* Institute of Botany, University of Agricultural Sciences Vienna, Vienna, Austria
Department of Genetics and Evolution, Max-Planck-Institute for Chemical Ecology, Jena, Germany
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Abstract |
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Key Words: apomixis Arabis Boechera Brassicaceae phylogeography concerted evolution hybrid speciation internal transcribed spacer
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Introduction |
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Molecular tools have greatly improved our knowledge about hybrid speciation, because such tools allow characterization of parental genomes that can then be followed in the offspring. This characterization could be random (e.g., amplified fragment length polymorphism [AFLP]; random amplified polymorphic DNA [RAPD]) or highly specific (e.g., microsatellites, genomic mapping). In many cases the characterization of strictly uniparentally inherited genomes, such as the plastome in many angiosperms (Harris and Ingram 1991), allows identification of the paternal or maternal crossing partner. Recent studies of the total genome structure of hybrid and polyploid taxa provide new insight into the dynamic nature of complete genomes analyzed either on the basis of artificial hybrids or by comparative mapping (Kowalski et al. 1994; Lagercrantz 1998; Rieseberg, Whitton, and Gardner 1999; Rieseberg and Linder 1999). In their comparative genome analysis of some Brassicaceae, Acarkan et al. (2000) showed that structural rearrangements occurred with a significantly higher frequency in polyploid Brassica than in diploid Arabidopsis thaliana or Capsella rubella.
DNA analyses of the nuclear and plastid genomes have greatly increased the possibility of detecting and distinguishing allopolyploids and autopolyploids, following paternal and maternal genome lineages, and documenting hybridization, introgression, and reticulate evolution. Through such analyses, several polyploid complexes within the Brassicaceae have been characterized in significant detail, including those of the genera Microthlaspi (Koch, Mummenhoff, and Hurka 1998; Koch and Hurka 1998), Draba (Brochmann 1992; Brochmann and Elven 1992; Brochmann, Soltis, and Soltis 1992; Brochmann, Nilsson, and Gabrielsen 1996; Widmer and Baltisberger 1999; Koch and Al-Shehbaz 2002), Cochlearia (Koch, Huthmann, and Hurka 1998; Koch, Mummenhoff, and Hurka 1999), Yinshania (Koch and Al-Shehbaz 2000), Cardamine (Franzke et al. 1998; Urbanska et al. 1997), Biscutella (König 1998; Tremetsberger et al. 2002), Brassica and related genera (Anderson and Warwick 1999), and Nasturtium (Bleeker, Huthmann, and Hurka 1999). In some of these complexes ITS sequence evolution has been analyzed in hybrid systems; the phenomenon of concerted evolution of ITS DNA loci has been demonstrated several times in the Brassicaceae. Concerted evolution describes the molecular process of DNA sequence homogenization among different loci within multigene families (Arnheim et al. 1980; Dover 1982; Avise 1994). DNA sequence homogenization via concerted evolution is driven by two molecular processes, gene conversion and unequal crossing over. The relative contribution of each as a homogenizing agent, however, continues to be the subject of debate (Muir, Fleming, and Schlötterer 2001).
The rDNA loci in particular serve as a classic example of concerted evolution of tandemly repeated gene families and have been analyzed in detail (for references see Buckler, Ippolito, and Holtsford 1997; Muir, Fleming, and Schlötterer 2001). In principle, there are three different ways in which two different ITS copies evolve within a single individual: (1) unidirectional concerted evolution leads to the loss of one copy and fixation of the second (e.g., Wendel, Schnabel, and Seelanan 1995a; Koch and Al-Shehbaz 2000); (2) concerted evolution leads to a new ITS type that represents a mixture of the two original ITS sequences (Van Houten, Scarlett, and Bachmann 1993; Wendel, Schnabel, and Seelanan 1995b; Mummenhoff, Franzke, and Koch 1997; Franzke and Mummenhoff 1999; Koch and Al-Shehbaz 2000); (3) both ITS copies are still present, which might be mostly the case in young hybridogenous taxa (Kim and Jansen 1994; O'Kane, Schaal, and Al-Shehbaz 1996; Koch and Al-Shehbaz 2000). However, the third possibility has also been described in the genus Rosa as a stable situation and has been defined as "nonconcerted" evolution (Wissemann 1999; 2000). In some cases these paralogues are old and might have lost their function and turned into pseudogenes (Buckler and Holtsford 1996; Hartmann, Nason, and Bhattacharya 2001; Muir, Fleming, and Schlötterer 2001). Functional analysis on the transcriptional level provided additional insight into concerted evolution of rDNA (Chen and Pikaard 1997; Chen, Comai, and Pikaard 1998; Frieman et al. 1999; Muir, Fleming, and Schlötterer 2001) and the phenomenon of nucleolar dominance (Volkov et al. 1999).
