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Systematics |
Department of Biological Sciences, Idaho State University, Pocatello, Idaho 83209-8007 USA
Received for publication June 29, 2000. Accepted for publication November 9, 2000.
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ABSTRACT |
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 TOP ABSTRACT INTRODUCTIONMATERIALS AND METHODSRESULTSDISCUSSIONLITERATURE CITED |
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Key Words: 26S rDNA • combining data • Cornaceae • Cornus • cpDNA • molecular evolution • molecular phylogeny
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INTRODUCTION |
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TOPABSTRACTINTRODUCTIONMATERIALS AND METHODSRESULTSDISCUSSIONLITERATURE CITED |
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55 species that are mostly trees and shrubs and rarely perennial herbs with woody rhizomes. The genus is widely distributed in the northern hemisphere, with centers of diversity in eastern Asia, eastern North America, and western North America. Two species of the genus are endemic to South America and one species is endemic to tropical Africa (see Table 1). Species of Cornus are morphologically diverse. Various types of inflorescences are found within the genus, including open compound cymes with minute, nonmodified bracts; umbellate cymes with four basal, scale-like bracts; capitate cymes with four large, basal, and showy bracts; and minute compound cymes with four basal showy bracts. In addition, the color of fruits also varies among species (see Table 1). Due to the great morphological diversity encompassed by the Linnaean circumscription of Cornus, the taxonomy and phylogenetic relationships of subgroups within the genus are highly controversial (see Eyde, 1988
; Murrell, 1993
; Xiang et al., 1996
). The genus has been divided into several distinct genera (e.g., Rafinesque, 1838
; von Berchtold and Opiz, 1838
; Spach, 1839
; Nakai, 1909
; Hutchinson, 1942
; Pojarkova, 1950
; also see Murrell, 1993
), or into various numbers of subgenera (e.g., Harms, 1898
; Wangerin, 1910
; Ferguson, 1966
; Eyde, 1987, 1988
; Xiang, 1987
). Following the broad view of Cornus, a total of ten subgenera have been recognized by different authors at one time or another (see Table 1; Ferguson, 1966
; Xiang, 1987
; Eyde, 1988
; Murrell, 1993
).
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; Xiang, Soltis, and Soltis, 1998
) and morphological characters (Murrell, 1993
). Phylogenetic analyses of these data identified five major lineages within Cornus: (1) C. oblonga, an enigmatic blue-fruited dogwood, (2) other blue- or white-fruited dogwoods, (3) the cornelian cherries, (4) the big-bracted dogwoods, and (5) the dwarf dogwoods (the herbaceous species). However, relationships among these groups suggested by cpDNA data are different from those suggested by morphological data. The cpDNA data (combined rbcL and matK sequences and restriction sites) suggested that the dwarf dogwoods are sisters of the big-bracted dogwoods with the cornelian cherries sister to them, and C. oblonga is a member of the blue- or white-fruited dogwoods and sister to the remainder of the group (see Fig. 1; Xiang et al., 1996
; Xiang, Soltis, and Soltis, 1998
). These results are consistent with the hypothesis of Eyde (1988)
based on synthesis of information available without performing phylogenetic analyses. In contrast, cladistic analysis of 28 morphological, anatomical, chemical, and cytological characters of Cornus by Murrell (1993)
suggested that the cornelian cherries and the big-bracted dogwoods are sister groups, and the dwarf dogwoods are sister to them, with C. oblonga being the first-branching lineage in Cornus (see Fig. 2; Murrell, 1993
; Hardin and Murrell, 1997
). To explore possible sources of incongruence between the cpDNA and morphological data, additional phylogenetic analyses, especially analyses of molecular data from the nuclear genome, are necessary.
