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Genetics and Molecular Biology |
Graduate School of Agriculture, Kyoto University, Nakajoh 1, Mozume-cho, Mukoh 617-0001, Japan
Received for publication July 17, 2002. Accepted for publication October 24, 2002.
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ABSTRACT |
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 TOP ABSTRACT INTRODUCTIONMATERIALS AND METHODSRESULTSDISCUSSIONLITERATURE CITED |
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Key Words: autotetraploid • biogeography • chloroplast DNA • Fagopyrum cymosum • multiple origin • Tartary buckwheat
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INTRODUCTION |
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TOPABSTRACTINTRODUCTIONMATERIALS AND METHODSRESULTSDISCUSSIONLITERATURE CITED |
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), Thailand (Anderson, 1986
), and Nepal (Malla and Shakya, 1983
). In Nepal, naturally growing plants are harvested as forage for cattle. Both diploid (2n = 2x = 16) and tetraploid (2n = 4x = 32) cytotypes are known in F. cymosum (Darlington and Wylie, 1955
; Sharma and Chatterji, 1960
). The approximate ranges of distribution of diploid and tetraploid F. cymosum are shown in Fig. 1 (see Ohnishi, 1998
; Tsuji et al., 1999
). The range of the tetraploid cytotype is far wider than the diploid cytotype, the widest among the wild species of Fagopyrum. Its habitat is near roadsides, in margins of cultivated fields, and near housing areas.
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, 1995
, 1998
, 2000
; see Fig. 1).
Recently, several molecular systematic studies have been conducted to assess phylogenetic relationships within the genus Fagopyrum (Kishima et al., 1995
; Ohnishi and Matsuoka, 1996
; Yasui and Ohnishi, 1996
, 1998a
, b
; Ohsako and Ohnishi, 1998
, 2000
). These studies indicated that 15 species of the genus Fagopyrum can be divided into two major phylogenetic groups. One group, with a large achene (the cymosum group), consists of two cultivated species, common buckwheat (F. esculentum Moench) and Tartary buckwheat, and two wild species, F. homotropicum Ohnishi and F. cymosum. The other group, with a small achene (the urophyllum group), includes F. urophyllum (Bur. et. Franch) Gross and 11 other wild species. A close genetic relationship between F. cymosum and F. tataricum was first pointed out by Kishima et al. (1995)
through an analysis of cpDNA restriction sites. Ohnishi and Matsuoka (1996)
confirmed this finding. This relationship exists in spite of differences in morphological characters and breeding traits. Interspecific hybrids between F. cymosum and F. tataricum are very difficult to obtain by conventional breeding methods, i.e., the reproductive isolation between these two species is strict (Woo et al., 1999
).
Yasui and Ohnishi (1998a
, b
) investigated the phylogenetic relationships among Fagopyrum species using nucleotide sequence variation in cpDNA and in the internal transcribed spacer (ITS) region of nuclear ribosomal RNA. As for the cymosum groups, they clarified intraspecific relationships among local populations of diploid and tetraploid cytotypes of F. cymosum and proposed the following two suggestions. First, they claimed that F. tataricum speciated from a population of F. cymosum in the maternal line. Second, they hypothesized that the tetraploid population of F. cymosum from Kathi, India, probably had arisen allopatrically and independently from tetraploid populations in China and Thailand. However, they investigated only two tetraploid accessions of F. cymosum and the diploid progenitor of the tetraploid cytotype in India was entirely unknown at that time. The samples of F. tataricum did not cover diversity of F. tataricum. It indicates that their used materials were insufficient for the assertions mentioned above. Moreover, phylogenetic relationships within F. cymosum showed poor resolution in their tree with a low level of bootstrap values.
Allozyme analyses of 20 populations of F. cymosum also supported the hypothesis of multiple origins for tetraploid F. cymosum (Yamane and Ohnishi, 2001
). Recently, Tsuji et al. (1999)
found a diploid sample of F. cymosum with seed morphology similar to that of wild Tartary buckwheat in the Yaruzampu river valley of eastern Tibet. This form of F. cymosum, reported under the name of F. pilus by Chen (1999)
, is a strong candidate for the diploid ancestor of the tetraploid cytotypes in India and Nepal.
