Ribosomal ITS sequences and plant phylogenetic inference

Adams, 2000, Ribosomal DNA evolution and phylogeny in Aloe (Asphodelaceae), Am. J. Bot., 87, 1578, 10.2307/2656733

Ainouche, 1997, On the origins of the tetraploid Bromus species (section Bromus, Poaceae): Insights from the internal transcribed spacer sequences of nuclear ribosomal DNA, Genome, 40, 730, 10.1139/g97-796

Álvarez Fernández, 2001, A phylogenetic analysis of Doronicum (Asteraceae, Senecioneae) based on morphological, nuclear ribosomal (ITS), and chloroplast (trnL-F) evidence, Mol. Phylogenet. Evol., 20, 41, 10.1006/mpev.2001.0954

Anamthawat-Jónsson, 2001, Molecular cytogenetics of introgressive hybridization in plants, Methods Cell Sci., 23, 139, 10.1023/A:1013182724179

Anamthawat-Jónsson, 2001, Genomic and genetic relationships among species of Leymus (Poaceae: Triticeae) inferred from 18S–26S ribosomal genes, Am. J. Bot., 88, 553, 10.2307/2657053

Arnheim, 1983, Concerted evolution of multigene families, 38

Ashworth, 2000, Phylogenetic relationships in Phoradendreae (Viscaceae) inferred from three regions of the nuclear ribosomal cistron. I. Major lineages and paraphyly of Phoradendron, Syst. Bot., 25, 349, 10.2307/2666647

Bailey, 1999, Potential phylogenetic utility of the low-copy nuclear gene pistillata in dicotyledonous plants: Comparison to nrDNA ITS and trnL intron in Sphaerocardamum and other Brassicaceae, Mol. Phylogenet. Evol., 13, 20, 10.1006/mpev.1999.0627

Bailey, C.D., Hughes, C.E., Harris, S.A., Carr, T.G., 2002. Characterization of angiosperm nrDNA polymorphism: Paralogy and pseudogenes. Unpublished manuscript

Baldwin, 1992, Phylogenetic utility of the internal transcribed spacers of nuclear ribosomal DNA in plants: An example from the Compositae, Mol. Phylogenet. Evol., 1, 3, 10.1016/1055-7903(92)90030-K

Baldwin, 1993, Molecular phylogenetics of Calycadenia (Compositae) based on ITS sequences of nuclear ribosomal DNA: Chromosomal and morphological evolution reexamined, Am. J. Bot., 80, 222, 10.1002/j.1537-2197.1993.tb13792.x

Baldwin, 1995, The ITS region of nuclear ribosomal DNA: A valuable source of evidence on angiosperm phylogeny, Ann. Missouri Bot. Gard., 82, 247, 10.2307/2399880

Barber, 2002, Origin of Macaronesian Sideritis L. (Lamioideae: Lamiaceae) inferred from nuclear and chloroplast sequence datasets, Mol. Phylogenet. Evol., 23, 293, 10.1016/S1055-7903(02)00018-0

Barkman, 2002, Hybrid origin and parentage of Dendrochilum acuiferum (Orchidaceae) inferred in a phylogenetic context using nuclear and plastid DNA sequence data, Syst. Bot., 27, 209

Baum, 1994, A phylogenetic analysis of Epilobium (Onagraceae) based on nuclear ribosomal DNA sequences, Syst. Bot., 19, 363, 10.2307/2419763

Baum, 1998, Biogeography and floral evolution of baobabs (Adansonia, Bombacaceae) as inferred from multiple data sets, Syst. Biol., 47, 181, 10.1080/106351598260879

Baumel, 2001, Molecular investigations in populations of Spartina anglica C.E. Hubbard (Poaceae) invading coastal Brittany (France), Mol. Ecol., 10, 1689, 10.1046/j.1365-294X.2001.01299.x

Beardsley, 2002, Redefining Phrymaceae: The placement of Mimulus, tribe Mimuleae, and Phryma, Am. J. Bot., 89, 1093, 10.3732/ajb.89.7.1093

Bechmann, 1990, Improvement of PCR amplified DNA sequencing with the aid of detergents, Nucleic Acids Res., 18, 1309, 10.1093/nar/18.5.1309

Bobola, 1992, Five major nuclear ribosomal repeats represent a large and variable fraction of the genomic DNA of Picea rubens and P. mariana, Mol. Biol. Evol., 9, 125