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; Soltis and Soltis, 1998
), our initial analyses within Cornus revealed a high level of ITS sequence divergence among species from the five major lineages, which made unambiguous alignment of sequences unfeasible (Xiang and Fan, unpublished data). Therefore, we turned to a more slowly evolving nuclear gene 26S rDNA. Recent studies have demonstrated the great potential of 26S rDNA sequences in elucidating phylogenetic relationship at various taxonomic levels of seed plants (at and above the generic level) (e.g., Mishler et al., 1994
, used rRNA sequences only; Ro, Keener, and McPheron, 1997
; Kuzoff et al., 1998
; Soltis and Soltis, 1998
; Stefanovic et al., 1998
; Ashworth, 2000
). In our ongoing study of 26S rDNA sequencing for Cornales, several species representing the five different subgroups of Cornus were included. Our preliminary results revealed that sufficient sequence variation exists among Cornus species. Thus, we employed comparative 26S rDNA sequencing to reconstruct a nuclear phylogeny of Cornus. The goals of this study were: (1) to determine phylogenetic relationships among subgroups of Cornus using nuclear 26S rDNA sequences; (2) to test the phylogenetic hypotheses based on morphology and cpDNA data; (3) to gain insights into the evolution of some subgroup-diagnostic morphological characters in Cornus. |
MATERIALS AND METHODS |
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TOPABSTRACTINTRODUCTIONMATERIALS AND METHODSRESULTSDISCUSSIONLITERATURE CITED |
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; Xiang, Soltis, and Soltis, 1998
). Thus, even without these two species our sampling represented well all major subgroups within the genus. Although subgenus Kraniopsis is the largest subgenus in Cornus (30 spp.), all species in the subgenus are morphologically very similar, and they formed a strongly supported monophyletic group in the cpDNA study (Xiang et al., 1996
). Therefore, only two species were sampled from this subgenus. All of the species sampled were included in previous matK and rbcL sequencing and chloroplast DNA restriction site analyses, except C. suecica (a dwarf dogwood) and C. volkensii (the single species from Africa). These two species had not been included in the cpDNA studies because of the lack of materials of these taxa at the time the studies were completed. Three genera, Nyssa, Alangium, and Schizophragma (Hydrangeaceae), were chosen as the outgroups for the present study based on the results of broad phylogenetic analyses of matK amd rbcL sequences for Cornaceae (Xiang, Soltis, and Soltis, 1998
), which suggested that Alangium is the sister of Cornus; Nyssa and Hydrangeaceae are close relatives of Cornus.
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; Xiang, Soltis, and Soltis, 1998
). The 26S rDNA sequences were amplified via PCR (polymerase chain reaction) from total DNA aliquots using the forward primer N-nc26S1 (5'-CGACCCCAGGTCAGGCG-3') and the reverse primer 3331rev (5'-ATCTCAGTGGATCG TGGCAG-3') following Kuzoff et al. (1998)
with slight modifications. Our PCR reactions contained the following: 5 µL of 10x Mg free buffer, 6 µL of 25 mmol/L MgCl2, 10 µL of 2.5 mmol/L dNTP, 1.0 µL of 20 µmol/L N-nc26S1 (forward primer), 1.0 µL of 20 µmol/L 3331 rev (reverse primer), 5 µL of DMSO (dimethyl sulfoxide), 0.3 µL of Taq polymerase (Promega), 2.0 µL of 20 ng/µL total DNA extract, and 19.7 µL of deionized water. The PCR reaction mix was covered with two drops of mineral oil and run on a Robocycle PCR machine as the following: (1) 94°C for 3 min for one cycle; (2) 30 cycles of 94°C for 1 min, 55°C for 1 min, 72°C for 3.5 min; and (3) a terminal phase at 72°C for 5 min.
The double-stranded (DS) PCR products were subsequently purified via precipitation with 60 µL of 20% PEG 8000/2.5 mol/L NaCl on ice for at least 1 h (Morgan and Soltis, 1993
; Soltis and Soltis, 1997
). The precipitated DS products were centrifuged for 15 min at 14 000 rpm at 4°C. The DNA pellets were then washed with 1000 µL of 75% ethanol (prechilled to 4°C) and centrifuged for 3 min. The DNA pellets were washed again with chilled 95% ethanol and centrifuged for 3 min at 4°C. The ethanol was decanted, and the pellets were dried in a vacuum. The dried DNA products were resuspended in 20–30 µL of ddH2O. One microliter of the clean PCR products was electrophoresed in a 1% agarose mini-gel for quantification.