We used a phylogenetically complex model system of naturally occurring hybrids within North American Arabis. Taxonomically, the species under study should be included in the genus Boechera (Koch, Bishop, and Mitchell-Olds 1999) and are not related to Eurasian Arabis (Koch, Haubold, and Mitchell-Olds 2000). But because of the traditional taxonomic treatment of these taxa herein, we continue to refer to them as Arabis: Arabis drummondii, a widespread North American perennial, mostly diploid, and Arabis holboellii, often apomictic on the triploid chromosomal level and also widespread on the North American continent, the putative parental taxa of Arabis divaricarpa. In contrast to Arabis drummondii, which contains only limited morphological variation, several variable morphological characters led to the recognition of multiple varieties among Arabis holboellii (Rollins 1993). However, Arabis divaricarpa is an intermediate morphotype between the parental taxa. Because of the wide distribution of the hybrid and its occurrence in pristine habitats, this system is ideally suited to the study of hybrid speciation on a broad scale and in an evolutionary context. Here, to gain some insight into rDNA evolution in natural populations on a temporal and spatial scale, we have chosen the ITS region of rDNA to study the fate of parental ITS copies in hybrids and their offspring.
This study is based exclusively on plant specimens from several herbaria, and we aim to demonstrate the value of this source of biological variation for fundamental, molecular-based research.
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Materials and Methods |
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All primary PCR products that resulted in ambiguous ITS sequences were subsequently cloned into the pGEM-T easy-cloning vector (PROMEGA) in order to separate ambiguous sites among the differing intraindividual ITS copies (A. drummondii: one of 85 accessions; A. holboellii: 36 of 187 accessions; A. divaricarpa: 34 of 130 accessions). Five to ten clones per each amplification product have been isolated, and ITS inserts have been reamplified and sequenced using the original ITS primer described above. This sequencing was performed using a Thermo Sequenase cycle sequencing kit (rpn2438 from Amersham Pharmacia Biotech) with IRD700- and IRD800-labeled primers (MWG Biotech, Ebersberg, Germany). Products of these direct cycle sequencing reactions were run on a LICOR L4200S-2 automated sequencer.
Analysis of Ploidy Levels
It is impossible to determine chromosome numbers from herbarium specimens directly. Therefore, we used an indirect procedure to obtain evidence of ploidy distribution in the taxa under study. It has been shown that there is a strong correlation of ploidy levels with morphometric parameters such as stomata density, branching pattern of trichomes, or size of pollen grains. We used pollen grain size as an indicator of ploidy level by measuring length and width of the pollen grains under a microscope. Mature pollen was sampled from flowers of single specimens. We measured 20 to 30 pollen grains per individual examined. The dimensions of Arabis pollen grains range from 15 to 36 µm. Additionally, pollen quality was summarized in six categories, for which we estimated the percentage of highly degraded pollen (subsequently converted into percentage of well-developed pollen: 0%, 0%10%, 10%50%, 50%80%, 80%90%, 90%100%, based on more than 100 pollen grains) as an indicator for pollen sterility, which is frequently accompanied by apomixis in Arabis species.
Data Analysis
Alignment and Outgroup Comparisons
Alignment was performed by hand, and ITS sequence data were submitted to GenBank (AF165313AF165439). Automated alignments were not necessary because of nearly identical sequence lengths in the ingroup taxa. We used ITS sequences from Cusickiella douglasii (AF146515) and C. quadricostata (AF146514) (Koch and Al-Shehbaz 2002), Halimolobus perplexa ssp. lemhiensis (AJ232927) and H. perplexa ssp. perplexa (AJ232926) (Koch, Bishop, and Mitchell-Olds 1999), and from Polyctenium fremontii (AF183109) (Roy 2001) for outgroup comparisons.
Sequence Conservation and Secondary Structure Analysis of ITS Regions
Secondary structures were generated for the ITS1 and ITS2 regions separately under the RNA folding option using the online version 3.0 of Mfold (Jaeger, Turner, and Zuker 1989; Zuker 1989; Zuker, Mathews, and Turner 1999) and the standard options. The Mfold server is accessible under the URL http://bioinfo.math.rpi.edu/zukerm/ or alternatively under http://mfold.burnet.edu.au/. The distributions of variable nucleotide positions were subsequently mapped onto the plotted secondary structures of the ITS1 and ITS2 from ingroup and outgroup taxa. A sliding window analysis to test recombination and analysis of linkage disequilibrium of the DNA sequences has been performed with DnaSP software version 3.51 (Rozas and Rozas 1999).
Phylogenetic Analysis
To analyze the relative position of the outgroups, a Neighbor-Joining distance analysis was conducted with all five outgroups and sequences from Arabis drummondii, (AJ232887), A. holboellii (accession 009, Supplementary Material online), and some additional related Arabis taxa (Koch, Bishop, and Mitchell-Olds 1999: A. lyallii AJ232897, A. lignifera AJ232898, A. microphylla AJ232929, A. parishii AJ232901). The analyses were run using TREECON for Windows (version 1b [Van de Peer and De Wachter 1997]). Distance matrices according to Kimura (1980) were generated using the GAPS INCLUDED option. The bootstrap option (1,000 replicates) was used to assess relative support of the branching pattern. Phylogenetic analysis of ITS sequences of the various Arabis accessions has been performed in two ways: (1) only sequences of the parental taxa A. drummondii and A. holboellii were considered in obtaining information about within-species variation; (2) in addition all A. divaricarpa sequences were considered to test their phylogenetic position with respect to their parents.