During the last decade, the most widely utilized tool for phylogeny reconstruction in plants has been the analysis of chloroplast (cp) DNA, which is haploid, multicopy, and nonrecombining. A low evolutionary rate of cpDNA genomes generally makes this type of analysis unsuitable for the study of phylogenetic relationships among closely related taxa. However, several informative studies on intraspecific variation of cpDNA sequences have focused on rapidly evolving regions in the chloroplast genome (Jordan et al., 1996
; Fujii et al., 1997
, 1999
; Yasui and Ohnishi, 1998a
; Segraves et al., 1999
; Widmer and Baltisberger, 1999
; Inamura et al., 2000
; Ohsako and Ohnishi, 2000
, 2001
). In the genus Fagopyrum, 3' end of rbcL, accD, and associated intergenic spacer region of cpDNA (Yasui and Ohnishi, 1998a
), the trnC-rpoB spacer, and the trnK/matK region (Ohsako and Ohnishi, 2000
, 2001
) can be used to study genetic relationships at lower taxonomic levels such as within a species.
In the present study, we used these three regions of cpDNA to confirm the multiple origins of the tetraploid cytotype of F. cymosum and the speciation of F. tataricum from F. cymosum. We included 12 natural populations of F. cymosum, including a diploid population from eastern Tibet, which covers almost the whole range of species. We also included one cultivated and three natural populations of F. tataricum, which represented wide variation within F. tataricum. By choosing these plant materials, we may arrive at more solid conclusions about the allopatrical multiple origin of tetraploid cytotypes of F. cymosum and the speciation of F. tataricum from F. cymosum than those asserted by Yasui and Ohnishi (1998a
, b
). Moreover, we estimated the nucleotide diversities within the species. The assertions mentioned above now have the basis of the variation of nucleotide sequences. Furthermore, we speculated the time and place of intraspecific divergence in F. cymosum.
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MATERIALS AND METHODS |
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TOPABSTRACTINTRODUCTIONMATERIALS AND METHODSRESULTSDISCUSSIONLITERATURE CITED |
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), whereas YC9806b has normal seed morphology. Although accession YC9806a of F. cymosum was designated as F. pilus by Chen (1999)
, we designated it as F. cymosum because "F. pilus" can easily be crossed with F. cymosum (Woo et al., 1999
), and all the molecular data so far obtained suggest that F. cymosum and F. pilus are the same species (Yamane and Ohnishi, 2001
; K. Yamane et al., unpublished data). Both the diploid and tetraploid cytotypes of F. cymosum that were used in this study were analyzed cytologically to verify chromosome numbers. The F. tataricum samples (see Table 1) were carefully selected from those used by Tsuji and Ohnishi (2000
, 2001a
, b
) so that a small number of samples would encompass the entire variation revealed by RAPDs and AFLPs. In this study, Fagopyrum esculentum (C9106) was included as the outgroup, since F. esculentum is known to be the closest relative to both F. cymosum and F. tataricum (Yasui and Ohnishi, 1998a
, b
). One individual was examined for each accession, except for YC9806. All plant materials were selected from the collection at the Laboratory of Crop Evolution, Graduate School of Agriculture, Kyoto University. These seed samples were originally established from randomly collected seeds (100–1000 seeds) from natural or cultivated populations by the second and third authors during their expeditions from 1985 through 1998.
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. For the trnC (GCA)-rpoB spacer region and the trnK (UUU) intron and matK region, the PCR method was described by Ohsako and Ohnishi (2000)
. Nucleotide sequencing reactions were carried out using the Taq dye deoxy terminator sequencing kit (Applied Biosystems, Foster, California, USA). The sequencing primers were as follows: (1) 5'-GGT ATT CAT GTT TGG GA-3' and 5'-TAT CCG CAT TCA TCA CAA A-3' for the rbcL-accD region; (2) 5'-TGC CTT ACC ACT CGG CCA T-3' and 5'-GTA GAT ATT CCC TCA TTT CC-3' for the trnC-rpoB region; (3) 5'-GGG GTT GCT AAC TCA ACG G-3' and 5'-AAC TAG TCG GAT GGA GTA G-3' for the trnK/matK region. Sequences were determined using a 373 A DNA sequencer (Applied Biosystems).
Data analyses
Nucleotide sequences were aligned manually using DNASIS version 3.0 (Hitachi Software Engineering, Tokyo, Japan), with manual modifications to minimize the number of gaps. Aligned sequences in the NEXUS files were analyzed with DnaSP version 3.00 (Rozas and Rozas, 1999
) for estimating polymorphisms, the number of polymorphic sites (Pn) and the nucleotide diversity (
) (Nei and Li, 1979
). We also used DnaSP version 3.00 to estimate the number of net nucleotide substitutions between two populations (DA) (Nei, 1987
). These measures of variation were originally defined for populations; however, we used them for groups of individuals representing populations.