The purified DS DNA products were used as the templates for sequencing on an ABI-377 automated sequencer following the standard protocol recommended by the company (Applied Biosystems, Foster City, CA 94404 USA). For some species, DMSO was added to the sequencing reactions to obtain clear sequences. Sixteen sequencing primers (N-nc26S1, N-nc26S3, N-nc26S4, N-nc26S5, N-nc26S6, N-nc26S8, N-nc26S10, N-nc26S12, N-nc26S14, 268rev, 641rev, 950rev, 1449rev, 2134rev, 2782rev, and 3331rev) described in Kuzoff et al. (1998)
were used to obtain the entire sequence of 26S rDNA. The sequence chromatogram output files for all species were checked and edited base by base before being aligned manually.
Phylogenetic analysis
The 26S rDNA sequences representing 16 taxa comprise 3380 aligned bp with small gaps (see RESULTS). The data matrix was analyzed with both parsimony and maximum likelihood (ML) methods using PAUP 4.0b4 (Swofford, 2000)
. For parsimony analysis, gaps were coded as missing data; branch-and-bound search was conducted. Branch-and-bound search was performed using furthest taxon addition sequence and initial upper bound computed via stepwise addition. To evaluate relative robustness of the clades found in the most parsimonious trees, bootstrap and decay analyses were conducted. Bootstrap analysis (Felsenstein, 1985
) of 1000 replicates was conducted using fast heuristic search and TBR branch-swapping. The method for decay analysis (Bremer, 1988
) was described in Xiang et al. (1996)
, which followed Eernisse and Kluge (1993)
. This method involves examining each node of interest in turn using a constraint statement that specifies only the node of interest being monophyletic and saving the shortest trees that do not satisfy this criterion. The difference between the length of these trees and the true shortest trees is used as the decay value for that node.
Maximum likelihood analyses were first conducted using heuristic searches with random taxon addition of five replicates with default settings of the ML program (i.e., empirical base frequency, HKY [Hasegawa, Kishino, and Yano, 1985
] two-parameter model variant for unequal base frequency, ti/tv = 2, and equal rates for all sites). The resulting tree was simultaneously used to estimate values for base frequency, ti/tv ratio, proportion of invariable sites, and shape of the discrete gamma distribution of rates across sites, through maximum likelihood. A subsequent ML analysis using the estimated values of these parameters (A = 0.220264, C = 0.272649, G = 0.307582, T = 0.199505; ti/tv ratio = 1.343463 [kappa = 2.741222]; proportion of invariable sites = 0.704318; shape value for discrete gamma distribution = 0.848768) was then conducted to see whether adjusting these parameters to the estimated values resulted in significant differences in tree topologies.
Since the results of analyses of 26S rDNA sequences suggested phylogenetic relationships within Cornus are highly congruent with those achieved via cpDNA data (combined matK, rbcL sequences, and restriction sites), the 26S rDNA sequences were combined with cpDNA data for further parsimony and ML analyses to obtain a comprehensive view of relationships. The combined data matrix included ten species of Cornus and two outgroups (Alangium and Nyssa), each of 6338 characters, among which 3380 bp were from 26S rDNA, 1212 bp from matK, 1504 bp from rbcL, and 242 from restriction sites. Phylogenetic analyses of the combined 26S rDNA and cpDNA were conducted as above.
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RESULTS |
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TOPABSTRACTINTRODUCTIONMATERIALS AND METHODSRESULTSDISCUSSIONLITERATURE CITED |
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) and Tragopogon dubius Scop. (AFO36493, Kuzoff et al., 1998
), obtained from GenBank. The aligned 26S rDNA sequences in Cornus and outgroups contained a total length of 3380 bp. Sequences for all species are complete except for C. controversa and C. sessilis. In C. controversa, 166 bp (bases 1542–1707) are missing and in C. sessilis, 476 bp (bases 1217–1692) are missing. Despite repeated efforts, these missing data in these two species could not be obtained due to potential primer divergence or heterogeneity of temperate DNA. Among the 16 sequences of Cornus and outgroups, 391 of the 3380 sites are variable (11.56%) and 137 sites (4.05%) are phylogenetically informative. The alignment sequences of Cornus and outgroups required the addition of 20 small alignment gaps (1–5 bp in length). Eleven of these gaps appear to be autapomorphies, and nine of them are potentially phylogenetically informative within Cornus (Table 3, also see Fig. 3).