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Results |
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Pollen Measurements, Pollen Quality, and Ploidy Levels
A canonical discriminant analysis evaluating means of pollen grain length and breadth has been conducted for the three Arabis taxa under study. The results are shown in figure 5. Major differences can be detected among the taxa: Arabis drummondii is mostly diploid with only a few triploid and tetraploid individuals. In contrast, Arabis holboellii shows a remarkably high proportion of triploid individuals. However, according to the pollen size measurements, numerous diploid accessions of A. holboellii have been detected. In contrast, the putative hybrid A. divaricarpa had very few diploid individuals, and most genomes exist at the triploid level. Remarkably, in the case of A. drummondii and A. holboellii, the slope of the pollen size distribution is relatively steep compared to A. divaricarpa. We took this as strong evidence that in A. divaricarpa aneuploids are more frequent than in the parental taxa (fig. 5). This finding is in congruence with cytological data compiled by Rollins (1993). Herein numerous reports of aneuploids and the occurrence of B chromosomes can be found.
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Discussion |
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Nonetheless, it is clear that during speciation processes among the different taxa, hybridization, introgression, and reticulation resulted in up to eight intra-individual ITS copies in A. holboellii and in A. divaricarpa. If it is taken into account that most of the accessions are triploid (with and without extra chromosomes; cf. Sharbel and Mitchell-Olds 2001), the variation can be explained by intralocus variation with the two parental genotypes as the original source. Nonetheless, interlocus variation is also likely. Different modes of concerted evolution of ITS regions detected within a particular species group have been reported and discussed extensively (Wendel, Schnabel, and Seelanan 1995a; 1995b; Koch and Al-Shehbaz 2000; 2002). The same is true for the Arabis species hybrid system analyzed here. The morphologically defined hybrid A. divaricarpa is represented (1) with accessions possessing only a single ITS sequence typically found in A. drummondii accessions (57 accessions), (2) with accessions possessing only a single ITS type typically found in A. holboellii (24 accessions), (3) with accessions possessing multiple ITS types, of which at least one resamples an original A. drummondii ITS type but no original A. holboellii ITS type (7 accessions), (4) with accessions possessing multiple ITS types, of which at least one resamples an original A. holboellii ITS type but no original A. drummondii ITS type (6 examples), (5) with accessions possessing multiple ITS types, of which both parental original ITS types are still present (18 accessions), (6) with accessions possessing a single intermediate ITS type (no example found), and (7) with accessions possessing several intermediate ITS types (one accession). These different findings can be explained by dominance of one parental ITS type in cases (1) and (2). In our analysis, dominance of A. drummondii has been more frequently found in A. drummondii than in A. holboellii, which is also suggested by cases (3) and (4). However, dominance is not as strong as in cases (1) and (2), and additional "intermediate" ITS types have been observed. Interestingly, even here more A. drummondiidominated accessions have been detected than A. holboelliidominated accessions. The situation described in case (5) might demonstrate very recent hybridization, whereas cases (6) and (7), with differing complexity, illustrate evolutionary processes affected by recombinations and gene conversions leading to mosaic ITS types. The high frequency of accessions showing ITS types of case (5) suggests that many accessions of A. divaricarpa have been constituted "recently" and can be explained by postglacial migration, range extension, and subsequent hybridization.
The situation for A. holboellii is more complex. Even in this species we detected strong evidence for hybridization, introgression, and reticulation, although not as extensive as in A. divaricarpa. Most likely, this difference is due to existing classification. Both parental species, A. drummondii and A. holboellii, and the hybrid have been recognized based on morphological characters (fruit and trichome characteristics). It is possible, however, that after hybridization and constitution of some populations of A. divaricarpa, introgression and reticulation involving A. holboellii has also taken place. In addition, more complex reticulation patterns might be present in A. holboellii only. Such introgression and reticulation should have resulted in morphotypes more similar to A. holboellii but showing increased molecular variation. This hypothesis is supported by taxonomical-morphological investigations characterizing several varieties within an A. holboellii species group (Rollins 1993). Preliminary morphometric analyses (Koch and Dobe, unpublished) support this view. Additional evidence came from pollen size measurements as an indicator of ploidy levels (fig. 5). Accordingly, most accessions carrying multiple ITS types (either A. holboellii or A. divaricarpa) turned out to be triploid (as inferred from pollen size measurements), with and without extra chromosomes. The only exceptions are diploid accessions (accession numbers 489, 736, 741, 753, 754, 761, and 762). Interestingly, these diploid accessions have been described based on morphological data exclusively as A. holboellii var. retrofracta. Here we assume that hybrid speciation on the diploid level of A. holboellii with another unknown parental Arabis species occurred, resulting in this new variety with multiple ITS types. In summary, an analysis of the several cases (1 to 7) described for A. divaricarpa has shown that in A. holboellii only 5 accessions carried typical A. drummondii ITS types, which might indicate either backcrosses of A. divaricarpa with A. holboellii or the rare event of introgression of A. holboellii into A. drummondii (rare because of high levels of pollen sterility in A. holboellii). This explanation is supported by plastome type variation characterizing these five accessions with typical A. drummondii plastome types (Koch and Dobe
, in preparation).
