| HOME | HELP | FEEDBACK | SUBSCRIPTIONS | ARCHIVE | SEARCH | TABLE OF CONTENTS |
|
|
|
|||||||
|
|||||||||
Systematics |
Department of Crop Sciences, University of Illinois, 1102 South Goodwin Avenue, Urbana, Illinois 61801 USA
Received for publication December 21, 2000. Accepted for publication April 3, 2001.
 |
ABSTRACT |
|---|
 TOP ABSTRACT INTRODUCTIONMATERIALS AND METHODSRESULTSDISCUSSIONLITERATURE CITED |
|---|
Key Words: cpDNA • Glycininae • Leguminosae • molecular phylogeny • rps16 intron
|
INTRODUCTION |
|---|
|
TOPABSTRACTINTRODUCTIONMATERIALS AND METHODSRESULTSDISCUSSIONLITERATURE CITED |
|---|
). Lackey (1981)
recognized that Glycininae is a very natural group with the exception of Teramnus, Diphyllarium, and Mastersia but is confused with Diocleinae due to a paucity of unique characters to define the subtribe. Almost all Glycininae are distributed in the Old World with the exceptions of Amphicarpaea bracteata (L) Fernald, several species of Teramnus, and Cologania (Table 1; Lackey, 1981
).
|
recognized 16 genera of Glycininae, which he subdivided into two groups, Glycine and Shuteria, based on morphological alliances. The Glycine group is characterized by the presence of bristly fruits, often-black nodes, and generally rough seeds. This group is distributed in the Old World with the exception of Teramnus, which has pantropical distribution. The Shuteria group represents all other Glycininae and is characterized by the presence of smooth-surfaced seeds with long and slender funiculi, thin ovary walls, united upper calyx lobes and long petal claws (Lackey, 1977a
).
Since subtribe Glycininae was established by Bentham (1837)
, there has been controversy in delimiting the boundary of subtribe Glycininae. In order to resolve this taxonomic problem, there have been several attempts. For instance, Viviani et al. (1991)
conducted a phenetic analysis of tribe Phaseoleae. They scored 126 morphological characters and included 11 taxa from 8 genera of Glycininae sensu Polhill (1994)
. Their results revealed that Glycininae was not clustered into a single group because several taxa of Clitoriinae, Diocleinae, and Kennediinae were included within the Glycininae clade. They suggested that the most similar genus to Glycine was Pueraria, a genus that has been considered primitive among Glycininae by Lackey (1977a)
owing to several primitive characters, such as branched or stipule-bearing inflorescences, woody habit, fish-poison chemicals, and more or less attached vexillary filaments. Viviani et al. (1991)
produced a similar result from the sero-systematic study using three taxa from three genera of Glycininae sensu Polhill (1994)
.
Phylogenetic relationships were investigated within tribe Phaseoleae based on chloroplast DNA (cpDNA) restriction-site mapping of the inverted repeat regions (Doyle and Doyle, 1993
; Bruneau, Doyle, and Doyle, 1994
). Glycininae was represented by 12 genera from Lackey's subtribe Glycininae. The cpDNA restriction study suggested that Glycininae sensu Lackey (1981)
are not monophyletic, with Calopogonium and Pachyrhizus of subtribe Diocleinae arising within the Glycininae clade and with Shuteria placed outside of Glycininae. Moreover, the sister genus (or genera) to Glycine within Glycininae was not clearly resolved. On the basis of these restriction site-based phylogenies, Polhill (1994)
transferred Calopogonium and Pachyrhizus from the subtribe Diocleinae sensu Lackey (1977a)
to Glycininae and reorganized 18 genera within Glycininae.