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; Dover and Flavell, 1984
; Flavell, 1986
). The location of expansion segments of 26S rDNA sequences appears to be highly conserved over a wide range of taxa (Bult, Sweere, and Zimmer, 1995
). According to the coordinates for expansion segment positions in the sequence of Oryza sativa (Kuzoff et al. 1998
), 12 expansion segments were identified in the 26S rDNA sequence data of Cornus and outgroups (Table 4). These expansion segments of 26S rDNA in Cornus and outgroups span a total of 1034 bp, among which 233 bp (22.53%) are variable and 97 sites (9.38%) are phylogenetically informative. These values are much higher than those for the conserved core regions, which contain 2346 bp, of which 158 (6.73%) are variable and have only 40 sites (1.71%) that are phylogenetically informative. The expansion segments also have a higher average G + C content (68.5%) than the entire 26S rDNA (58.1%) and the conserved core regions (52.6%).
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The ML analysis using default setting (see MATERIALS AND METHODS) found a tree with the best score of -Ln = 8531 with a topology identical to the parsimony tree (Fig. 4). The ML analysis using estimated values found a tree with a higher likelihood (-Ln = 8219), but showing the same relationships as described above.
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DISCUSSION |
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TOPABSTRACTINTRODUCTIONMATERIALS AND METHODSRESULTSDISCUSSIONLITERATURE CITED |
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; Kuzoff et al., 1998
; Stefanovic et al., 1998
; Ashworth, 2000
). Our phylogenetic study of Cornus using 26S rDNA sequences provides an example of phylogenetic utility of this gene at an intrageneric level. Although the rate of evolution of 26S rDNA is relatively conservative (comparable to rbcL), the gene contains several expansion segments that evolve faster than the conserved core regions (see Bult, Sweere, and Zimmer, 1995
; Kuzoff et al., 1998
). The variable rate of evolution in the expansion segments and the conserved core regions makes the gene useful for phylogenetic analyses at different taxonomic levels depending on the regions employed (see Kuzoff et al., 1998
). The expansion segments can be used at lower taxonomic levels, whereas the conserved core regions are suitable at higher levels. In addition, the large size of the gene provides more variable characters for phylogenetic analysis than rbcL; the low sequence variation as a result of the conservative rate of the gene is well compensated by its large size. Although only 11.56% of the sites are variable, and 4.05% is phylogenetically informative in the 26S rDNA matrix of Cornus, the total number of variable sites from the entire sequence is 391, and the number of total informative sites is 137. These numbers are nearly two times higher than those for rbcL and matK, respectively, in the combined data matrix (see RESULTS). Analyses of the 26S rDNA sequences of Cornus resulted in a completely resolved phylogeny of the genus and suggested relationships congruent with the cpDNA-based phylogeny (Figs. 3, 4). This suggests that the 26S rDNA sequences as a whole contain sufficient phylogenetic information at the intrageneric level of Cornus and are useful for elucidating phylogenetic relationships within the genus.
To explore differential utilities of the expansion segments and conserved core regions of 26S rDNA sequences in Cornus, we conducted phylogenetic analyses of the sequences from the expansion segments and conserved core regions separately. The analyses of these portions of 26S rDNA did not produce topologies that were as fully resolved. The results indicated that the analysis of the expansion segments alone produced a weakly supported phylogeny inconsistent with both the cpDNA-based phylogeny and the morphology-based phylogeny. In this phylogeny, the monophyly of the cornelian cherries was unsupported and species of the group appear in different clades. Similar results were obtained from the analysis of the conserved core regions. In the trees resulting from the analysis of the conserved core sequences, the monophyly of Cornus was even unsupported. These odd results may be explained as the effect of insufficient variable characters in either the expansion segments or the conserved core regions. Although the expansion segments contain a higher percentage of phylogenetically informative sites (9.38%) than that of the entire 26S rDNA (4.05%), the total number of phylogenetically informative sites in the expansion segments is only 97, 40 sites less compared to 137 sites in the entire gene. The conserved core regions contain only 40 potentially phylogenetically informative sites. Moreover, the expansion segments have a significantly higher average G + C content (68.5%) than that of the entire 26S rDNA (58.1%) and that of the conserved core regions (52.6%). The higher G + C content in the 26S rDNA expansion segments poses a potential problem for phylogenetic analysis if the algorithm used to construct a tree assumes equally abundant nucleotides (see Kuzoff et al., 1998
).