Important for the understanding of the evolutionary scenario is the mode of reproduction. Apomixis has been shown to play a major role in the evolution of North American Arabis (Rollins 1993, Sharbel and Mitchell-Olds 2001). This finding fits with our analysis of pollen quality (fig. 6). In correlation with the findings described above, A. drummondii is a mostly diploid species that produces well-developed pollen, whereas A. divaricarpa and, to a lesser extent, A. holboellii mostly produce infertile pollen. We can assume that apomixis is widely distributed in A. holboellii and most likely in A. drummondii as well. However, pollen fertility in these taxa cannot be excluded totally, as shown above. These finding are strongly supported by analysis of plastome type variation and distribution of aneuploidy in A. holboellii (Sharbel and Mitchell-Olds 2001). From our ITS data it can be assumed that A. drummondii regularly served as a paternal hybridization partner. Triploids and aneuploids predominate in A. holboellii and A. divaricarpa, which favors the hypothesis that the hybrids reproduce by apomixis. However, subsequent reticulate evolution is also apparent. In these cases, the hybrid A. divaricarpa most likely served as the maternal plant because of high levels of pollen sterility.
In summary, this hybrid complex shows strongly directed gene flow from A. drummondii into A. holboellii and A. divaricarpa. This scenario is supported by morphological data indicating a clearly defined A. drummondii but more variable A. holboellii and A. divaricarpa.
Phylogeography and Multiple Origin
In the context of this article we do not discuss phylogeographic aspects in detail. A comprehensive screening of maternally inherited plastidic genetic variation with more than 1,000 accessions has been finished and the published study will focus on speciation and phylogeography (Koch and Dobe, in preparation). Here, we will concentrate on some aspects of the general spatial distribution of ITS types. If we compare the present-day distribution of those accessions with multiple ITS types found in A. holboellii (fig. 1), it is obvious that more complex hybrid ITS types are distributed outside the range of the last maximum glaciation in North America (Wisconsin glaciation 18,000 years ago). Only a few accessions with multiple ITS types are distributed within this range; moreover, all those accessions showed ITS types differing by a single mutation only. In contrast, in A. divaricarpa numerous accessions within the formerly glaciated area carry multiple, hybrid ITS types. This scenario is best explained by the assumption that hybrids formed postglacially in relic areas southwest of the maximum ice shield and followed the retreating glaciers in a north and north-east direction.
Many other accessions of A. divaricarpa within the formerly glaciated area have only a single ITS type (either a fixed parental type or a fixed mosaic structured type), which indicates ongoing hybridization and reticulation. A few accessions distributed within the formerly glaciated area have ITS types that suggest a single recombination event between two parental copies from A. drummondii and A. holboellii from the same area. These findings suggest that, from a glacial refugium southwest of the maximum ice shield of the Wisconsin glaciation, Arabis started the recolonization of northern parts of its current range. Both, A. drummondii and A. holboellii recolonized the formerly glaciated areas successfully. Sequence data from the plastome indicating maternal seed dispersal and migration agree with this hypothesis (Koch and Dobe, in preparation), and for A. drummondii they show a two-way migration of two different plastome types of A. drummondii, resulting in a western clade distributed along the mountain regions in the western United States and an eastern clade following the Great Lakes.
For A. holboellii, such a simple migration scenario was not observed. Instead, different plastome types are distributed randomly in this taxon, and plastome type diversity decreased with increasing distance from the assumed relic area in the southwestern United States. However, overall present-day distribution and the occurrence of several diverse ITS types in Alaska might indicate that for this taxon a second glacial refugium existed in unglaciated areas of Alaska and the Great Lakes. However, this hypothesis has to be substantiated by analysis of plastome type variation and microsatellite variation (Koch and Dobe, in preparation).
Disjunct populations of A. holboellii have been described from the St. Lawrence River Valley in Québec (Böcher 1951), which may have been a glacial refugium (Marie-Victorin and Rolland-Germain 1964). Typical refugia south of the glacial maximum have been recognized, such as the Klamath-Siskiyou Mountains in California (Whittaker 1961; Smith and Sawyer 1988). Several other possible northern refugia have been reviewed in Soltis et al. (1997) and comprise coastal refugia such as northwestern Vancouver Island or the Queen Charlotte Islands.