Bortiri, 2001, Phylogeny and Syatematics of Prunus (Rosaceae) as determined by sequence analysis of ITS and the chloroplast trnL-trnF spacer DNA, Syst. Bot., 26, 797

Bortiri, 2002, The phylogenetic utility of nucleotide sequences of sorbitol 6-phosphate dehydrogenase in Prunus (Rosaceae), Am. J. Bot., 89, 1697, 10.3732/ajb.89.10.1697

Brochmann, 1996, A classic example of postglacial allopolyploid speciation re-examined using RAPD markers and nucleotide sequences: Saxifraga osloensis (Saxifragaceae), Symb. Bot. Ups., 31, 75

Brown, 1993, Preliminary karyotype and chromosomal localization of ribosomal DNA sites in white spruce using fluorescence in situ hybridization, Genome, 36, 310, 10.1139/g93-043

Buckler, 1996, Zea ribosomal repeat evolution and substitution patterns, Mol. Biol. Evol., 13, 623, 10.1093/oxfordjournals.molbev.a025622

Buckler, 1996, Zea systematics: Ribosomal ITS evidence, Mol. Biol. Evol., 13, 612, 10.1093/oxfordjournals.molbev.a025621

Buckler, 1997, The evolution of ribosomal DNA: Divergent paralogous and phylogenetic implications, Genetics, 145, 821, 10.1093/genetics/145.3.821

Camacho, 1997, Endophytic fungal DNA, the source of contamination in spruce needle DNA, Mol. Ecol., 6, 983, 10.1046/j.1365-294X.1997.00266.x

Campbell, 1997, Persistent nuclear ribosomal DNA sequence polymorphism in the Amelanchier agamic complex (Rosaceae), Mol. Biol. Evol., 14, 81, 10.1093/oxfordjournals.molbev.a025705

Catalán, 1997, Phylogeny of Poaceae subfamily Pooideae based on chloroplast ndhF gene sequences, Mol. Phylogenet. Evol., 8, 150, 10.1006/mpev.1997.0416

Chase, 1993, Phylogenetics of seed plants: An analysis of nucleotide sequences from the plastid gene rbcL, Ann. Missouri Bot. Gard., 80, 528, 10.2307/2399846

Clegg, 1993, Chloroplast gene sequences and the study of plant evolution, Proc. Natl. Acad. Sci. USA, 90, 363, 10.1073/pnas.90.2.363

Clevinger, 2000, Phylogenetic analysis of Silphium and subtribe Engelmanniinae (Asteraceae: Heliantheae) based on ITS and ETS sequence data, Am. J. Bot., 87, 565, 10.2307/2656600

Comes, 2001, Molecular phylogeography, reticulation, and lineage sorting in Mediterranean Senecio sect. Senecio (Asteraceae), Evolution Int. J. Org. Evolution, 55, 1943, 10.1111/j.0014-3820.2001.tb01312.x

Compton, 2002, Phylogeny and circumscription of tribe Actaeae (Ranunculaceae), Syst. Bot., 27, 502

Cronn, 1999, Duplicated genes evolve independently after polyploid formation in cotton, Proc. Natl. Acad. Sci. USA, 96, 14406, 10.1073/pnas.96.25.14406

Cronn, 2002, PCR-mediated recombination in amplification products derived from polyploid cotton, Theor. Appl. Genet., 104, 482, 10.1007/s001220100741

Cronn, 2002, Rapid diversification of the cotton genus (Gossypium: Malvaceae) revealed by analysis of sixteen nuclear and chloroplast genes, Am. J. Bot., 89, 707, 10.3732/ajb.89.4.707

Dagne, 2000, Number and sites of rDNA loci of Guizotia abyssinica (L. f.) Cass. as determined by fluorescence in situ hybridization, Hereditas, 132, 63, 10.1111/j.1601-5223.2000.00063.x

Danna, 1996, 5S rRNA genes in tribe Phaseoleae: Array size, number, and dynamics, Genome, 39, 445, 10.1139/g96-056

Davis, 1998, Data decisiveness, data quality, and incongruence in phylogenetic analysis: An example from the monocotyledons using mitochondrial atp A sequences, Syst. Biol., 47, 282, 10.1080/106351598260923

Dixon, 1993, Ribosomal RNA secondary structure: Compensatory mutations and implications for phylogenetic analysis, Mol. Biol. Evol., 1, 256