Phylogenetic relationships within Cornus
The phylogenetic tree derived from the analysis of 26S rDNA sequences of Cornus shows a topology identical to the tree derived from cpDNA data (Fig. 1; Xiang et al., 1996
; Xiang, Soltis, and Soltis, 1998
), although some nodes in the 26S rDNA tree are not strongly supported by bootstrap and decay analyses (Figs. 3, 4). This 26S rDNA tree is also congruent with the tree derived from analyses of the combined 26S rDNA and cpDNA data (Fig. 5). Thus all of the molecular data from both nuclear and chloroplast genomes of Cornus are concordant. These data suggest that the genus diverged early into two large lineages: (1) the blue- or white-fruited group and (2) the red-fruited group. The red-fruited group subsequently separated into the cornelian cherries and a clade bearing showy bracts, which then diverged into the big-bracted dogwoods and the dwarf dogwoods. Within the blue- or white-fruited group, C. oblonga was the first lineage to branch off. This phylogenetic pattern is consistent with the scheme proposed by Eyde (1988)
, but at odds with the morphology-based phylogeny (Murrell, 1993
). Phylogenetic analysis of morphological characters by Murrell (1993)
placed the cornelian cherries (rather than the dwarf dogwoods as in the molecular tree) as the sister of the big-bracted dogwoods. This relationship was supported by five inflorescence characters that were treated as independent characters, including protective bracts, precocious peduncle, inflorescence preformed in the previous fall and developed from a mixed bud, reduced primary inflorescence branches, and reduced secondary inflorescence branches. However, three of these characters (protective bracts, precocious peduncle, and reduced secondary inflorescence branches) are homoplasious on the morphological trees, whereas they are reversed one or two times in some other clades or terminal taxa. In addition, these five inflorescence characters may not be independent because these characters may be developmentally correlated. Thus, differences in inflorescence may be overweighted in the morphological analysis, resulting in an incongruence between the morphological and molecular phylogeny. Based on the molecular phylogeny derived from multiple molecular data sets, the synapomorphies used to unite the cornelian cherries and the big-bracted dogwoods appear to be plesiomorphic characters evolved in the ancestor of the red-fruited group, but were later lost in the dwarf dogwoods (see discussion in Xiang et al., 1996
). Alternatively, these features may have evolved independently in the big-bracted dogwoods and the cornelian cherries. However, these two hypotheses cannot be distinguished without fossils representing the ancestor of the red-fruited group.
The second major incongruence between the molecular and morphological phylogenies involves the placement of C. oblonga (subg. Yinquania). Cornus oblonga was placed as the basal group within Cornus in the morphological tree (Fig. 2; Murrell, 1993
), whereas in the molecular phologeny, C. oblonga is a distinct lineage sister to the remainder of the blue- or white-fruited dogwoods, a relationship strongly supported by bootstrap and decay analyses (Figs. 3, 5). A single morphological character (displaced bracts, present in the remainder of the genus, absent in C. oblonga) separated C. oblonga and the remainder of the genus in the morphological tree (Murrell, 1993
). Based on the molecular phylogenies, this character is better explained as a plesiomorphic condition, and the nondisplaced bract in C. oblonga is a derived state (perhaps a reversal). Several morphological, anatomical, biochemistry characters (blue fruits, lack of iridoids, crassinucellate ovule, open cyme with minute bracts) also support the placement of C. oblonga as a member of the blue- or white-fruited group.