North American Arabis (Boechera) as a Study System
The North American Arabis are an ideal model system in which to study historical and ongoing evolutionary processes. In this genus many different species have been described (Rollins 1993), providing a suitable source for morphological, ecological, and physiological variation. Some of this variation has been used recently to study evolutionary aspects such as phenotypic plasticity and adaptation (McKay et al. 2001), apomixis (Roy 1995; Roy and Rieseberg 1989; Sharbel and Mitchell-Olds 2001), flower biology and host-pathogen interaction and evolution (Roy 2001), or the evolution of genes and gene families (Bishop, Dean, and Mitchell-Olds 2000; Koch, Haubold, and Mitchell-Olds 2000). The distribution pattern of the species indicates postglacial range extension and recolonization. However, the existence of a center of species diversity in the southwestern United States, which is also a center of molecular diversity (within and between species) suggests multiple range fluctuations during the Pleistocene. Preliminary plastid data showed that within-species variation is comparable with between-species variation (Koch and Dobe, in preparation), and, moreover, many plastome types are distributed across species. Two explanations for this are possible. First, extensive hybridization and reticulation may have occurred. Second, all of the genetic variation was present before pleistocenic speciation of the genus started, and plastome types have been distributed randomly among the several lineages. We believe that both explanations need to be invoked to describe the distribution of molecular variation and the complex evolutionary scenario. Reticulation and hybridization have been demonstrated herein for the A. divaricarpa example. However, the existence of a diverse "ancient" gene pool is supported by cpDNA sequence distances. ITS sequences of the different Arabis species used for outgroup analysis (fig. 2) revealed pairwise DNA sequence differences ranging from 0.3% to 1.3%. These are values that have been expected for Pleistocene differentiation. Although molecular clock hypotheses are still under debate, for ITS a substitution rate of approximately 0.5% to 2.5% nucleotide divergence per 1 million years can be assumed (for comparison: highest substitution rates with 5.3 x 109 substitutions/site/year, Wendel, Schnabel, and Seelanan 1995a; lowest rates with 0.35 x 10-9 substitutions/site/year, Suh et al. 1993). In the case of the North American Arabis these literature-based comparisons of ITS substitution rates would account for Pleistocene speciation. In strong contrast, plastidic sequence variation of the trnL intron and the trnL-F spacer region from the different populations exceed those of the ITS region by far (up to 2.1% sequence differences), although these sequences evolve with much lower substitution rates than the ITS region.
The closest relatives that can serve as outgroups from the genera Halimolobus, Cusickiella, or Polyctenium are also restricted to the North American continent. Phylogenetic hypothesis among these taxa are available and robust (Koch, Bishop, and Mitchell-Olds 1999; Koch, Haubold, and Mitchell-Olds 2000; 2001). In contrast to numerous other species selected for fundamental research in plant sciences, the North American Arabis are mostly restricted to pristine habitats. This enables us to study evolutionary processes in nature not biased by direct human activities.
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Acknowledgements |
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Footnotes |
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William Martin, Associate Editor
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Literature Cited |
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Acarkan, A., M. Rossberg, M. Koch, and R. Schmidt. 2000. Comparative genome analysis reveals extensive conservation of genome organisation for Arabidopsis thaliana and Capsella rubella. Plant J. 32:55-62.[CrossRef]
An, S. S., L. T. Fried, and E. Hegewald. 1999. Phylogenetic relationships of Scenedesmus and Scenedesmus-like coccoid green algae as inferred from ITS-2 rDNA sequence comparisons. Plant Biol. 1:418-428.[ISI]
Anderson, J. K., and S. I. Warwick. 1999. Chromosome number evolution in the tribe Brassiceae (Brassicaceae): Evidence from isozyme number. Plant Syst. Evol. 215:255-285.[ISI]
Arnheim, N., M. Krystal, R. Schmickel, G. Wilson, O. Ryder, and E. Zimmer. 1980. Molecular evidence for genetic exchanges among ribosomal genes on nonhomologous chromosomes in man and apes. Proc. Natl. Acad. Sci. USA 77:7323-7327.[Abstract]
Arnold, M. L. 1997. Natural hybridization and evolution. Oxford University Press, Oxford.
Avise, M. L. 1994. Molecular markers, natural history and evolution. Chapman & Hall, New York.
Bishop, J., A. M. Dean, and T. Mitchell-Olds. 2000. Rapid evolution in plant chitinases: molecular targets of selection in plant pathogen coevolution. Proc. Natl. Acad. Sci. USA 97:5322-5327.
Bleeker, W., M. Huthmann, and H. Hurka. 1999. Evolution of hybrid taxa in Nasturtium R. Br. (Brassicaceae). Folia. Geobot. Phytotaxon. 34:421-433.
Böcher, T. W. 1951. Cytological and embryological studies in the amphi-apomictic Arabis holboellii complex. Kong. Danske Vidensk. Selsk. 6:1-59.
Brochmann, C. 1992. Polyploid evolution in arctic-alpine Draba (Brassicaceae). Sommerfeltia Suppl. 4:1-34.
Brochmann, C., and R. Elven. 1992. Ecological and genetic consequences of polyploidy in arctic Draba (Brassicaceae). Evol. Trends Pl. 6:111-124.[ISI]
Brochmann, C., T. Nilsson, and T. M. Gabrielson. 1996. A classic example of postglacial allopolyploid speciation re-examined using RAPD markers and nucleotide sequences: Saxifraga osloensis (Saxifragaceae). Acta Univ. Ups. Symb. Bot. Ups. 31:75-89.