The chloroplast DNA rps16 intron region was used for investigating phylogeny in this study. This region indicated somewhat slower sequence evolution than that of the nuclear ribosomal DNA ITS (internal transcribed spacer) region, which provides a valuable source of data for phylogenetic studies at the species level (Baker, Hedderson, and Dransfield, 2000
). The chloroplast gene rps16, encoding ribosomal protein S16, is found between trnQ and trnK within the large single copy region of the plastid genome of most flowering plants. It is interrupted by a long (790–967 bp [base pair]) group II intron (Shinozaki et al., 1986a
; Hiratsuka et al., 1989
; Neuhaus, Scholz, and Link, 1989
; Sexton, Jones, and Mullet, 1990
; Downie and Palmer, 1992
). Several sequencing studies have discovered that the gene is entirely or partially absent from the chloroplast genomes of Marchantia polymorpha L., Pinus thunbergii Parl., Pisum sativum L., the parasitic Epifagus virginiana (L.) Bart., in some other Leguminosae, and in a few other taxa (Downie and Palmer, 1992
; Doyle, Doyle, and Palmer, 1995
; Oxelman, Liden, and Berglund, 1997
). All examined representatives of Glycininae, however, contain the intron (Doyle, Doyle, and Palmer, 1995
).
Many cytological, chemical, and molecular investigations have been conducted on the cultivated soybean, G. max, because of its economic importance. Morphological and serological studies and phylogenetic investigations of the Phaseoleae have also been done. However, there is no rigorous analysis of phylogenetic relationships within subtribe Glycininae, which would provide broad information to other researchers, such as breeders. Therefore, a study of phylogenetic relationships among the genera of Glycininae is very much needed. Objectives of this study are to (1) identify the most closely related genus or genera to the soybean; (2) investigate intergeneric relationships within the subtribe; and (3) compare the phylogenetic hypothesis inferred from this study with Polhill's and Lackey's taxonomic treatments.
|
MATERIALS AND METHODS |
|---|
|
TOPABSTRACTINTRODUCTIONMATERIALS AND METHODSRESULTSDISCUSSIONLITERATURE CITED |
|---|
|
with slight modification. Fresh leaf tissues were ground using liquid nitrogen in a 1.5-mL microcentrifuge tube. Additional alcohol precipitation was followed. Herbaria materials (100 mg) were ground in a preheated mortar and pestle using the CTAB (hexadecytrimethylammonium bromide) procedure of Doyle and Doyle (1987)
. Proteins were removed with chloroform : isoamyl alcohol (24 : 1), followed by a final purification using equilibrium density-dependent ultracentrifugation in cesium chloride-ethidium bromide gradients. Purified DNAs were stored at –20°C until use.
PCR amplification of rps16 intron regions and sequencing
The intron region of rps16 in tobacco is illustrated in Fig. 1. The rps16 intron is 860 bp in size in tobacco cpDNA (Shinozaki et al., 1986b
). The primers 1 (3' exon primer: 5'-CTGTAGGTTGAGCNCCTCGTT-3') and 3 (5' exon primer: 5'-AAACGATGTGGTAGAAAGCA-3') were designed with some alteration specific for Leguminosae from similar degenerate sequences provided by S. Downie [cf. primers 3' exon rps16 (5'-CCTGTAGG(C/T)TGNGCNCC(C/T)TT-3') and 5' exon rps16 (5'-AAACGATGTGGNAGNAA(A/G)CA-3')] and sequences available from GenBank. Italicized sequences of S. Downie's primers were modified to boldface italicized sequences specific to Leguminosae. The primer 2 (3' intron primer: 5'-ATTTCATTT(A/T)TTGAGTGGTCT-3') was designed by choosing almost invariable regions among sequences of rps16 intron from taxa sequenced with only primers 1 and 3. Primers were synthesized by the W. M. Keck Center for Comparative and Functional Genomics (University of Illinois, Urbana, Illinois, USA). The cpDNA rps16 intron region for 34 taxa of Glycininae was amplified by the PCR (polymerase chain reaction) technique using primers 1 and 3 in an equimolar ratio. Primer 2 was used if needed. One hundred microliters PCR reactions contained (in order of addition) 78.6 µL of sterile water, 10.0 µL of 10 x Taq polymerase reaction buffer (Gibco BRL Life Technologies, Gaithersberg, Maryland, USA), 2.0 µL of dNTP mixture containing 10 mmol/L of each nucleotide (final concentration of 0.2 mmol/L each; Pharmacia Biotech, Piscataway, New Jersey, USA), 3.0 µL of 50 mmol/L MgCl2 (final concentration of 1.5 mmol/L), 2.0 µL (8 pmol) each of the two 3' exon and 5' exon primers, 2.0 unit of Taq polymerase (Gibco BRL Life Technologies) and 2.0 µL (40–50 ng) of template DNA. The amplification was performed using a thermocycler (PTC-100, MJ Research, Watertown, Massachusetts, USA) that was set to run at 95°C for 3 min for initial denaturation followed by 40 cycles of 94°C for 30 sec to denature the double-stranded template DNA, 50°C for 1 min to anneal primers to single-stranded template DNA, and 72°C for 1 min 30 sec to extend primers. To allow completion of unfinished DNA strands and to terminate the PCR reaction, a 5-min 72°C extension period followed. Successful PCR amplifications resulted in a single DNA band in a 1.25% agarose gel.
