  • Baldwin, B. G., 1992: Phylogenetic utility of the internal transcribed spacers of nuclear ribosomal DNA in plants: an example from theCompositae. — Mol. Phyl. Evol.1: 3–16.

    Google Scholar 

  • —, 1993: Molecular phylogenetics ofCalycadenia (Compositae) based on ITS sequences of nuclear ribosomal DNA: chromosomal and morphological evolution re-examined. — Amer. J. Bot.80: 222–238.

    Google Scholar 

  • Barker, R. F., Harberd, N. P., Jarvis, M. G., Flavell, R. B., 1988: Structure and evolution of the intergenic region in a ribosomal DNA repeat unit of wheat. — J. Mol. Biol.201: 1–17.

    Google Scholar 

  • Bechmann, B., Lüke, W., Hunsmann, G., 1990: Improvement of PCR amplified DNA sequencing with the aid of detergents. — Nucl. Acids Res.18: 1309.

    Google Scholar 

  • Blackmore, S., 1981: Palynology and intergeneric relationships in subtribeHyoseridinae (Compositae: Lactuceae). — Bot. J. Linn. Soc.82: 1–13.

    Google Scholar 

  • Bremer, K., 1990: Combinable component consensus. — Cladistics6: 369–372.

    Google Scholar 

  • Bull, J. J., Huelsenbeck, J. P., Cunningham, C. W., Swofford, D. L., Waddell, P. J., 1993: Partitioning and combining data in phylogenetic analysis. — Syst. Biol.42: 384–397.

    Google Scholar 

  • Chambers, C. L., 1965: An allopolyploidKrigia from the southern Appalachians. — Amer. J. Bot. (Abstr.)52: 654.

    Google Scholar 

  • Chatterton, N. J., Hsiao, C., Asay, K. H., Jensen, K. B., Wang, R. R.-C., 1992a: Nucleotide sequence of the internal transcribed spacer region of rDNA in the primitive oat species,Avena longiglumis Durieu (Gramineae). — Pl. Mol. Biol.20: 163–164.

    Google Scholar 

  • —, 1992b: Nucleotide sequence of the internal transcribed spacer region of rDNA in barley,Hordium vulgare L. (Gramineae). — Pl. Mol. Biol.20: 165–166.

    Google Scholar 

  • Chinnappa, C. C., 1981: Cytological studies inKrigia (Asteraceae). — Canad. J. Genet. Cytol.23: 671–678.

    Google Scholar 

  • Donoghue, M. J., Sanderson, M. J., 1992: The suitability of molecular and morphological evidence in reconstructing plant phylogeny. — InSoltis, P. S., Soltis, D. E., Doyle, J. J., (Eds): Molecular systematics of plants, pp. 340–368. — New York: Chapman and Hall.

    Google Scholar 

  • Dorado, O., Rieseberg, L. H., Arias, D. M., 1992: Chloroplast introgression in southern California sunflowers. — Evolution46: 566–572.

    Google Scholar 

  • Dover, G. A., 1982: Molecular drive: a cohesive mode of species evolution. — Nature299: 159–165.

    Google Scholar 

  • D'Ovidio, R., 1992: Nucleotide sequence of a 5.8 S rDNA gene and of the internal transcribed spacers fromPopulus deltoides. — Pl. Mol. Biol.19: 1069–1072.

    Google Scholar 

  • Doyle, J. J., 1992: Gene trees and species trees: molecular systematics as one character taxonomy. — Syst. Bot.17: 144–163.

    Google Scholar 

  • —, 1987: A rapid DNA isolation procedure for small quantities of fresh leaf tissue. — Phytochem. Bull.19: 11–15.

    Google Scholar 

  • Felsenstein, J., 1985: Confidence limits on phylogenies: an approach using the bootstrap. — Evolution39: 783–791.

    Google Scholar 

  • —, 1991: PHYLIP (Phylogeny inference package), version 3.4. Computer program distributed by the author. — St Louis: The University of Washington.

    Google Scholar 

  • Feuer, S., Tomb, A. S., 1977: Pollen morphology and detailed structure of familyCompositae, tribeCichorieae II. subtribeMicroseridinae. — Amer. J. Bot.64: 230–245.

    Google Scholar 

  • Field, G. F., Olsen, G. L., Lane, D. J., Giovannoni, S. J., Ghiselin, M. T., Raff, E. C., Pace, N. R., Raff, R. A., 1988: Molecular phylogeny of the animal kingdom. — Science239: 748–753.

