New Trends in Plant Systematics
New Trends in Plant Systematics
Daniel J. Crawford,
Mark E. Mort,
Daniel J. Crawford
Department of Ecology and Evolutionary Biology & The Museum of Natural History and Biodiversity Research Center, University of Kansas, Lawrence, Kansas, 66045 U.S.A.
Search for more papers by this authorMark E. Mort
Department of Ecology and Evolutionary Biology & The Museum of Natural History and Biodiversity Research Center, University of Kansas, Lawrence, Kansas, 66045 U.S.A.
Search for more papers by this author
Daniel J. Crawford,
Mark E. Mort,
Daniel J. Crawford
Department of Ecology and Evolutionary Biology & The Museum of Natural History and Biodiversity Research Center, University of Kansas, Lawrence, Kansas, 66045 U.S.A.
Search for more papers by this authorMark E. Mort
Department of Ecology and Evolutionary Biology & The Museum of Natural History and Biodiversity Research Center, University of Kansas, Lawrence, Kansas, 66045 U.S.A.
Search for more papers by this author
Literature Cited
- Bachmann, K. 2001. Evolution and the genetic analysis of populations: 1950-2000. Taxon 50: 7-45.
- Brennan, R., Jorgensen, L., Woodhead, M. & Russell, J. 2002. Development and characterization of SSR markers in Ribes species. Molec. Ecol. Notes 2: 327–330.
- Chippindale, P. T. & Wiens, J. J. 1994. Weighting, partitioning, and combining characters in phylogenetic analysis. Syst. Biol. 43: 278–287.
- Constance, L. 1964. Systematic botany—an unending synthesis. Taxon 13: 257–273.
10.2307/1216193 Google Scholar
- Crawford, D. J. 2000. Plant macromolecular systematics in the past 50 years: one view. Taxon 49: 479–501.
- Cron, R. C., Small, R. L. & Wendel, J. F. 1999. Duplicated genes evolve independently after polyploid formation in cotton. Proc. Natl. Acad. Sci. U.S.A. 96: 14406–14411.
- Cruzan, M. B. 1998. Genetic markers in plant evolutionary ecology. Ecology 79: 400–412.
- Decker-Walters, D. S., Chung, S. M., Staub, J. E., Quemada, H. D. & Lopez-Sese, A. I. 2002. The origin and genetic affinities of wild populations of melon (Cucumis melo, Cucurbitaceae) in North America. Pl. Syst. Evol. 233: 183–197.
- Dirlewanger, E., Cosson, P., Tavaud, M., Aranzana, M. J., Poizat, C., Zanetto, A., Arus, P. & Laigret, F. 2002. Development of microsatellite markers in peach [Prunus persica (L.) Batsch] and their use in genetic diversity analysis in peach and sweet cherry. Theor. Appl. Genet. 105: 127–138.
- Felsenstein, J. 1983. Parsimony in systematics: biological and Statistical issues. Ann. Rev. Ecol. Syst. 14: 313–333.
- Felsenstein, J. 1985. Phylogenies and the comparative method. Amer. Naturalist 125: 1–15.
- Fineschi, S., Anzidei, M., Cafasso, D., Cozzolino, S., Garfi, G., Pastorelli, R., Salvini, D., Taurchini, D. & Vendramin, G. G. 2002. Molecular markers reveal a strong genetic differentiation between two European relic tree species: Zelkova abelicea (Lam.) Boissier and Z. sic-ula Di Pasquale, Garfi & Quezel (Ulmaceae). Conserv. Genet. 3: 145–153.
- Ford, V. S. & Gottlieb, L. D. 1999. Molecular characterization of PgiC in a tetraploid plant and its diploid relatives. Evolution 53: 1060–1067.
- Garland, T., Jr., Harvey, P. H. & Ives, A. R. 1992. Procedures for analyses of comparative data using phylogenetically independent contrasts. Syst. Biol. 41: 18–31.
- Garland, T., Jr., Dickerman, A. W., Janis, C. M. & Jones, J. A. 1993. Phylogenetic analysis of covariance by computer simulation. Syst. Biol. 42: 265–292.
- Ge, X.-J., Chiang, Y.-C., Chou, C.-H. & Chiang, T.-Y. 2002. Nested clade analysis of Dunnia sinensis (Rubiaceae), a monotypic genus from China based on organelle DNA sequences. Conser. Genet. 3: 351–362.
- Gottlieb, L. D. & Ford, V. S. 1996. Phylogenetic relationships among the sections of Clarkia (Onagraceae) inferred from the nucleotide sequences of PgiC. Syst. Bot. 21: 45–62.