Doyle, 1992, Gene trees and species trees: Molecular systematics as one-character taxonomy, Syst. Bot., 17, 144, 10.2307/2419070

Doyle, 1999, Nuclear protein-coding genes in phylogeny reconstruction and homology assessment: Some examples from Leguminosae

Dubcovsky, 1995, Ribosomal RNA multigene loci: Nomads of the Triticeae genomes, Genetics, 140, 1367, 10.1093/genetics/140.4.1367

Elder, 1995, Concerted evolution of repetitive DNA sequences in eukaryotes, Quart. Rev. Biol., 70, 297, 10.1086/419073

Erdogan, 2000, Phylogenetic relationships of Corylus species (Betulaceae) based on nuclear ribosomal DNA ITS region and chloroplast matK gene sequences, Syst. Bot., 25, 727, 10.2307/2666730

Farris, 1989, The retention index and the rescaled consistency index, Cladistics, 5, 417, 10.1111/j.1096-0031.1989.tb00573.x

Ferguson, 1999, Relationships of Eastern North American Phlox (Polemoniaceae) based on ITS sequence data, Syst. Bot., 24, 616, 10.2307/2419646

Franzke, 1999, Recent hybrid speciation in Cardamine (Brassicaceae) -conversion of nuclear ribosomal ITS sequences in statu nascendi, Theor. Appl. Genet., 98, 831, 10.1007/s001220051140

Fuertes Aguilar, 1999, Nuclear ribosomal DNA (nrDNA) concerted evolution in natural and artificial hybrids of Armeria (Plumbaginaceae), Mol. Ecol., 8, 1341, 10.1046/j.1365-294X.1999.00690.x

Fuertes Aguilar, 1999, Molecular evidence for the compilospecies model of reticulate evolution in Armeria (Plumbaginaceae), Syst. Biol., 44, 735, 10.1080/106351599259997

Fulnec̀ek, 2002, Evolution and structure of 5S rDNA loci in allotetraploid Nicotiana tabacum and its putative parental species, Heredity, 88, 19, 10.1038/sj.hdy.6800001

Gatesy, 1994, Rate limits for mispairing and compensatory change: The mitochondrial ribosomal DNA of antelopes, Evolution, 4, 188, 10.1111/j.1558-5646.1994.tb01305.x

Gaut, 1998, Molecular clocks and nucleotide substitution rates in higher plants, 93

Germano, 1999, Species-specific nuclear and chloroplast single nucleotide polymorphisms to distinguish Picea glauca, P. mariana, and P. rubens, Theor. Appl. Genet., 99, 37, 10.1007/s001220051206

Gernandt, 1999, Internal transcribed spacer region evolution in Larix and Pseudotsuga (Pinaceae), Am. J. Bot., 86, 711, 10.2307/2656581

Gernandt, 2001, Variation in the nrDNA ITS of Pinus subsection Cembroides: Implications for molecular systematic studies of pine species complexes, Mol. Phylogenet. Evol., 21, 449, 10.1006/mpev.2001.1026

Goff, 2002, A draft sequence of the rice genome (Oryza sativa L. ssp. japonica), Science, 296, 92, 10.1126/science.1068275

Grant, 1981

Gravendeel, 2001, Molecular phylogeny of Coleogyne (Epidendroideae; Orchidaceae) based on plastid RFLPs, matK, and nuclear ribosomal ITS sequences: Evidence for polyphyly, Am. J. Bot., 88, 1915, 10.2307/3558367

Hadjiolova, 1984, Localization and structure of endonuclease cleavage sites involved in the processing of the rat 32S precursor to ribosomal RNA, Biochem. J., 220, 105, 10.1042/bj2200105

Hadjiolova, 1994, Processing of truncated mouse or human rRNA transcribed from ribosomal minigenes transfected into mouse cells, Mol. Cell Biol., 14, 4044

Hancock, 2000, How slippage-derived sequences are incorporated into rRNA variable-region secondary structure: Implications for phylogeny reconstruction, Mol. Phylogenet. Evol., 14, 366, 10.1006/mpev.1999.0709

Hartmann, 2001, Extensive ribosomal DNA genic variation in the columnar cactus Lophocereus, J. Mol. Evol., 53, 124, 10.1007/s002390010200