    Google Scholar 

  • Gonzalez, I. L., Sylvester, J. E., Smith, T. F., Stambolian, D., Schmickel, R. D., 1990: Ribosomal RNA gene sequences and hominoid phylogeny. — Mol. Biol. Evol.7: 203–219.

    Google Scholar 

  • Gray, A., 1886:Apogon andKrigia. — In: Synoptical flora of North America, pp. 410–412. — New York: Ivison, Baikeman, Taylor.

    Google Scholar 

  • Gyllensten, U. B., Erlich, H. A., 1988: Generation of single-stranded DNA by the polymerase chain reaction and its application to direct sequencing of the HLA-DQA locus. — Proc. Natl. Acad. Sci. USA85: 7652–7656.

    Google Scholar 

  • Hamby, R. K., Zimmer, E. A., 1992: Ribosomal RNA as a phylogenetic tool in plant systematics. — InSoltis, P. S., Soltis, D. E., Doyle, J. J., (Eds): Molecular systematics of plants, pp. 50–91. — New York: Chapman and Hall.

    Google Scholar 

  • Harborne, J. B., 1977: Variations in pigment patterns inPyrrhopappus and related taxa of theCichorieae. — Phytochemistry16: 927–928.

    Google Scholar 

  • Harrison, R. G., 1991: Molecular changes at speciation. — Annu. Rev. Ecol. Syst.22: 281–308.

    Google Scholar 

  • Hendy, M. D., Penny, D., 1982: Branch and bound algorithms to determine minimal evolutionary trees. — Math. Biosci.59: 227–290.

    Google Scholar 

  • Hillis, D. M., 1987: Molecular versus morphological approaches to systematics. — Annu. Rev. Ecol. Syst.18: 23–42.

    Google Scholar 

  • —, 1991: Discriminating between phylogenetic signal and random noise in DNA sequences. — InMiyamoto, M. M., Cracraft, J., (Eds): Phylogenetic analysis of DNA sequences, pp. 278–294. — New York: Oxford University Press.

    Google Scholar 

  • —, 1989: Vertebrate phylogeny: evidence from 28 S ribosomal DNA sequences. — InFernholm, B., Bremer, K., Jornvall, H., (Eds): The hierarchy of life, pp. 355–367. Nobel Symposium70. — Amsterdam: Elsevier.

    Google Scholar 

  • —, 1991: Evidence for biased gene conversion in concerted evolution of ribosomal DNA. — Science251: 308–310.

    Google Scholar 

  • Jansen, R. K., Wallace, R. S., Kim, K.-J., Chambers, K. L., 1991: Systematic implications of chloroplast DNA variation in the subtribeMicroseridinae (Asteraceae: Lactuceae). — Amer. J. Bot.78: 1015–1027.

    Google Scholar 

  • Jeffrey, C., 1966: Notes onCompositae: I. TheCichorieae in east tropical Africa. — Kew Bull.18: 427–482.

    Google Scholar 

  • Jorgensen, R. A., Cluster, P. D., 1988: Modes and tempos in the evolution of nuclear ribosomal DNA: new characters for evolutionary studies and new markers for genetic and population studies. — Ann. Missouri Bot. Gard.75: 1238–1247.

    Google Scholar 

  • Jukes, T. H., Cantor, C. R., 1969: Evolution of protein molecules. — InMunro, H. N., (Ed.): Mammalian protein metabolism, pp. 21–123. — New York: Academic Press.

    Google Scholar 

  • Kavanagh, T. A., Timmis, J. N., 1988: Structure of melon rDNA and nucleotide sequence of the 17–25 S spacer region. — Theor. Appl. Genet.76: 673–680.

    Google Scholar 

  • Kim, K.-J., Mabry, T. J., 1991: Phylogenetic and evolutionary implications of nuclear ribosomal DNA variation in dwarf dandelions (Krigia, Lactuceae, Asteraceae). — Pl. Syst. Evol.177: 53–69.

    Google Scholar 

  • —, 1992: Systematic overview ofKrigia (Asteraceae: Lactuceae). — Brittonia44: 173–198.

    Google Scholar 

  • —, 1992a: Phylogenetic and evolutionary implications of interspecific chloroplast DNA variation inKrigia (Lactuceae-Asteraceae). — Syst. Bot.17: 449–469.

    Google Scholar 

  • —, 1992b: Evolutionary implications of intraspecific chloroplast DNA variation in dwarf dandelions (Krigia-Asteraceae). — Amer. J. Bot.79: 708–715.