- Gottlieb, L. D. & Ford, V. S. 1997. A recently silenced, duplicate Pgi locus in Clarkia. Molec. Biol. Evol. 14: 125–132.
- Harvey, P. H. & Pagel, M. D. 1991. The Comparative Method in Evolutionary Biology. Oxford Univ. Press, New York.
10.1093/oso/9780198546412.001.0001 Google Scholar
- Heiser, C. B., Jr. 1947. Hybridization between the sunflower species Helianthus annuus and H. petiolaris. Evolution 1: 249-262.
- Heiser, C. B., Jr., Smith, D. M., Clevenger, S. B. & Martin W. C., Jr. 1969. The North American sunflowers. Mem. Torrey Bot. Club 22: 1–113.
- Hillis, D. M. 1987. Molecular versus morphological approaches to systematics. Ann. Rev. Ecol. Syst. 18: 23–42.
- Hillis, D. M., Bull, J. J., White, M. E., Badgett, M. R. & Molineux, I. J. 1992. Experimental phylogenetics: generation of a known phylogeny. Science 255: 589–592.
- Howarth, D. G. & Baum, D. A. 2002a. Phylogenetic utility of a nuclear intron from nitrate reductase for the study of closely related species. Molec. Phylog. Evol. 23: 525–528.
- Howarth, D. G. & Baum, D. A. 2002b. Comparing three variable nuclear intron regions and nrDNA ITS to determine the phylogenetic history and a possible hybrid origin in a closely related Hawaiian clade in Scaevola (Goodeniac-eae). Amer. J. Bot. 89 (6, suppl.): 128. [Abstr.]
- Huelsenbeck, J. P. 1995. The performance of phylogenetic methods in simulation. Syst. Biol. 44: 17–48.
- Huelsenbeck, J. P. & Hillis, D. M. 1993. Success of phyloge-netic methods in the four-taxon case. Syst. Biol. 42: 247–264.
- Huelsenbeck, J. P., Ronquist, F., Nielsen, R. & Bollback, J. P. 2001. Bayesian inference of phylogeny and its impact on evolutionary biology. Science 294: 2310–2314.
- Jiang, C.-X., Wright, R. J., El-Zik, K. M. & Paterson, A. H. 1998. Polyploid formation created unique avenues for response to selection in Gossypium (cotton). Proc. Natl. Acad. Sci. U.S.A. 95: 4419–4424.
- Johnson, L. A., Weese, T. L. & Liljenquist, N. J. 2002. Phylogenetic potential of IDH sequences in Polemon-iaceae I: copy number and gene organization. Amer. J. Bot. 89 (6, suppl.): 129. [Abstr.]
- Kumar, L. S., Sawant, A. S., Gupta, V. S. & Ranjekar, P. K. 2001. Comparative analysis of genetic diversity among Indian populations of Scirpophaga incertulas by ISSR- PCR and RAPD-PCR. Biochem. Genet. 39: 297–309.
- Lewis, H. 1953. The mechanism of evolution in the genus Clarkia. Evolution 7: 1–20.
- Lewis, H. & Lewis, M. E. 1955. The genus Clarkia. Univ. Calif. Publ. Bot. 20: 241–392.
- Lewis, H. & Roberts, M. R. 1956. The origin of Clarkia lin-gulata. Evolution 10: 126–138.
- Liebhard, R., Gianfranceschi, L., Koller, B., Ryder, C. D., Tarchini, R., Van de Wag, E. & Gessler, C. 2002. Development and characterization of 140 new microsatellites in apple (Malus xdomestica Borkh.). Molec. Breeding 10: 217–241.
- Lim, K. Y., Matysek, R., Lichtenstein, C. P. & Leitch, A. R. 2000. Molecular cytogenetic analyses and phylogenetic studies of Nicotiana section Tomentosae. Chromosoma 109: 245–258.
- Liu, B., Brubaker, C. L., Mergeai, G., Cronn, R. C. & Wendel, J. F. 2001. Polyploid formation in cotton is not accompanied by rapid genomic changes. Genome 44: 321–330.
- Liu, B. & Wendel, J. F. 2001. Intersimple sequence repeat (ISSR) polymorphisms as a genetic marker system in cotton. Molec. Ecol. Notes 1: 205–208.
- Lopez-Sese, A. I., Staub, J., Katzir, N. & Gomez-Guillamon, M. L. 2002. Estimation of between and within accession variation in selected Spanish melon germplasm using RAPD and SSR markers to assess strategies for large collection evaluation. Euphytica 127: 41–51.