|
The DNA was sequenced using an Applied Biosystems (Foster City, California, USA) 377 automated DNA sequencer with Stretch upgrade at the W. M. Keck Center for Comparative and Functional Genomics. Cycle sequencing reactions were carried out in a PTC-100 thermocycler (MJ Research) using purified PCR products, AmpliTaq® DNA polymerase, and fluorescent dye-labeled terminators (Perkin Elmer, Norwalk, Connecticut, USA). The reaction conditions were modified to contain 5% dimethylsulfoxide (DMSO). The sequencing products, after purification with Centri-Sep spin columns (Princeton Separations, Adelphia, New Jersey, USA), were resolved by electrophoresis in 4% acrylamide gels.
Phylogenetic analyses
The rps16 intron DNA sequences were aligned manually and gaps were positioned to minimize nucleotide mismatches. Some regions were difficult to align because of simple nucleotide repeats. These ambiguously aligned sequences were not included in the phylogenetic analysis (see Appendix 2 in Lee, 2000
). Pairwise nucleotide differences of unambiguously aligned positions were determined using the distance matrix option in PAUP* version 4.01.beta (Swofford, 1998
). In the phylogenetic analysis, all gaps were treated as missing data. Transition/transversion ratios over all maximally parsimonious trees were calculated using MacClade version 3.01 (Maddison and Maddison, 1992
). The rps16 intron DNA sequences have been submitted to GenBank (accession numbers in Table 2). All data matrices are available upon request.
Cladistic analyses were performed to find the shortest trees using PAUP* version 4.01.beta (Swofford, 1998
) on a Power Macintosh 7100/80 computer. A heuristic search was carried out with 100 random addition replicates and tree bisection-reconnection (TBR) branch swapping. The options with MULPARS, STEEPEST DESCENT, COLLAPSE, and ACCTRAN optimization were selected to search for the most parsimonious trees. Bootstrap analysis (Felsenstein, 1985
) of 100 replicates was performed using heuristic option, simple addition, TBR branch swapping, and MULPARS to evaluate the degree of support for each branch. Decay analysis (Bremer, 1988
) was conducted up to four steps greater than the most parsimonious. The search was limited to four additional steps because of the computational constraints. The amount of phylogenetic information in the parsimony analyses was estimated using the consistency index (Kluge and Farris, 1969
), retention index (Farris, 1989
), and g1 statistic (Hillis, 1991
; Hillis and Huelsenbeck, 1992
). The g1 statistic was achieved by calculating the tree length distribution of 100 000 random parsimony trees using PAUP'S RANDOM TREES selection, and was used to assess the amount of nonrandom structure in the data. In order to evaluate the distribution of insertion and deletion events (indels) against a phylogeny constructed using nucleotide substitutions, each indel was optimized visually onto one of the resultant minimal-length trees.