Hillis, 1991, Ribosomal DNA: Molecular evolution and phylogenetic inference, Quart. Rev. Biol., 66, 411, 10.1086/417338

Hillis, 1991, Evidence of biased gene conversion in concerted evolution of ribosomal DNA, Science, 251, 308, 10.1126/science.1987647

Hizume, 1994, Allodiploid nature of Allium wakegi Araki revealed by genomic in situ hybridization and localization of 5S and 18S rDNAs, Jpn. J. Genet., 69, 407, 10.1266/jjg.69.407

Hodkinson, 2002, The use of DNA sequencing (ITS and trnL-F), AFLP, and fluorescent in situ hybridization to study allopolyploid Miscanthus (Poaceae), Am. J. Bot., 89, 279, 10.3732/ajb.89.2.279

Hughes, 2002, Divergent and reticulate species relationships in Leucaena (Fabaceae) inferred from multiple data sources: insights into polyploid origins and nrDNA polymorphism, Am. J. Bot., 89, 1057, 10.3732/ajb.89.7.1057

Innis, 1990, PCR with 7-deaza-2’-deoxyguanosine triphosphate, 54

Kelchner, 1997, Molecular evolution and phylogenetic utility of the chloroplast rpl16 intron in Chusquea and the Bambusoideae (Poaceae), Mol. Phylogenet. Evol., 8, 385, 10.1006/mpev.1997.0432

Kim, 1994, Comparisons of phylogenetic hypothesis among different data sets in dwarf dandelions (Krigia): Additional information from internal transcribed spacer sequences of nuclear ribosomal DNA, Plant Syst. Evol., 190, 157, 10.1007/BF00986191

Kim, 1996, Phylogenetic implications of rbcL and ITS sequence variation in the Berberidaceae, Syst. Bot., 21, 381, 10.2307/2419666

Kita, 2000, Nuclear ribosomal ITS sequences and phylogeny in East Asian Aconitum subgenus Aconitum (Ranunculaceae), with special reference to extensive polymorphism in individual plants, Plant Syst. Evol., 225, 1, 10.1007/BF00985455

Kluge, 1969, Quantitative phyletics and the evolution of anurans, Syst. Zool., 18, 1, 10.2307/2412407

Ko, 2002, Three nonorthologous ITS1 types are present in a polypore fungus Trichaptum abietinum, Mol. Phylogenet. Evol., 23, 112, 10.1016/S1055-7903(02)00009-X

Kress, 2002, The phylogeny and a new classification of the gingers (Zingiberaceae): evidence from molecular data, Am. J. Bot., 89, 1682, 10.3732/ajb.89.10.1682

Leggett, 1995, The genomic identification of some monosomics of Avena sativa L. cv. Sun II using genomic in situ hybridization, Genome, 38, 747, 10.1139/g95-094

Levinson, 1987, Slipped-strand mispairing: A major mechanism for DNA sequence evolution, Mol. Biol. Evol., 4, 203

Li, 2002, Physical localization of the 18S–5.8S–26S rDNA and sequence analysis of ITS regions in Thinopyrum ponticum (Poaceae: Triticeae): Implications for concerted evolution, Ann. Bot., 90, 445, 10.1093/aob/mcf213

Liston, 1995, Internal transcribed spacer sequences of conifers: There is a fungus among us, Inoculum, 46, 26

Liston, 1996, Length variation in the nuclear ribosomal DNA internal transcribed spacer region of non-flowering seed plants, Syst. Bot., 21, 109, 10.2307/2419742

Liu, 1994, A conserved sequence in internal transcribed spacer 1 of plant nuclear rRNA genes, Plant Mol. Biol., 26, 775, 10.1007/BF00013763

Ma, 1997, In situ hybridization of ribosomal DNA to rose chromosomes, J. Hered., 88, 158, 10.1093/oxfordjournals.jhered.a023078

Maggini, 2000, Nucleotide sequence of the internal transcribed spacers of ribosomal DNA in Picea abies Karst, DNA Seq., 11, 87, 10.3109/10425170009033973

Mai, 1997, The Internal Transcribed Spacer 2 exhibits a common secondary structure in green algae and flowering plants, J. Mol. Evol., 44, 258, 10.1007/PL00006143

Manos, 1999, Phylogeny, biogeography and processes of molecular differentiation in Quercus subgenus Quercus (Fagaceae), Mol. Phylogenet. Evol., 12, 333, 10.1006/mpev.1999.0614