    Google Scholar 

  • Kimura, M., 1980: A simple method for estimating evolutionary rates of base substitution through comparative studies of nucleotide sequences. — J. Mol. Evol.16: 111–120.

    Google Scholar 

  • —, 1981: Estimation of evolutionary distances between homologous nucleotide sequences. — Proc. Natl. Acad. Sci. USA78: 454–458.

    Google Scholar 

  • Kiss, T., Mihály, K., Steffen, A., Solymosy, F., 1988: Nucleotide sequence of the 17S–25S spacer region from tomato rDNA. — Nucl. Acids Res.16: 7179.

    Google Scholar 

  • Kluge, A. G., 1989: A concern for evidence and a phylogenetic hypothesis of relationships amongEpicrates (Boidae, Serpentes). — Syst. Zool.38: 7–25.

    Google Scholar 

  • Lake, A. J., 1985: Evolving ribosome structure: domains in archaebacteria, eubacteria, eocytes, and eukaryotes. — Annu. Rev. Biochem.54: 507–530.

    Google Scholar 

  • Lee, S. B., Taylor, J. W., 1992: Phylogeny of five fungus-like protoctistanPhytophthora species, inferred from the internal transcribed spacers of ribosomal DNA. — Mol. Biol. Evol.9: 636–653.

    Google Scholar 

  • Levinson, G., Gutman, G. A., 1987: Slipped-strand mispairing: a major mechanism for DNA sequence evolution. — Mol. Biol. Evol.4: 203–221.

    Google Scholar 

  • McDade, L. A., 1992: Hybrids and phylogenetic systematics II. The impact of hybrid on cladistic analysis. — Evolution46: 1329–1346.

    Google Scholar 

  • Mickevich, M. F., Farris, J. S., 1981: The implications of congruence inMenidia. — Syst. Zool.30: 351–370.

    Google Scholar 

  • Miyamoto, M. M., 1985: Consensus cladograms and general classifications. — Cladistics1: 186–189.

    Google Scholar 

  • Northington, D. K., 1974: Systematic studies of the genusPyrrhopappus (Compositae, Cichorieae). — Spec. Publ. Mus. Texas Tech. Univ.6: 1–38.

    Google Scholar 

  • O'Donnell, K., 1992: Ribosomal DNA internal transcribed spacers are highly divergent in the phytopathogenic ascomyceteFusarium sambucinum (Gibberella pulicaris). — Curr. Genet.22: 213–220.

    Google Scholar 

  • Olsen, G. J., 1987: Earliest phylogenetic branchings: comparing rRNA-based evolutionary trees inferred with various techniques. — Cold Spring Harbor Symp. Quant. Biol.52: 825–837.

    Google Scholar 

  • Rathgeber, J., Capesius, I., 1989: Nucleotide sequence of the 18 S–25 S spacer region from mustard DNA. — Nucl. Acids Res.17: 7522.

    Google Scholar 

  • Rieseberg, L. H., Soltis, D. E., Palmer, J. D., 1988: A molecular re-examination of introgression betweenHelianthus annuus andH. bolanderi (Compositae). — Evolution42: 227–238.

    Google Scholar 

  • Rogers, S. O., Bendich, A. J., 1987: Ribosomal RNA genes in plants: variability in copy number and in the intergenic spacer. — Pl. Mol. Biol.9: 509–520.

    Google Scholar 

  • Saghai-Maroof, M. A., Soliman, K. M., Jorgensen, R. A., Allard, R. W., 1984: Ribosomal DNA spacer-length polymorphisms in barley: mendelian inheritance, chromosomal location, and population dynamics. — Proc. Natl. Acad. Sci. USA81: 8014–8018.

    Google Scholar 

  • Sanderson, M. J., Donoghue, M. J., 1989: Patterns of variation in levels of homoplasy. — Evolution43: 1781–1795.

    Google Scholar 

  • Saitou, N., Nei, M., 1987: The neighbor-joining method: a new method for reconstructing phylogenetic trees. — Mol. Biol. Evol.4: 406–425.

    Google Scholar 

  • Schiebel, K., Hemleben, V., 1989: Nucleotide sequence of the 18 S–25 S spacer region from rDNA of mung bean. — Nucl. Acids Res.17: 2852.

    Google Scholar 

  • Shaffer, H. B., Clark, J. M., Kraus, F., 1991: When molecules and morphology clash: a phylogenetic analysis of North American ambystomatid salamanders (Caudata: Ambystomatidae). — Syst. Zool.40: 284–303.

    Google Scholar 

  • Shinners, L. H., 1947: Revision of the genusKrigia Schreber. — Wrightii1: 187–206.