Brochmann, C., P. S. Soltis, and D. E. Soltis. 1992. Recurrent formation and polyphyly of Nordic polyploids in Draba (Brassicaceae). Pl. Syst. Evol. 182:35-70.[ISI]
Buckler, E. S., IV, T. Holtsford. 1996. Zea ribosomal repeat evolution and substitution patterns. Mol. Biol. Evol. 13:623-632.[Abstract]
Buckler, E. S., A. Ippolito, and T. P. Holtsford. 1997. The evolution of ribosomal DNA: divergent paralogues and phylogenetic implications. Genetics 145:821-832.
Chen Z. J., L. Comai, and C. S. Pikaard. 1998. Gene dosage and stochastic effects determine the severity and direction of uniparental ribosomal RNA gene silencing (nucleolar dominance) in Arabidopsis thaliana. Proc. Natl. Acad. Sci. USA 95:14891-14896.
Chen, Z. J., and C. S. Pikaard. 1997. Transcriptional analysis of nucleolar dominance in polyploid plants: biased expression/silencing of progenitor rRNA genes is developmentally regulated in Brassica. Proc. Natl. Acad. Sci. USA 94:3442-3447.
Darlington, C. D. 1937. Recent advances in cytology. 2nd edition. Churchill, London.
Denduangboripant, J., and Q. C. B. Cronk. 2001. Evolution and alignment of the hypervariable arm 1 of Aeschynanthus (Gesneriaceae) ITS2 nuclear ribosomal DNA. Mol. Phyl. Evol. 20:163-172.[CrossRef][ISI][Medline]
Dover, G. 1982. Molecular drive: a cohesive mode of species evolution. Nature 299:111-117.[ISI][Medline]
Doyle, J. J., and J. L. Doyle. 1997. A rapid isolation procedure for small quantities of fresh leaf tissue. Phytochem. Bull. 19:11-15.
Franzke, A., and K. Mummenhoff. 1999. Recent hybrid speciation in Cardamine (Brassicaceae)conversion of nuclear ribosomal ITS sequences in statu nascendi. Theor. Appl. Genet. 98:831-834.[CrossRef][ISI]
Franzke, A., K. Pollmann, W. Bleeker, R. Kohrt, and H. Hurka. 1998. Molecular systematics of Cardamine and allied genera (Brassicaceae): ITS and non-coding chloroplast DNA. Folia Geobot. Phytotax. 33:225-240.
Frieman, M., Z. J. Chen, J. Saez-Vasquez, L. A. Shen, and C. S. Pikaard. 1999. RNA polymerase I transcription in a Brassica interspecific hybrid and its progenitors: tests of transcription factor involvement in nucleolar dominance. Genetics 152:451-460.
Goldblatt, P. 1980. Polyploidy in angiosperms: monocotyledones. Pp. 219239 in W. H. Lewis, ed. Polyploidy, biological relevance. Plenum Press, New York.
Grant, V. 1963. The origin of adaptations. Columbia University Press, New York.
Harris, S. H., and R. Ingram. 1991. Chloroplast DNA and biosystematics: the effects of intraspecific diversity and plastid transmission. Taxon 40:393-412.[ISI]
Hartmann, S., Nason, J. D., and D. Bhattacharya. 2001. Extensive ribosomal DNA genic variation in the columnar cactus Lophocereus. J. Mol. Evol. 53:124-134.[ISI][Medline]
Jaeger, J. A., D. H. Turner, and M. Zuker. 1989. Improved predictions of secondary structures for RNA. Proc. Natl. Acad. Sci. USA 86:7706-7710.[Abstract]
Kim, K. J., and R. K. Jansen. 1994. Comparisons of phylogenetic hypotheses among different data sets in dwarf dandelions (Krigia, Asteraceae): additional information from internal transcribed spacer sequences of nuclear ribosomal DNA. Plant Syst. Evol. 190:157-185.[ISI]
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.[ISI][Medline]
Kita, Y., and M. Ito. 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. 225:1-13.[ISI]
Koch, M., and I. A. Al-Shehbaz. 2000. Molecular systematics of the Chinese Yinshania (Brassicaceae): evidence from plastid trnL intron and nuclear ITS DNA sequence data. Ann. Missouri Bot. Gard. 87:246-272.[ISI]
Koch, M., and I. A. Al-Shehbaz. 2002. Molecular data indicate complex intra- and intercontinental differentiation of American Draba (Brassicaceae). Ann. Missouri Bot. Gard. 88:88-109.
Koch, M., J. Bishop, and T. Mitchell-Olds. 1999. Molecular systematics and evolution of Arabis and Arabidopsis. Plant Biol. 1:529-537.[ISI]
Koch, M., B. Haubold, and T. Mitchell-Olds. 2000. Comparative evolutionary analysis of chalcone synthase and alcohol dehydrogenase loci in Arabidopsis, Arabis, and related genera (Brassicaceae). Mol. Biol. Evol. 17:1483-1498.
Koch, M., B. Haubold, and T. Mitchell-Olds. 2001. Molecular systematics of the cruciferae: evidence from coding plastome matK and nuclear CHS sequences. Am. J. Bot. 88:534-544.