Phylogenetic relationships were inferred by the maximum parsimony (MP) analysis that was performed using PAUP 4.0b2 (Swofford, 1999
). All informative substitutions were used in the analyses, and indels were treated as missing data in both methods. An heuristic search was carried out 100 times with random-addition sequence (RANDOM) and tree bisection-reconnection (TBR) branch swapping. We also examined phylogenetic relationships by the neighbor-joining (NJ) method (Saitou and Nei, 1987
) using PAUP. The number of nucleotide substitutions per site was estimated by Kimura's (1980)
two-parameter method and used to estimate the genetic distance. PAUP was also used to perform bootstrap analyses to estimate the relative support for clades (Felsenstein, 1985
). Bootstrap values were calculated from 1000 replicates using a heuristic search with the simple-addition sequence (SIMPLE) and TBR branch swapping. To assess congruence between data from the three regions of cpDNA and the combined data, we conducted the incongruence length difference (ILD) test (Farris et al., 1994
), as implemented in the partition homogeneity test in PAUP version 4.0b21. The analysis was conducted with 100 replicates using a heuristic search strategy.
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RESULTS |
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TOPABSTRACTINTRODUCTIONMATERIALS AND METHODSRESULTSDISCUSSIONLITERATURE CITED |
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The nucleotide diversity () among the accessions of F. cymosum was 0.00260, 0.00311, and 0.00304 in the three regions, respectively (Table 2). The highest value of 0.00502 was observed in the 3' intron of trnK, and the lowest value of 0.00113 was observed in the 5' intron of trnK. The values for the coding regions in the accD (0.00331) and matK (0.00418) genes were higher than the corresponding value for the associated spacer regions (0.00288 and 0.00113, respectively). The value for synonymous sites was 3.6 and 1.9 times higher than that of nonsynonymous sites in the accD and matK genes, respectively. Comparing diploids and tetraploids of F. cymosum, the respective values for diploid and tetraploid populations were 0.00340 and 0.00204 in the rbcL-accD and the associated spacer region, 0.00283 and 0.00315 in the trnC-rpoB spacer, and 0.00356 and 0.00315 in the trnK/matK region (Table 2).
Fagopyrum tataricum
The total number of polymorphic and informative sites within the species was only four. No polymorphic character was detected in the 1.1-kilobase (kb) rbcL-accD region and its associated spacer. Three out of four polymorphic sites were detected in the trnC-rpoB spacer region. One of the three polymorphic sites in this region was a parsimonious informative character. All the values for F. tataricum (0–0.00094) were lower than the corresponding values (0.00113–0.00502) for F. cymosum (Table 2). Fagopyrum tataricum had no length variation in the three regions.
Phylogenetic relationships
A heuristic search found the shortest trees based on the site-change data for each of the three regions in the cpDNA. The number of trees retained and characteristics of the trees are briefly summarized in Table 3 (trees themselves are not shown). All data sets exhibited low homoplasy levels (high consistency indexes and high retention indexes). The number of polymorphic sites Pn and the nucleotide diversity values shown in Table 2 varied considerably among the three genomic regions. However, the results of the pairwise ILD test for a comparison of the three regions vs. the combined data showed nonsignificant heterogeneity, meaning that little homoplasy arises when the data are combined. The phylogenetic relationships of the tree produced from the combined data were similar to the topology of the tree based on each region. The bootstrap probabilities were increased by combining the three data sets (see Table 3), and the same was true in NJ tree (data not shown). Therefore, we use the combined data and the trees produced from these data for further discussion. Figure 3 shows 1 of the 20 trees reconstructed using the combined data. The branches that collapsed in the strict consensus of 20 shortest trees are shown by dashed lines. As shown in Fig. 3, F. cymosum consists of two major clades. All reconstructed trees showed that the phylogenetic relationships within F. cymosum coincide with the geographic locations of the accessions; one consists of the accessions from Tibet and the Himalayan hills, Nepal, Bhutan, and India, including the accessions of F. tataricum (Tibet-Himalayan clade), and the other consists of the accessions from Yunnan and Sichuan provinces of China and Thailand (Yunnan-Sichuan clade). The topology of the combined NJ tree (not shown) was similar to the most parsimonious tree, except the branches marked by asterisks. Furthermore, the combined tree (Fig. 3) shows that tetraploid accessions of F. cymosum apparently are not monophyletic.