    Google Scholar 

  • Smith, G. P., 1976: Evolution of repeated DNA sequences by unequal crossover. — Science191: 528–535.

    Google Scholar 

  • Standley, P. C., 1911: A revision of the cichoriaceous generaKrigia, Cynthia, andCymbia. — Contr. U. S. Natl. Herb.13: 351–357.

    Google Scholar 

  • Stebbins, G. L., 1953: A new classification of the tribeCichorieae, familyCompositae. — Madroño12: 33–64.

    Google Scholar 

  • —, 1953: Chromosomes and phylogeny in theCompositae, tribeCichorieae. — Univ. Calif. Publ. Bot.26: 401–429.

    Google Scholar 

  • Swofford, D. L., 1991a: When are phylogeny estimates from molecular and morphological data incongruent. — InMiyamoto, M. M., Cracraft, J., (Eds): Phylogenetic analysis of DNA sequences, pp. 295–333. — New York: Oxford University Press.

    Google Scholar 

  • —, 1991b: PAUP: phylogenetic analysis using parsimony, version 3.0 r. Computer program distributed by the author. — Urbana-Champain: Illinois Natural History Survey.

    Google Scholar 

  • Sytsma, K. J., Schaal, B. A., 1990: Ribosomal DNA variation within and among individuals ofLisianthus (Gentianaceae) populations. — Pl. Syst. Evol.170: 97–106.

    Google Scholar 

  • Takaiwa, F., Oono, K., Sugiura, M., 1985: Nucleotide sequence of the 17 S–25 S spacer region from mice rDNA. — Pl. Mol. Biol.4: 355–364.

    Google Scholar 

  • Turner, B. L., Kim, K.-J., 1990: Overview of the genusPyrrhopappus (Asteraceae: Lactuceae) with emphasis upon chloroplast DNA restriction site data. — Amer. J. Bot.77: 845–850.

    Google Scholar 

  • Ueki, M., Uchizawa, E., Yakura, K., 1992: The nucleotide sequence of the rRNA intergenic spacer region in a wild species of the genusVicia, V. angustifolia. — Pl. Mol. Biol.18: 175–178.

    Google Scholar 

  • Venkateswarlu, K., Nazar, R., 1991: A conserved core structure in the 18 S–25 S rRNA intergenic region from tobacco,Nicotiana rustica. — Pl. Mol. Biol.17: 189–194.

    Google Scholar 

  • Wang, B., Fang, Q., Williams, W. V., Weiner, D. B., 1992: Double-stranded DNA sequencing by linear amplification withTaq DNA polymerase. — Biotechniques13: 527–530.

    Google Scholar 

  • White, T. J., Bruns, T., Lee, S., Taylor, J., 1990: Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. — InInnis, M. A., Gelfand, D. H., Sninsky, J. J., White, T. J., (Eds): PCR protocols: a guide to methods and applications, pp. 315–322. — San Diego: Academic Press.

    Google Scholar 

  • Winship, P. R., 1989: An improved method for direct sequencing PCR amplified material using dimethyl sulphoxide. — Nucl. Acids Res.17: 1266.

    Google Scholar 

  • Yakura, K., Kato, A., Tanifuji, S., 1984: Length heterogeneity in the large spacer ofVicia fava rDNA is due to differing number of 325 bp repetitive elements. — Mol. Gen. Genet.139: 400–405.

    Google Scholar 

  • —, 1992: The nucleotide sequences of the rDNA spacer region between the 25 S and 18 S rRNA genes in a species of the genusVicia, V. hirsuta. — Pl. Mol. Biol.19: 537–539.

    Google Scholar 

  • Yokota, Y., Kawata, T., Iida, Y., Kata, A., Tanifuji, S., 1989: Nucleotide sequences of the 5.8 S rRNA gene and internal transcribed spacer regions in carrot and broad bean ribosomal DNA. — J. Mol. Evol.29: 294–301.

    Google Scholar 

  • Zhang, W., Reading, C., Deisseroth, A. B., 1992: Improved PCR sequencing with formamide. — Trends Genet.8: 332.

    Google Scholar 

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  1. Department of Botany, University of Texas, 78713-7640, Austin, TX, USA

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Kim, K.J., Jansen, R.K. Comparisons of phylogenetic hypotheses among different data sets in dwarf dandelions (Krigia, Asteraceae): Additional information from internal transcribed spacer sequences of nuclear ribosomal DNA. Pl Syst Evol 190, 157–185 (1994). https://doi.org/10.1007/BF00986191

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