- Lynch, M. & Milligan, B. G. 1994. Analysis of population structure with RAPD markers. Molec. Ecol. 3: 91–99.
- Maddison, W. P. & Maddison, D. R. 1992. MacClade: Analysis of Phylogeny and Character Evolution. Sinauer Associates, Sunderland, Massachusetts.
- Matzke, M. A., Scheid, O. M. & Matzke, A. J. M. 1999. Rapid structural and epigenetic changes in polyploid and aneuploid genomes. BioEssays 21: 761–767.
10.1002/(SICI)1521-1878(199909)21:9<761::AID-BIES7>3.0.CO;2-C CASPubMedWeb of Science®Google Scholar
- Mort, M. E., Crawford, D. J., Esselman, E. J., Santos-Guerra, A., Wolfe, A. D. & Francisco-Ortega, J. In press. Relationships among the Macaronesian members of Tolpis (Asteraceae: Lactuceae) based upon analyses of inter-simple sequence repeat (ISSR) markers. Taxon 52.
- Olson, K. M. 2002. Population history of Manihot esculenta (Euphorbiaceae) inferred from nuclear DNA sequences. Molec. Ecol. 11: 901–911.
- Parker, P. G., Snow, A. A., Schug, M. D., Booton, B. C. & Fuerst, P. A. 1998. What molecules can tell us about populations: choosing and using a molecular marker. Ecology 79: 361–382.
- Patzak, J. 2001. Comparison of RAPD, STS, ISSR and AFLP molecular methods used for assessment of genetic diversity in hop (Humulus lupulus L.). Euphytica 121: 9–18.
- Pires, J. C., Sherwood, A. M., Lim, K. Y., Leitch, I. J., Bennett, M. D., Soltis, P. S. & Soltis, D. E. 2001. Integrating molecular cytogenetics and phylogenetics: genome evolution in diploid and polyploid Tragopogon (Asteraceae). Amer. J. Bot. 88 (6, suppl.): 134. [Abstr.]
- Rieseberg, L. H. 1991. Homoploid reticulate evolution in Helianthus: evidence from ribosomal genes. Amer. J. Bot. 78: 1218–1237.
- Rieseberg, L. H. 1996. Homology among RAPD fragments in interspecific comparisons. Molec. Ecol. 5: 99–105.
- Rieseberg, L. H., Choi, H., Chan, R. & Spore, C. 1993. Genomic map of a diploid hybrid species. Heredity 70: 285–293.
- Rieseberg, L. H., Sinervo, H. B., Linder, C. R., Ungerer, M. & Arias, D. M. 1996. Role of gene interactions in hybrid speciation: evidence from ancient and experimental hybrids. Science 272: 741–745.
- Rieseberg, L. H., Soltis, D. E. & Palmer, J. D. 1988. A molecular reexamination of introgression between Helianthus annuus and H. bolanderi (Compositae). Evolution 42: 227–238.
- Rieseberg, L. H., Van Fossen, C. & Desrochers, A. 1995. Hybrid speciation accompanied by genomic reorganization in wild sunflowers. Nature 375: 313–316.
- Sang, T. 2002. Utility of low-copy nuclear gene sequences in plant phylogenetics. Crit. Rev. Biochem. Molec. Biol. 37: 121–147.
- Schaal, B. A., Hayworth, D. A., Olsen, K. M., Rauscher, J. T. & Smith, W. A. 1998. Phylogeographic studies in plants: problems and prospects. Molec. Ecol. 7: 465–474.
- Schaal, B. A. & Leverich, W. J. 2001. Plant population biology and systematics. Taxon 50: 679–695.
- Schaal, B. A. & Olsen, K. M. 2000. Gene genealogies and population variation in plants. Proc. Natl. Acad. Sci. U.S.A. 97: 7024–7029.
- Silvertown, J. & Dodd, M. 1996. Comparing plants and connecting traits. Phil. Trans. Royal Soc. London Ser. B 351: 1233–1239.
- Soltis, D. E. & Soltis, P. S. 1998. Choosing an approach and an appropriate gene for phylogenetic analysis. Pp. 1–42 in: D. E. Soltis, P. S. Soltis & J. J. Doyle (eds.), Molecular Systematics of Plants II. Kluwer, Boston.
10.1007/978-1-4615-5419-6_1 Google Scholar
- Stace, C. A. 2000. Cytology and cytogenetics as a fundamental taxonomic resource for the 20th and 21st centuries. Taxon 49: 451–477.