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DISCUSSION |
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TOPABSTRACTINTRODUCTIONMATERIALS AND METHODSRESULTSDISCUSSIONLITERATURE CITED |
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; Fujii et al., 1997
, 1999
; Yasui and Ohnishi, 1998a
; Segraves et al., 1999
; Widmer and Baltisberger, 1999
; Inamura et al., 2000
; Ohsako and Ohnishi, 2000
, 2001
).
The evolutionary rates of coding and noncoding regions differed in this study (Table 2). Compared to noncoding regions, the accD and matK genes had an unexpectedly high evolutionary rate. Yasui and Ohnishi (1998a)
first noticed the high evolutionary rate of the accD gene in Fagopyrum and suggested that a weak selection constraint exists on this gene. A similar result was obtained for the accD gene in F. cymosum (Table 2). Cuenoud et al. (2002)
found that in the Caryophyllales the matK gene has a high proportion of amino-acid-changing substitutions. Ohsako and Ohnishi (2001)
also pointed out a high ratio of nonsynonymous changes in the matK gene of F. leptopodum. The ratio of nonsynonymous changes to synonymous changes in the matK gene was higher than in the accD gene, and the evolutionary rate of matK was 1.3 times higher than that of accD in F. cymosum. These results suggest that a less functional constraint may exist not only in the accD gene but also in the matK gene. Recently, noncoding regions of the cpDNA genome have been used to study phylogenetic relationships at lower taxonomic levels because of their relatively rapid evolutionary rate (e.g., Morton and Clegg, 1993
; Johnson and Hattori, 1996
; Kelchner and Wendel, 1996
; Sang et al., 1997
; Small et al., 1998
). The present study indicates that the accD and matK genes have a high evolutionary rate and would therefore provide potentially useful phylogenetic resolution within a species.
Multiple origins of tetraploid Fagopyrum cymosum
A polyphyletic origin for tetraploid F. cymosum was first proposed based on nucleotide sequence analyses of cpDNA (Yasui and Ohnishi, 1998a
). Allozyme analyses in F. cymosum also supported this hypothesis (Yamane and Ohnishi, 2001
). Furthermore, because the tree in Fig. 3 shows that tetraploid accessions are not monophyletic, tetraploid F. cymosum apparently has arisen allopatrically from a diploid progenitor at least twice—in the Tibet-Himalayan and Yunnan-Sichuan regions.
Autopolyploids have generally been considered much less prevalent in nature than allopolyploids (reviewed by Stebbins, 1950
). Ramsey and Schemske (1998)
claimed that autopolyploids in nature are much more common than recognized in crossing experiments. However, autopolyploids have been reported less frequently than allopolyploids because of the difficulty in detecting them (Ramsey and Schemske, 1998
). Furthermore, until recently most polyploid species have been thought to have a single origin. Molecular phylogenetic studies, however, suggest that most polyploid species are polyphyletic (Soltis and Soltis, 2000
). In fact, several examples of polyphyletic autopolyploid species have been reported, e.g., Heuchera micrantha (Saxifragaceae) by Soltis et al. (1989)
; Heuchera grossulariifolia (Saxifragaceae) by Wolf et al. (1990)
and Segraves et al. (1999)
; Draba norvegica (Brassicaceae) by Brochmann and Elven (1992)
; and Plantago media (Plantaginaceae) by Van Dijk and Bakx-Schotman (1997)
.
On the basis of karyotypic analyses, Gohil and Rathar (1983)
proposed that F. cymosum in Kashmir is an autotetraploid. Yamane and Ohnishi (2001)
demonstrated tetrasomic segregation of allozymes in tetraploids, which implies that tetraploid F. cymosum may be an autopolyploid. These findings are consistent with the present report that the putative autotetraploid F. cymosum had multiple origins.
Levin (1983)
argued that polyploids might have wider ecological niches than their diploid progenitors because of their increased genetic and biochemical diversity. Tetraploid F. cymosum may have extended its habitat after polyploidization, so that tetraploid F. cymosum now has a wider range than its diploid counterpart (see Fig. 1). Ohnishi (1998)
found a similar phenomenon in F. gracilipes; tetraploid F. gracilipes has more colonizing ability and hence a wider range than its diploid progenitor, F. capillatum.