Besides parsimony analysis, distance trees based on rps16 intron sequencing data were constructed using the neighbor-joining method (Saitou and Nei, 1987
) implemented using the Neighbor program in Felsenstein's (1993)
phylogeny inference package (PHYLIP, version 3.5s). Distance matrices were calculated using the DNADIST program of PHYLIP and the numbers of nucleotide substitutions (excluding gaps) were estimated using the two-parameter method of Kimura (1980)
. Transitions were weighted relative to transversions, with a transition/transversion (ts/tv) rate ratio of 0.62 inferred from the parsimony analysis used to construct the neighbor-joining tree. A bootstrap analysis of these data was carried out using 100 resampled data sets, which were generated using the SEQBOOT program prior to calculating the distance matrices and neighbor-joining trees. PHYLIP's CONSENSE program was then implemented in order to construct a strict consensus tree.
|
RESULTS |
|---|
|
TOPABSTRACTINTRODUCTIONMATERIALS AND METHODSRESULTSDISCUSSIONLITERATURE CITED |
|---|
|
For the proper alignment of rps16 intron sequences, the introduction of 48 gaps was required. The length of the gaps ranged from 1 to 23 bp (averaging 4 bp), with the largest representing an insertion in Glycine tabacina. Of these 48 gaps, 21 were potentially informative for parsimony analysis and the remainder were autapomorphic. Those gaps are randomly scattered throughout the sequences.
Phylogenetic analyses
Parsimony analysis of 34 rps16 intron sequences using equally weighted character states resulted in 12 parsimonious trees; the strict consensus of these trees, with accompanying bootstrap and decay values, is presented in Fig. 2. These trees each have a length of 402 steps, consistency indices of 0.627 (excluding uninformative characters) and 0.769 (including uninformative characters), and a retention index of 0.751. Bootstrap values ranged from 29 to 100%. The g1 statistic calculated from 100 000 random trees was –0.784 (Table 3). This indicates that the tree length distribution was significantly skewed to the left, suggesting that there is a strong phylogenetic signal in the data (Hillis and Huelsenbeck, 1992
). One of these 12 trees was arbitrarily selected in order to show the number of nucleotide substitutions supporting each branch, as optimized by ACCTRAN in PAUP (Fig. 3), and the distribution of the 21 phylogenetically informative length mutations. Six of 21 potentially informative length mutations are uniquely synapomorphic (represented by solid bars in Fig. 3). Sixteen homoplastic indels have occurred twice (indels 1, 5, 18, 27, 30, 31, 34, 40, 45, 47, and 48), three times (indels 22, 29, 30, and 42) or four times (indel 32). These homoplastic indels are represented by open bars in Fig. 3. Character numbers are as in Appendix 2 in Lee (2000)
; Appendix 2 is available upon request.
|
|
|
Glycininae is not monophyletic. Pachyrhizus and Calopogonium of subtribe Diocleinae sensu Lackey (1981)
show a close relationship to Pueraria phaseoloides var. phaseoloides or Cologania, respectively. Glycininae expanded to include the two genera above is tentatively divided into three branches (I, II, and III) but two of them consist entirely of Pueraria wallichii (II) or of Mastersia (III). The large clade (I) comprising the rest of the examined taxa is supported by a relatively low bootstrap and low decay values (44% and 1, respectively) (Fig. 2). Shuteria, sister taxon to all remaining members within this clade in the parsimony showed a sister relationship with Mastersia and Pueraria wallichii in the neighbor-joining analysis, although bootstrap supports its weak relationship (Fig. 4). The remaining members are temporarily divided into three subclades, designated by groups 1, 2, and 3 (Figs. 2–4). The first of these three subclades consists of Teramnus, Glycine, Amphicarpaea, Pueraria pulcherrima, P. montana var. lobata, and Nogra. Teramnus appears to be the genus most closely related to Glycine; Amphicarpaea is sister to this clade. The second subclade, comprising Teyleria, Neonotonia, Pseudovigna, Pseudeminia, Pachyrhizus, Pueraria stricta, and P. phaseoloides var. phaseoloides, shows a sister relationship to group 1. The last subclade consists of Cologania, Calopogonium, and Dumasia. The monophyly of group 1 is supported relatively strongly by the parsimony tree (80%), whereas the monophyly of groups 2 and 3 is supported weakly (29 and 45%, respectively). Distance tree inferred from the neighbor-joining analysis of rps16 intron sequence data, with ts/tv rate ratio of 0.62, is not congruent with the maximally parsimonious trees. The most striking difference between the neighbor-joining and parsimonious trees is that two clades (Groups 2 and 3) constructed from parsimony were not supported by the similarity-based analysis. A cluster consisting of two species of Pueraria (P. stricta, P. phaseoloides var. phaseoloides), Teyleria, Neonotonia, and Pachyrhizus is basal to Group 1. Other members of Group 2 (Pseudeminia and Pseudovigna) collapsed with Dumasia, which were assigned into Group 3 in the parsimony analysis. A cluster comprising Cologania and Calopogonium is basal within clade I.