Marrocco, 1996, Nucleotide sequence of the internal transcribed spacers and 5.8S region of ribosomal DNA in Pinus pinea L, DNA Seq., 6, 175, 10.3109/10425179609010206

Masterson, 1994, Stomatal size in fossil plants: Evidence for polyploidy in majority of angiosperms, Science, 264, 421, 10.1126/science.264.5157.421

Mayol, 2001, Why nuclear ribosomal DNA spacers (ITS) tell different stories in Quercus, Mol. Phylogenet. Evol., 19, 167, 10.1006/mpev.2001.0934

McDade, 1992, Hybrids and phylogenetic systematics II. The impact of hybrids on cladistic analysis, Evolution, 46, 1329, 10.1111/j.1558-5646.1992.tb01127.x

McDade, 1995, Hybridization and phylogenetics, 305

Miller, 1999, Phylogenetic systematics of Ipomoea (Convolvulaceae) based on ITS and waxy sequences, Syst. Bot., 24, 209, 10.2307/2419549

Mishima, 2002, Trends in site-number change of rDNA loci during polyploid evolution in Sanguisorba (Rosaceae), Chromosoma, 110, 550, 10.1007/s00412-001-0175-z

Möller, 1997, Origin and relationships of Saintpaulia (Gesneriaceae) based on ribosomal DNA internal transcribed spacer (ITS) sequences, Am. J. Bot., 84, 956, 10.2307/2446286

Molvray, 1999, Phylogenetic relationships within Korthalsella (Viscaceae) based on nuclear ITS and plastid trnL-F sequence data, Am. J. Bot., 86, 249, 10.2307/2656940

Mort, 2002, Phylogenetics and evolution of the Macaronesian clade of Crassulaceae inferred from nuclear and chloroplast sequence data, Syst. Bot., 27, 271

Muir, 2001, Three divergent rDNA clusters predate the species divergence in Quercus petraea (Matt.) Liebl. and Quercus robur L, Mol. Biol. Evol., 18, 112, 10.1093/oxfordjournals.molbev.a003785

Murray, 2002, Trees, maps and FISH: The application of genome based technologies to the analysis of chromosome evolution, Curr. Genom., 3, 539, 10.2174/1389202023350192

Musters, 1990, Functional analysis of transcribed spacers of yeast ribosomal DNA, EMBO J., 9, 3989, 10.1002/j.1460-2075.1990.tb07620.x

Nakayama, 2001, Additional locus of rDNA sequence specific to the X chromosome of the liverwort, Marchantia polymorpha, Chromosome Res., 9, 469, 10.1023/A:1011676328165

Nashimoto, 1988, In vitro sequence-specific cleavage in transcribed spacer of mouse precursor ribosomal RNA, J. Biochem., 103, 992, 10.1093/oxfordjournals.jbchem.a122399

O’Donnell, 1997, Two divergent intragenomic rDNA ITS2 types within a monophyletic lineage of the fungus Fusarium are nonorthologous, Mol. Phylogenet. Evol., 7, 103, 10.1006/mpev.1996.0376

Olmstead, 1994, Chloroplast DNA systematics: A review of methods and data analysis, Am. J. Bot., 81, 1205, 10.1002/j.1537-2197.1994.tb15615.x

Olmstead, 1995, Evidence for the polyphyly of the Scrophulariaceae based on chloroplast rbcL and ndhF sequences, Ann. Missouri Bot. Garden, 82, 176, 10.2307/2399876

Panzera, 1996, Nucleolar organizer expression in Allium cepa L. chromosomes, Chromosoma, 105, 12, 10.1007/BF02510034

Pedersen, 1994, Chromosomal locations of four minor rDNA loci and a marker microsatellite sequence in barley, Chrom. Res., 2, 65, 10.1007/BF01539456

Raina, 2001, GISH technology in plant genome research, Methods Cell Sci., 23, 83, 10.1023/A:1013197705523

Rauscher, 2002, Internal transcribed spacer repeat-specific primers and the analysis of hybridization in the Glycine tomentella (Leguminosae) polyploid complex, Mol. Ecol., 11, 2691, 10.1046/j.1365-294X.2002.01640.x

Ray, 1995, Systematics of Lavatera and Malva (Malvaceae, Malveae)- a new perspective, Plant Syst. Evol., 198, 29, 10.1007/BF00985106