- Stace, C. A. & Bailey, J. P. 1999. The value of genomic in situ hybridization (GISH) in plant taxonomy and evolutionary studies. Pp. 199–210 in: P. M. Hollinsworth, R. M. Bateman & R. J. Gornall (eds.), Molecular Systematics and Plant Evolution. Taylor and Francis, London.
- Stephens, S. G. 1949. The cytogenetics of speciation in Gossypium. I. Selective elimination of the donor parent genotype in interspecific backcrosses. Genetics 34: 627–637.
- Stephens, S. G. 1950. The internal mechanisms of speciation in Gossypium. Bot. Rev. 16: 115–149.
- T. F. Stuessy, E. Hörandl & V. Mayer (eds.). 2001. Plant Systematics: A Half Century of Progress (1950-2000) and Future Challenges. Intern. Assoc. Pl. Tax., Vienna.
- Sytsma, K. J. & Gottlieb, L. D. 1986a. Chloroplast DNA evidence for the origin of the genus Heterogaura from within a species of Clarkia. Proc. Natl. Acad. Sci. U.S.A. 83: 555–557.
- Sytsma, K. J. & Gottlieb, L. D. 1986b. Chloroplast DNA evolution and phylogenetic relationships in Clarkia sect. Peripetasma (Onagraceae). Evolution 40: 1248–1261.
- Sytsma, K. J., Smith, J. F. & Gottlieb, L. D. 1990. Phylogenetics in Clarkia (Onagraceae): restriction site mapping of chloroplast DNA. Syst. Bot. 15: 280–295.
- Systsma, K. J. & Pires, J. C. 2001. Plant sytematics in the next 50 years—remapping the new frontier. Taxon 50: 713–732.
- Templeton, A. R. 1998. Nested clade analyses of phylogeo-raphic data: testing hypotheses about gene flow and population history. Molec. Ecol. 7: 381–397.
- Templeton, A. R., Maskas, S. D. & Cruzan, M. B. 2000. Gene trees: a powerful tool for exploring the evolutionary biology of species and speciation. Pl. Spec. Biol. 15: 211–222.
10.1111/j.1442-1984.2000.00041.x Google Scholar
- Varshney, R. K., Thiel, T., Stein, N., Langridge, P. & Graner, A. 2002. In silico analysis on frequency and distribution of microsatellites in ESTs of some cereal species. Cell. Molec. Biol. Letters 7: 537–546.
- Wendel, J. F. 1989. New World tetraploid cottons contain Old World cytoplasm. Proc. Natl. Acad. Sci. U.S.A. 86: 4132–4136.
- Wendel, J. F. 2000. Genome evolution in polyloids. Pl. Molec. Biol. 42: 225–249.
- Wendel, J. F., Schnabel, A. & Seelanan, T. 1995. Bidirectional interlocus concerted evolution following allopolyploid speciation in cotton (Gossypium). Proc. Natl. Acad. Sci. U.S.A. 92: 280–284.
- Wendel, J. F., Stewart, J. M. & Rettig, J. H. 1991. Molecular evidence for homoploid reticulate evolution among Australian species of Gossypium. Evolution 45: 694–711.
- Whitton, J. Rieseberg, L. H. & Ungerer, M. C. 1997. Microsatellite loci are not conserved across the Asteraceae. Molec. Biol. Evol. 14: 204–209.
- Wolfe, A. D. & Liston, A. 1998. Contributions of PCR-based methods to plant systematics and evolutionary biology. Pp. 43–86 in: D. E. Soltis, P. S. Soltis & J. J. Doyle (eds.), Molecular Systematics of Plants II. Kluwer, Boston.
10.1007/978-1-4615-5419-6_2 Google Scholar
- Wolfe, A. D. & Randle, C. P. 2001. Relationships within and among species of the holoparasitic genus Hyobanche (Orobanchaceae). Syst. Bot. 26: 120–130.
- Wolfe, A. D., Xiang, Q.-Y. & Kephart, S. 1998. Assessing hybridization in natural populations of Penstemon (Scrophulariaceae) using hypervariable intersimple sequence repeat bands. Molec. Ecol. 7: 1107–1125.
- Zelenin, A. V., Badaeva, E. D. & Muravenko, O. V. 2001. Introduction into plant genomics. Molec. Biol. 35: 285–293.
- Zhang, D. & Sang, T. 1999. Physical mapping of ribosomal RNA genes in Peonies (Paeonia, Paeoniaceae) by fluorescent in situ hybridization: implications for phylogeny and concerted evolution. Amer. J. Bot. 86: 735–740.