The monophyly of Glycininae sensu Polhill (1994)
, representing 15 genera investigated here, was supported. Several of the Lackey's (1981)
genera were supported by their monophyly. The genus Pueraria is not monophyletic because the five species of Pueraria examined occur a minimum of four times throughout the tree. For example, only two species, P. pulcherrima and P. montana var. lobata, formed a clade, whereas the remaining three species examined here were scattered elsewhere in the trees.
|
DISCUSSION |
|---|
|
TOPABSTRACTINTRODUCTIONMATERIALS AND METHODSRESULTSDISCUSSIONLITERATURE CITED |
|---|
) suggests that cpDNA in Glycininae may be evolving rapidly. Rapid evolution and divergence of cpDNA rps16 introns is consistent with high levels of divergence in the nuclear ribosomal DNA internal transcribed spacer (ITS) regions of Glycininae (J. Lee and T. Hymowitz, unpublished data). We could not compare homologous sequences among genera within Glycininae due to alignment ambiguity of ITS sequences.
Comparison with other classification systems
The phylogeny derived from cpDNA rps16 intron sequences provided does not support Lackey's (1981)
delimitation of Glycininae. He reluctantly added Pachyrhizus and Calopogonium as members of Diocleinae because he had no hypotheses for a better relationship. However, Polhill (1994)
expanded the boundary of the subtribe, including Pachyrhizus and Calopogonium on the basis of the results of a restriction-site study in the conserved, inverted repeat region of the chloroplast genome (Doyle and Doyle, 1993
; Bruneau, Doyle, and Doyle, 1994
). The cpDNA restriction-site data suggested that Calopogonium and Pachyrhizus (both Diocleinae) are sister taxa and that they are closely related to members of Glycininae. The rps16 intron studies support the inclusion of these two genera within Glycininae, but do not yield the same sister relationship. The close relationships of these two genera with other taxa of Glycininae are congruent with phytochemical data (Ingham, 1990
). On a survey of phytoalexins within the tribe Phaseoleae, he reported that Calopogonium and Pachyrhizus produce phytoalexins sufficiently distinct from those of other Diocleinae to suggest that these two genera were closely related to Glycininae, which also produce phytoalexins.
The differences between the cpDNA restriction site and rps16 intron phylogenies are largely attributable to the number of taxa included in each study. More inclusion of taxa here, such as Mastersia and Pueraria wallichii, affects resolution of intergeneric relationships within Glycininae, which were uncertain in the cpDNA restriction-site derived phylogeny. Detailed information of intergeneric relationships is described in the following section.
Intergeneric relationships within Glycininae inferred from the phylogenetic analysis
On the basis of the rps16 intron phylogeny, subtribe Glycininae (Lackey, 1981
) and two genera (Pachyrhizus and Calopogonium) of subtribe Diocleinae are temporarily divided into three major branches. One branch (I) comprises most of the examined taxa and each of the two other branches consists of a single member of Pueraria wallichii (II) or Mastersia (III) (Fig. 2). This expanded assemblage (I), including two genera, Pachyrhizus and Calopogonium, parallels the subtribe Glycininae sensu Polhill (1994)
and is divided tentatively into three groups. Teramnus is revealed as the most closely related genus to Glycine with moderate bootstrap value support (69%), although the decay value of 1 does not strongly support this relationship. Traditionally, either Teramnus was confused with Glycine or alliance between these two genera was suggested by shared characters, such as hairy fruits, rough seeds, small flowers, and often-sculptured seeds (Verdcourt, 1970
; Lackey, 1977a
). Lackey (1977a)
, however, thought these similarities were superficial because of their different distribution patterns (Table 1). The pantropical distribution of Teramnus is different from the mostly Asiatic distribution of the remaining Glycininae. Also, Teramnus is anomalous from other members of subtribe Glycininae in having alternately aborted or sterile anthers, and pods with a hooked, persistent style (Verdcourt, 1970
). The somatic chromosome number (x = 7) reinforces its uniqueness (Krukoff and Barneby, 1981
) compared with other members of Glycininae sensu Polhill, which have x = 9, 10, or 11 (1994).