Genetic diversity within Fagopyrum cymosum
The genetic relationships of F. cymosum populations in the phylogenetic tree (Fig. 3) coincided with the geographic location of these populations. The same result was obtained from an analysis of allozyme variation (Yamane and Ohnishi, 2001
).
The phylogenetic tree (Fig. 3) shows two major clades in F. cymosum: a Tibet-Himalayan clade and Yunnan-Sichuan clade. Eight nucleotide substitutions in the three cpDNA regions divide F. cymosum into the two clades, and the 7-bp indel in the trnC-rpoB spacer region also supports these two clades. How did this intraspecific divergence occur? The Hengduanshan mountains, which span three large rivers (Nu River, Lancang River, and Jinsha River) on the eastern edge of the Tibetan Plateau, clearly separate F. cymosum into the two groups (see Fig. 1). When did these two groups differentiate? The divergence time, T, for two groups is given by T = DA/2
(Nei, 1987
), where is the rate of nucleotide substitution per site per year. The number of net nucleotide substitutions (DA) between the Tibet-Himalayan clade and Yunnan-Sichuan clade was 0.00359 for the matK-gene-coding region. For the rbcL gene of dicots, is approximately 1.3 x 10–9 substitution · synonymous site–1 · yr–1 (Zurawski and Clegg, 1987
; Clegg, 1993
). The number of different nucleotide sequences per site in matK was approximately 3.1-fold greater than that in the rbcL gene in 25 Saxifragaceous taxa (Johnson and Soltis, 1995
). Hence, we may estimate as 4.0 x 10–9 substitution · synonymous site–1 · yr–1. Because the substitution rate at synonymous sites in the matK gene was 1.9 times higher than that at nonsynonymous sites (Table 2), is estimated to be 2.1 x 10–9 substitution · nonsynonymous site–1 · yr–1. As a result, we obtained a putative divergence time of 0.70 million years ago (Mya).
The Himalayan Range and the adjacent Tibetan Plateau, including the Hengduanshan mountains, constitute an exceptional topographic anomaly as a result of the collision of Indian and Asian plates. Hsü (1978)
and Li et al. (1979)
insisted a hypothesis of the recent uplift (Late Pliocene and Pleistocene) of this region. However, Fort (1996)
and other authors claimed that the uplift of Tibet-Himalayan ensemble was probably ended by Late Tertiary. Our estimated divergence period (0.7 Mya) might support the recent uplift (Late Pliocene and Pleistocene). Zhou (1985)
argued that the great uplift of the Qinghai-Xizang Plateau occurred in the Late Pliocene and Pleistocene and the global climate around Tibet turned cold and dry. These changes in climate and landform might have caused geographic isolation and subsequently led to genetic divergence between the populations of F. cymosum to the east and west of the Hengduanshan mountains.
Speciation of Fagopyrum tataricum from F. cymosum
Fagopyrum cymosum is morphologically similar to cultivated common buckwheat (F. esculentum); hence, it was once considered to be the wild ancestor of common buckwheat (Campbell, 1976
), until the discovery of F. esculentum Moench subsp. ancestrale Ohnishi (the true wild ancestor of common buckwheat) by Ohnishi (1991)
. Kishima et al. (1995)
first clarified that F. cymosum is more closely related to F. tataricum than to F. esculentum based on a survey of chloroplast DNA restriction sites. Yasui and Ohnishi (1998a
, b
) confirmed this conclusion by observing a synapomorphic deletion in the F. cymosum-F. tataricum clade. Figure 3 shows that F. tataricum is monophyletic and entirely within the Tibet-Himalayan clade of F. cymosum. Thus, we may conclude that F. tataricum speciated from a population of F. cymosum in the Tibet-Himalayan area. Harrison (1991)
represented a model of speciation, i.e., the paraphyletic genealogies reflect a mode of speciation in which descendant species arose from one of several populations of the ancestral species. A low level of cpDNA sequence diversity within F. tataricum probably indicates that self-fertilizing F. tataricum has been relatively recently speciated from self-incompatible F. cymosum, by breaking of the self-incompatible system and rapid reproductive isolation from the progenitor. An alternative hypothesis of speciation of F. tataricum by introgression of chloroplast genome as a result of introgressive hybridization is not supported for the following reasons: difficulty of interspecific crosses between F. cymosum and F. tataricum and same interspecific relationships obtained by nuclear ITS phylogeny (Yasui and Ohnishi, 1998b
).
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FOOTNOTES |
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2 Author for correspondence (m52297{at}mbox.kudpc.kyoto-u.ac.jp
)
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