Koch, M., and H. Hurka. 1998. Isozyme analysis in the polyploid complex Microthlaspi perfoliatum (L.) F. K. Meyer: morphology, biogeography and evolutionary history. Flora 194:33-48.[ISI]
Koch, M., M. Huthmann, and H. Hurka. 1998. Isozymes, speciation and evolution in the polyploid complex Cochlearia L. (Brassicaceae). Bot. Acta 111:451-466.
Koch, M., K. Mummenhoff, and H. Hurka. 1998. Molecular biogeography and evolution of the Microthlaspi perfoliatum s. l. polyploid complex (Brassicaceae): chloroplast DNA and nuclear ribosomal DNA restriction site variation. Can. J. Bot. 76:382-396.[CrossRef][ISI]
Koch, M., K. Mummenhoff, and H. Hurka. 1999. Molecular phylogenetics of Cochlearia L. and allied genera based on nuclear ribosomal ITS DNA sequence analysis contradict traditional concepts of their evolutionary relationships. Plant Syst. Evol. 216:1483-1498.
König, C. 1998. Infraspecific morphometric and nuclear genome size variation in polyploid Biscutella laevigata (Brassicaceae). Am. J. Bot. 85: (Suppl.): 140.
Kowalski, S. P., T. H. Lan, K. A. Feldmann, and A. H. Paterson. 1994. Comparative mapping of Arabidopsis thaliana and Brassica oleracea chromosomes reveals islands of conserved organization. Genetics 138:499-510.
Lagercrantz, U. 1998. Comparative mapping between Arabidopsis thaliana and Brassica nigra indicates that Brassica genomes have evolved through extensive genome replication accompanied by chromosome fusions and frequent rearrangements. Genetics 150:1217-1228.
Liu, J.-S., and L. Schardl. 1994. A conserved sequence in internal transcribed spacer 1 of plant nuclear rRNA genes. Plant Mol. Biol. 26:775-778.[ISI][Medline]
Mai, J. C., and A. W. Coleman. 1997. The internal transcribed spacer 2 exhibits a common secondary structure in green algae and flowering plants. J. Mol. Evol. 44:258-271.[ISI][Medline]
Marie-Victorin, F., and F. Rolland-Germain. 1964. Flore de l'Anticosti-Minganie. Les Press de l'Université de Montréal, Montréal.
Masterson, J. 1994. Stomatal size in fossil plants: evidence for polyploidy in majority of angiosperms. Science 264:421-424.[ISI]
McKay, J. K., J. G. Bishop, J.-Z. Lin, J. H Richards, A. Sala, and T. Mitchell-Olds. 2001. Local adaptation across a climatic gradient despite small effective population size in the rare sapphire rockcress. Proc. R. Soc. Biol. Sci. Ser. B 268:1715-1721.[CrossRef][ISI][Medline]
Muir, G., C. C. Flemming, and C. Schlötterer. 2001. Three divergent rDNA clusters predate the species divergence in Quercus petraea (Matt.) Liebl. and Quercus robur L. Mol. Biol. Evol. 18:112-119.
Mummenhoff, K., A. Franzke, and M. Koch. 1997. Molecular phylogenetics of Thlaspi s. l. (Brassicaceae) based on chloroplast DNA restriction site variation and sequences of the internal transcribed spacers of nuclear ribosomal DNA. Can. J. Bot. 75:469-482.[ISI]
Müntzing, A. 1936. The evolutionary significance of autopolyploidy. Hereditas 21:263-378.
O'Kane Jr., S. L., B. A. Schaal, and I. Al-Shehbaz. 1996. The origins of Arabidopsis suecica as indicated by nuclear rDNA sequences. Syst. Bot. 21:559-566.[ISI]
Petit, C., F. Bretagnolle, and F. Felber. 1999. Evolutionary consequences of diploid-polyploid hybrid zones in wild species. Trends Ecol Evol 14:306-311.[CrossRef][ISI][Medline]
Ramsey, J., and D. W. Schemske. 1998. Pathways, mechanisms, and rates of polyploid formation in flowering plants. Annu. Rev. Ecol. Syst. 29:467-501.[CrossRef][ISI]
Rieseberg, L. H., and C. R. Linder. 1999. Hybrid classification: insights from genetic map-based studies of experimental hybrids. Ecology 80:361-370.[ISI]
Rieseberg, L. H., J. Whitton, and K. Gardner. 1999. Hybrid zones and the genetic architecture of a barrier to gene flow between two sunflower species. Genetics 152:713-727.
Rollins, R. 1993. The cruciferae of continental North America. Stanford University Press, Stanford, Calif.
Roy, B. 1995. The breeding system of six species of Arabis. Am. J. Bot. 82:869-877.[ISI]
Roy, B. 2001. Patterns of association between crucifers and their flower mimic pathogens: host shifts are more common than coevolution or cospeciation. Evolution 55:41-53.[ISI][Medline]
Roy, B., and L. H. Rieseberg. 1989. Evidence for apomixis in Arabis. J. Hered. 80:506-508.[ISI]
Rozas, J., and R. Rozas. 1999. DnaSP version 3: an integrated program for molecular population genetics and molecular evolution analysis. Bioinformatics 15:174-175.