Amphicarpaea has been thought to have the closest relationship to Cologania, supported by the fact that it shares cleistogamous flowers with this genus (Turner and Fearing, 1964
). Furthermore, Taubert (1894)
incorporated Cologania into Amphicarpaea. However, Fearing (1959)
, on the basis of morphological and cytological data, concluded that Cologania should be treated as an independent genus, but closely related to Amphicarpaea. He discussed the generic position of Amphicarpaea, particularly with the respect to its close relationship with Cologania, suggesting their common origin from some pantropical ancestors. Most taxonomists, including Lackey (1977a)
, have had little doubt regarding their close relationship. Interestingly, however, Amphicarpaea was sister to the clade comprising Glycine and Teramnus rather than to Cologania in this study. Two species of Amphicarpaea (A. edgeworthii, which has distribution in Asia, and A. bracteata, which has distribution in North America) were regarded as almost identical by Bentham (1858)
and Turner and Fearing (1964)
. Phylogenies investigated here, however, support that these two taxa should stand as separate species. Relatively high difference in sequences (36 bp difference between these two species: Appendix 2 in Lee, 2000
) and 1.31% pairwise sequence distance support their separate identity.
Pueraria is the largest and most problematic genus in Glycininae. Pueraria was suggested as the most closely related genus to Glycine (Lackey, 1977a
). On the basis of morphological characters, such as number of flowers per node, types of stipule and calyx, callosities on the vexillum, and pod types, Lackey (1977a)
tentatively reorganized this genus into four groups designated as groups A, B, C, and D (Table 4). The molecular phylogeny partially supports Lackey's (1977a)
grouping of the genus. Five taxa representing the four different groups within Pueraria were distributed four times independently on the phylogenetic trees. The taxonomic position of P. wallichii (group D), which forms a separate branch (II) in the molecular phylogeny (Fig. 2), is consistent with Lackey's claim (1977a, b). He suggested that P. wallichii should be removed from Pueraria based on morphological anomaly and the presence of the free amino acid canavanine. Lackey (1977a)
suggested that those plants belonging to group C also should be removed from Pueraria and allied with Neonotonia and Shuteria because they share some characters of inflorescence, flower, and general habit. The relationship among group C (P. stricta), Teyleria, and Neonotonia supports Lackey's claim, in part. Furthermore, Lackey (1977a)
stated that the plants of Group B were distinct enough to form an independent genus. His opinion is congruent with the result of the molecular phylogeny produced here in the sense that P. phaseoloides var. phaseoloides (Group B) belongs to a clade separate from any other Pueraria species investigated. Later, van der Maesen (1985)
revised this genus into three sections: Pueraria, Schizophyllon, and Breviramulae. He included 17 species as members of Pueraria based upon Lackey's (1977a)
grouping to reach somewhat natural groups of species more closely related to each other than to those in different groups. The molecular phylogeny derived from the rps16 intron sequences does not support his suggestion of a close relationship between P. wallichii and P. stricta, which were included in the section Breviramulae. Our results are more congruent with Lackey's reorganization (1977a) than van der Maesen's (1985)
. To resolve the relationships and definition of Pueraria, more taxa of Pueraria that represent all four groups should be included in a rigorous molecular investigation. The result of our study suggests that Pueraria is not sister to Glycine and is polyphyletic (Figs. 2–4).