The tropical African species C. volkensii is the only dioecious species in Cornus. Due to its morphological uniqueness, the species was treated as a separate subgenus (subg. Afrocrania Harms) or as a distinct genus (Afrocrania Hutch.) (Hutchinson, 1942
; Ferguson, 1966
; also see Murrell, 1993
; Xiang et al., 1993
). Eyde (1988)
considered C. volkensii as a member of the cornelian cherries based mainly on similarities in fruit morphology and inflorescence type between C. volkensii and other cornelian cherries. Our 26S rDNA sequence data and the combined 26S rDNA-cpDNA data strongly supported C. volkensii being a member of the cornelian cherries (Figs. 3, 5) and recognized it as either the sister of all of the other cornelian cherries (Fig. 3) or as the sister of C. sessilis (Fig. 5). However, neither of these placements of C. volkensii within the cornelian cherries are highly supported by bootstrap and decay analyses (Figs. 3, 5). At present, no synapomorphic morphological characters can be identified to support either of these relationships of C. volkensii in the cornelian cherries. Both Eyde (1988)
and Murrell (1993)
suggested that C. volkensii is sister to all of the other cornelian cherries (also Fig. 2) based on the autopomorphies found in C. volkensii (e.g., dioecy, reduced secondary inflorescence branches). Neither Eyde nor Murrell identified any synapomorphies to unite the rest of the cornelian cherries. Eyde (1988)
further proposed that the divergence of C. volkensii from the other cornelian cherries might have occurred in the Paleocene or early Eocene based on morphological and fossil evidence. For example, C. volkensii has dioecious breeding system, spiny pollen, up to nine or ten ripe fruits per umbel, a broad apical depression in the fruit-stones, whereas all the other cornelian cherries have a synoecious breeding system, smooth pollen, only one to five ripe fruits per umbel, and no apical depression in the fruit-stones. According to Eyde (1988)
fossil fruits of an ancient, extinct lineage of cornelian cherries, C. multilocularis, were found in the early Tertiary in the London Clay, suggesting that the divergence of this lineage and the extant cornelian cherries occurred in or before the early Tertiary; the divergence of C. volkensii from the other cornelian cherries was subsequent to this event. Therefore, the basal placement of C. volkensii within the cornelian cherries as suggested by 26S rDNA sequence data is concordant with hypotheses of Eyde (1988)
and Murrell (1993)
.
The dwarf dogwoods are the only herbaceous members of the dogwood genus Cornus. This group comprises three species, C. canadensis, C. suecica, and C. unalaschkensis. Evidence from cytology, phytogeography, and morphology suggests that C. unalaschkensis may be an allotetroploid species derived from past hybridization between C. canadensis and C. suecica followed by chromosomal doubling (Love and Love, 1975
; Bain and Denford, 1979
; Murrell, 1994
). The 26S rDNA sequence data suggested that C. unalaschkensis is more closely related to C. canadensis than it is to C. suecica. This result may indicate that, if C. unalaschkensis is indeed an allotetroploid, as has been hypothesized, the 26S rDNA in C. unalaschkensis has converted to the type of C. canadensis. However, more extensive analyses (e.g., analyses of both nuclear and cpDNA data including all three species with more extensive sampling) are needed to test the hypothesis and to determine whether C. unalaschkensis is of hybrid origin.
In summary, the entire 26S rDNA sequence of Cornus shows a low level of sequence divergence, but because of its great length, provides sufficient variable characters (compared to rbcL and matK) to resolve the phylogenetic relationships within Cornus. Analyses of 26S rDNA sequence data result in a phylogeny of Cornus that is congruent with that inferred from combined cpDNA data, but at odds with the phylogeny derived from morphological analyses. Combining data for phylogenetic analysis can minimize sampling error and maximize the explanatory power of the data if congruent hypotheses are generated from separate analyses (see review by Johnson and Soltis, 1998
). This was also demonstrated in our analysis of the combined 26S rDNA and cpDNA data in Cornus, which not only suggested congruent phylogenetic relationships to those inferred from separate data analyses within Cornus, but also significantly increased supports for most of the clades recognized in the tree (compare Figs. 3 and 5).
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FOOTNOTES |
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2 Author for reprint requests (Tel: 919 515-3345; FAX: 919 515-3436; e-mail: cfan3{at}unity.ncsu.edu
).
3 Current address: Dept. of Botany, North Carolina State University, Campus Box 7612, Raleigh, NC 27695-7612 USA.
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TOPABSTRACTINTRODUCTIONMATERIALS AND METHODSRESULTSDISCUSSIONLITERATURE CITED |
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