Raymundez, 2002, Coding of insertion-deletion events of the chloroplastic intergene atp beta-rbcL for the phylogeny of the Valerianeae tribe (Valerianaceae), C. R. Biol., 325, 131, 10.1016/S1631-0691(02)01416-6

Rieseberg, 1990, Helianthus annus ssp. texanus has chloroplast DNA and nuclear ribosomal RNA genes of Helianthus debilis ssp. cucumerifolius, Proc. Natl. Acad. Sci. USA, 87, 593, 10.1073/pnas.87.2.593

Rieseberg, 1991, Phylogenetic consequences of cytoplasmic gene flow in plants, Evol. Trends Plant, 5, 65

Rieseberg, 1993, Introgression and its consequences in plants, 70

Rieseberg, 2000, Hybridization, introgression, and linkage evolution, Plant Mol. Biol., 42, 205, 10.1023/A:1006340407546

Ritland, 1993, Variation in the ribosomal internal transcribed spacers (ITS1 and ITS2) among eight taxa of the Mimulus guttatus species complex, Mol. Biol. Evol., 10, 1273

Roalson, 2001, Phylogenetic relationships in Cariceae (Cyperaceae) based on ITS (nrDNA) and trnT-L-F (cpDNA) region sequences: Assessment of subgeneric and sectional relationships in Carex with emphasis on section Acrocystis, Syst. Bot., 26, 318

Roelofs, 1997, Molecular evidence for an extinct parent of the tetraploid species Microseris acuminata and M. campestris (Asteraceae, Lactuceae), Mol. Ecol., 6, 641, 10.1046/j.1365-294X.1997.00225.x

Rossetto, 2002, Is the genus Cissus (Vitaceae) monophyletic? Evidence from plastid and nuclear ribosomal DNA, Syst. Bot., 27, 522

Samuel, 1998, ITS sequences from nuclear rDNA suggest phylogenetic relationships between Euro-Mediterranean, East Asiatic and North American taxa of Quercus (Fagaceae), Plant Syst. Evol., 211, 129, 10.1007/BF00984917

Sang, 1995, Documentation of reticulate evolution in peonies (Paeonia) using internal transcribed spacer sequences of nuclear ribosomal DNA: Implications for biogeography and concerted evolution, Proc. Natl. Acad. Sci. USA, 92, 6813, 10.1073/pnas.92.15.6813

Sang, 2002, Utility of low-copy nuclear gene sequences in plant phylogenetics, Crit. Rev. Biochem. Mol. Biol., 37, 121, 10.1080/10409230290771474

Schlötterer, 1994, Comparative evolutionary analysis of rDNA ITS regions in Drosophila, Mol. Biol. Evol., 11, 513

Schlötterer, 1994, Chromosomal homogeneity of Drosophila ribosomal DNA arrays suggests intrachromosomal exchanges drive concerted evolution, Current Biol., 4, 777, 10.1016/S0960-9822(00)00175-5

Schubert, 1985, In situ hybridization confirms jumping nucleolus organizing regions in Allium, Chromosoma, 92, 143, 10.1007/BF00328466

Seelanan, 1997, Congruence and consensus in the cotton tribe (Malvaceae), Syst. Bot., 22, 259, 10.2307/2419457

Seelanan, 1999, Molecular systematics of Australian Gossypium section Grandicalyx (Malvaceae), Syst. Bot., 24, 183, 10.2307/2419548

Senchina, 2003, Rate variation among nuclear genes and the age of polyploidy in Gossypium, Mol. Biol. Evol., 20, 633, 10.1093/molbev/msg065

Shishido, 2000, Ribosomal DNAs: An exception to the conservation of gene order in rice genomes, Mol. Gen. Genet., 263, 586, 10.1007/s004380051205

Simmons, 2000, Gaps as characters in sequence-based phylogenetic analyses, Syst. Biol., 49, 369, 10.1093/sysbio/49.2.369

Simmons, 2001, Incorporation, relative homoplasy, and effect of gap characters in sequence-based phylogenetic analyses, Syst. Biol., 50, 454, 10.1080/106351501300318049

Small, R.L., Cronn, R.C., Wendel, J.F., 2003. Nuclear genes and plant phylogeny reconstruction. Australian Syst. Bot. (in review)

Small, 1998, The tortoise and the hare: choosing between noncoding plastome and nuclear Adh sequences for phylogeny reconstruction in a recently diverged plant group, Amer. J. Bot., 85, 1301, 10.2307/2446640