Sharbel, T. F., and T. Mitchell-Olds. 2001. Recurrent polyploid origins and chloroplast phylogeography in the Arabis holboellii complex (Brassicaceae). Heredity 87:59-68.[CrossRef][ISI][Medline]
Smith, J. P., and J. O. Sawyer. 1988. Endemic, vascular plants of northwestern California and southwestern Oregon. Madroño 35:54-69.
Soltis, D. E., Gitzendanner, M. A., Strenge, D. D., and P. S. Soltis. 1997. Chloroplast DNA intraspecific phylogeography of plants from the Pacific Northwest of North America. Plant Syst. Evol. 206:53-373.
Soltis, D. E., and P. S. Soltis. 1993. Molecular data and dynamic nature of polyploidy. C.R.C. Crit. Rev. Plant Sci. 12:243-273.[ISI]
Soltis, D. E., and P. S. Soltis. 1999. Polyploidy: recurrent formation and genome evolution. Trends Ecol. Evol. 14:348-352.[CrossRef][ISI][Medline]
Stebbins, G. L. 1971. Chromosomal evolution in higher plants. Addison-Wesley, Reading, Mass.
Suh, Y., L. B. Thein, H. E. Reeve, and E. A. Zimmer. 1993. Molecular evolution and phylogenetic implications of internal transcribed spacer sequences of ribosomal DNA in Winteraceae. Am. J. Bot. 80:1042-1055.[ISI]
Thompson, J. D., and R. Lumaret. 1992. The evolutionary dynamics of polyploid plants: origins, establishment and persistence. Trends Ecol. Evol. 7:302-307.[CrossRef][ISI]
Tremetsberger, K., König, C., Samuel, R., Pinsker, W., and T. Stuessy. 2002. Infraspecific genetic variation in Biscutella laevigata (Brassicaceae): new focus on Irene Manton's hypothesis. Plant Syst. Evol. 233:163-181.[CrossRef][ISI]
Urbanska, K. M., H. Hurka, E. Landolt, B. Neuffer, and K. Mummenhoff. 1997. Hybridization and evolution in Cardamine (Brassicaceae) at Urner Boden, Central Switzerland: biosystematic and molecular evidence. Plant Syst. Evol. 204:233-256.[ISI]
Van de Peer, Y., and R. De Wachter. 1997. Construction of evolutionary distance trees with TREECON for Windows: accounting for variation in nucleotide substitution rate among sites. Comp. Appl. Biosci. 13:227-230.[ISI][Medline]
Van Houten, W. H. J., N. Scarlett, and K. Bachmann. 1993. Nuclear DNA markers of the Australian tetraploid Microseris scapigera and its North American diploid relatives. Theor. Appl. Genet. 87:498-505.[ISI]
Volkov, R. A., Borisjuk, N. V., Panchuk, I. I., Schweizer, D., and V. Hemleben. 1999. Elimination and rearrangement of parental rDNA in the allotetraploid Nicotiana tabacum. Mol. Biol. Evol. 16:11-320.
Wendel, J. F., A. Schnabel, and T. Seelanan. 1995a. An unusual ribosomal DNA sequence from Gossypium gossypioides reveals ancient, cryptic, intergenomic introgression. Mol. Phylogenet. Evol. 4:298-313.[CrossRef][ISI][Medline]
Wendel, J. F., A. Schnabel, and T. Seelanan. 1995b. Bidirectional interlocus concerted evolution following allopolyploid speciation in cotton (Gossypium). Proc. Natl. Acad. Sci. USA 92:280-284.[Abstract]
White T. J., T. Bruns, S. Lee, and J. Taylor. 1990. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. Pp. 315322 in M. Innis, D. Gelfand, J. J. Sninsky, and T. J. White, eds. PCR protocols: a guide to methods and applications. Academic Press, San Diego, Calif.
Whittaker, R. H. 1961. Vegetation history of the Pacific Coast states and the "central" significance of the Klamath region. Madroño 16:5-17.
Widmer, A., and M. Baltisberger. 1999. ITS molecular evidence for allopolyploid speciation and a single origin of the narrow endemic Draba ladina (Brassicaceae). Am. J. Bot. 86:1282-1289.
Wissemann, V. 1999. Genetic constitution of Rosa sect. Caninae (R. canina, R. jundzillii) and sect. Gallicanae (R. gallica). Angew. Bot. 73:191-196.
Wissemann, V. 2000. Molekulargenetische und morphologisch-anatomische Untersuchungen zur Evolution and Genomzusammensetzung von Wildrosen der Sektion Caninae (DC.) Ser. Bot. Jahrb. Syst. 122:357-429.
Zuker, M. 1989. On finding all suboptimal foldings of an RNA molecule. Science 244:48-52.[ISI][Medline]
Zuker, M., D. H. Mathews, and D. H. Turner. 1999. Algorithms and thermodynamics for RNA secondary structure prediction: a practical guide. Pp. 1143 in J. Barciszewski and B. F. C. Clark, eds. RNA biochemistry and biotechnology. NATO ASI Series, Kluwer Academic Publishers, Dordrecht, The Netherlands.