Smedmark, 2002, Phylogenetic relationships of Geum (Rosaceae) and relatives inferred from the nrITS and trnL-trnF regions, Syst. Bot., 27, 303

Smith, 1994, Phylogenetic inferences on the relationship of North American and European Picea species based on nuclear ribosomal 18S sequences and the internal transcribed spacer 1 region, Mol. Phylogenet. Evol., 3, 17, 10.1006/mpev.1994.1003

Snowdon, 1997, Chromosomal localization and characterization of rDNA loci in the Brassica A and C genomes, Genome, 40, 582, 10.1139/g97-076

1998

Soltis, 1991, Multiple origins of the allotetraploid Tragopogon mirus (Compositae): rDNA evidence, Syst. Bot., 16, 407, 10.2307/2419333

Soltis, 1995, Genetic variation in Tragopogon species: Additional origins of the allotetraploids T. mirus and T. miscellus (Compositae), Am. J. Bot., 82, 1329, 10.1002/j.1537-2197.1995.tb12666.x

Springer, 1995, Compensatory substitutions and the evolution of the mitochondrial 12S rRNA gene in mammals, Mol. Biol. Evol., 12, 1138

Stebbins, 1950

Suh, 1993, Molecular evolution and phylogenetic implications of internal transcribed spacer sequences of ribosomal DNA in Winteraceae, Am. J. Bot., 80, 1042, 10.1002/j.1537-2197.1993.tb15332.x

Tartof, 1976, Similarities and differences in the structure of X and Y chromosome rRNA genes of Drosophila, Nature, 263, 27, 10.1038/263027a0

The Arabidopsis Genome Initiative, 2000. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408, 796–815

Thomas, 2001, Gross chromosome rearrangements are occurring in an accession of the grass Lolium rigidum, Chrom. Res., 9, 585, 10.1023/A:1012499303514

Torres, 1990, GC balance in the internal transcribed spacers ITS 1 and ITS 2 of nuclear ribosomal RNA genes, J. Mol. Evol., 30, 170, 10.1007/BF02099943

van Ham, 1994, Molecular evolution of noncoding regions of the chloroplast genome in the Crassulaceae and related species, Curr. Genet., 25, 558, 10.1007/BF00351678

van Nues, 1994, Separate structural elements within Internal Transcribed Spacer 1 of Saccharomyces cerevisiae ribosomal DNA, J. Mol. Biol., 223, 899

Vanzela, 1998, Multiple locations of the rDNA sites in holocentric chromosomes of Rhynchospora (Cyperaceae), Chrom. Res., 6, 345, 10.1023/A:1009279912631

Varadaraj, 1994, Denaturants or cosolvents improve the specificity of PCR amplification of a G+C-rich DNA using genetically-engineered DNA-polymerases, Gene, 140, 1, 10.1016/0378-1119(94)90723-4

Vargas, 1999, Polyploid speciation in Hedera (Araliaceae): Phylogenetic and biogeographic insights based on chromosome counts and ITS sequences, Plant Syst. Evol., 219, 165, 10.1007/BF00985577

Vaughan, 1993, Loss of nucleolus-organizer regions during polyploid evolution in Scilla autumnalis, Heredity, 71, 574, 10.1038/hdy.1993.181

Veldman, 1981, The nucleotide sequence of the intergenic region between the 5.8S and 26S rRNA genes of the yeast ribosomal RNA operon. Possible implications for the interaction between 5.8S and 26S rRNA and the processing of the primary transcript, Nucleic Acids Res., 9, 4847, 10.1093/nar/9.19.4847

Venkateswarlu, 1991, A conserved core structure in the 18–25S rRNA intergenic region from tobacco, Nicotiana rustica, Plant Mol. Biol., 17, 189, 10.1007/BF00039493

Vining, 1997, Phylogenetic signal in sequence repeats within nuclear ribosomal DNA internal transcribed spacer 1 in Tsuga, Am. J. Bot., 84, 702

Vining, 1998, Nuclear ribosomal DNA (nrDNA) internal transcribed spacer 1 (ITS1) subrepeats and phylogeny of Pinaceae, Am. J. Bot., 85, 186

Wagner, 1994, Surveys of gene families using polymerase chain reaction: PCR selection and PCR drift, Syst. Biol., 43, 250, 10.1093/sysbio/43.2.250

Wagstaff, 2002, Patterns of diversification in New Zealand Stylidiaceae, Am. J. Bot., 89, 865, 10.3732/ajb.89.5.865

Wendel, 1998, Phylogenetic incongruence: Window into genome history and molecular evolution, 265

Wendel, 1995, Bidirectional interlocus concerted evolution following allopolyploid speciation in cotton (Gossypium), Proc. Natl. Acad. Sci. USA, 92, 280, 10.1073/pnas.92.1.280

Wendel, 2000, Genome evolution in polyploids, Plant Mol. Biol., 42, 225, 10.1023/A:1006392424384

Wendel, 2003, Polyploidy and the evolutionary history of cotton, Adv. Agronomy, 78, 139, 10.1016/S0065-2113(02)78004-8

Wheeler, 1988, Paired sequence difference in ribosomal RNAs: Evolution and phylogenetic implications, Mol. Biol. Evol., 5, 90

White, 1990, Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics, 315

Whitten, 2000, Subtribal and generic relationships of Maxillarieae (Orchidaceae) with emphasis on Stanhopeinae: Combined molecular evidence, Am. J. Bot., 87, 1842, 10.2307/2656837

Winship, 1989, An improved method for direct sequencing PCR amplified material using dimethyl sulphoxide, Nucleic Acids Res., 17, 1266, 10.1093/nar/17.3.1266

Wissemann, 1999, Genetic constitution of Rosa Sect. Caninae (R. canina, R. jundzillii) and Sect. Gallicanae (R. gallica), J. Appl. Botany, 73, 191

Wissemann, V. 2003. Hybridization and the evolution of the nrITS spacer region. In: Sharma, A.K., et al. (Eds.), Plant genome, biodiversity and evolution I: Phanerogams. Science Publishers, Inc. Enfield, New Hampshire 57–71 (in press)

Wissemann, 2002, Molecular evidence for allopolyploid origin of the Rosa canina complex (Rosaceae, Rosoideae), J. Appl. Bot., 76, 176

Worton, 1988, Human ribosomal RNA genes: Orientation of the tandem array and conservation of the 5’ end, Science, 239, 64, 10.1126/science.3336775

Xu, 1996, High resolution physical mapping of 45S (5.8S, 18S, and 25S) rDNA gene loci in the tomato genome using a combination of karyotyping and FISH of pachytene chromosomes, Chromosoma, 104, 545, 10.1007/BF00352294

Yang, 1999, Molecular phylogenetic studies of Brassica, Rorippa, Arabidopsis, and allied genera based on the internal transcribed spacer region of 18S–25S rDNA, Mol. Phylogenet. Evol., 13, 455, 10.1006/mpev.1999.0648

Yu, 2002, A draft sequence of the rice genome (Oryza sativa L. ssp. indica), Science, 296, 79, 10.1126/science.1068037

Zhang, 1995, Detection of maize DNA sequences amplified in wheat, Genome, 38, 946, 10.1139/g95-124

Zhang, 1994, Improved PCR sequencing with formamide, Trends Genet., 8, 332, 10.1016/0168-9525(92)90145-T

Zhang, 1997, Bamboozled again: Inadvertent isolation of fungal rDNA sequences from Bamboo (Poaceae: Bambusoideae), Mol. Phylogenet. Evol., 8, 205, 10.1006/mpev.1997.0422

Zimmer, 1980, Rapid duplication and loss of genes coding for the alpha-chains of hemoglobin, Proc. Natl. Acad. Sci. USA, 77, 2158, 10.1073/pnas.77.4.2158

Zimmer, 2002, Phylogenetic relationships in the Gesnerioideae (Gesneriaceae) based on nrDNA ITS and cpDNA trnL-F and trnE-T spacer region sequences, Am. J. Bot., 89, 296, 10.3732/ajb.89.2.296

Zoller, 2001, Comparative genomic in situ hybridization (cGISH) analysis on plant chromosomes revealed by labelled Arabidopsis DNA, Chromosome Res., 9, 357, 10.1023/A:1016767100766

Zomlefer, 2001, Generic circumscription and relationships in the tribe Melanthieae (Liliales, Melanthiaceae), with emphasis on Zigadenus: Evidence from ITS and trnL-F sequence data, Am. J. Bot., 88, 1657, 10.2307/3558411