|
distinguished the African genus Pseudovigna from Pseudeminia by the presence of dense, adpressed, silvery hairs on the undersurfaces of the leaves, spreading, brown, bristly hairs on the stems and pods, and style differences. Later, Lackey (1977a)
claimed these morphological differences were not significant for separating the monotypic genus Pseudovigna and suggested that Pseudovigna should be congeneric with Pseudeminia. However, the relatively high pairwise-sequence divergence value (3.14%) of rps16 intron sequences between these two genera compared with relatively low pairwise divergence values within the genera except Pueraria (Table 5) probably supports the independence of Pseudovigna. More species of Pseudeminia and of Eminia (not included in this study) should be examined to resolve relationships among these genera. Whether Pseudovigna is congeneric with Pseudeminia or not, strong bootstrap (99% in the strict consensus tree; 100% in the neighbor-joining tree) and decay values (greater than four steps) in the rps16 intron phylogeny support the close relationship between these two genera. Verdcourt (1970)
and Lackey (1977a)
suspected that these two genera and Eminia might be derivatives from Asian Pueraria-like ancestors due to morphological alliance, such as the dark, prominent, hair bases, the presence of lower alae spurs, the often-congested inflorescences, and the lobed leaflets. This study does not support a close relationship between these genera and any of the species of Pueraria examined.
|
). Traditionally, Cologania was closely related to Amphicarpaea (Harms, 1911
; Fearing, 1959
; Lackey, 1977a
) or was even merged into Amphicarpaea (Taubert, 1894
).
Bentham (1837, 1865)
, with some doubt, placed Pachyrhizus in subtribe Phaseolinae because of the presence of a stylar indument. He placed Calopogonium in Galactiinae (1865). Lackey (1977a)
, insisting that the stylar pubescence in Pachyrhizus is due to the extension of ovary hairs rather than to stylar hairs, placed this genus alongside Calopogonium in subtribe Diocleinae. Pachyrhizus is unique in stigma structure in having a median to subterminal globular process on the adaxial side. These two characters, together with its tuberous roots, define the genus as a homogeneous entity (Sørensen, 1988
). Since Lackey's treatment (1977a), most taxonomists have excluded Pachyrhizus and Calopogonium from Phaseolinae and Galactiinae, respectively (Baudet, 1978
; Maréchal, Mascherpa, and Stainier, 1978
; Lackey, 1981
; Sørensen, 1988
). Lackey (1977a, 1981)
, however, questioned whether these genera might be improperly placed in Diocleinae on the basis of some anomalous morphological characters, such as the peculiar stigma-style structure of Pachyrhizus and the anomalous somatic chromosome number (2n = 36) of Calopogonium. Baudet (1978)
included Pachyrhizus in Glycininae. The serological study conducted by Viviani et al. (1991)
concluded that Calopogonium was improperly placed in the Diocleinae. More recently, Doyle and Doyle (1993)
suggested that these two genera should be placed within Glycininae on the basis of a restriction-site mapping study of the cpDNA inverted repeat region.
Shuteria does not show close relationships with any of the genera that Lackey (1981)
included in the Shuteria group (Amphicarpaea, Cologania, Dumasia, Teyleria, Neonotonia, and Mastersia). The unclear relationship of Shuteria to other genera of Glycininae agrees with a phylogeny derived from restriction-site mapping of the cpDNA inverted repeat region (Doyle and Doyle, 1993
; Bruneau, Doyle, and Doyle, 1994
). According to their studies, Shuteria showed a sister relationship with the Kennediinae/Desmodieae clade. On the other hand, the phylogenetic study based on rps16 intron sequences suggests that Shuteria is a sister to the rest of Glycininae investigated (with the exception of Pueraria wallichii and Mastersia, which are not in the neighbor-joining tree). Since no taxa of Kennediinae or Desmodieae was included in this study, the taxonomic position and relationship of Shuteria with other genera remains uncertain until additional genera of Kennediinae and Desmodieae are considered.
Since Bentham (1865)
placed Mastersia near Calopogonium in Galactiinae, there has been controversy regarding the relationship of Mastersia. One year later, Bentham (1866)
associated the genus with Pueraria and Dioclea on the basis of shared common characters in habit and the general structure of the flower. Subsequently, Taubert (1894)
and Harms (1911)
supported Bentham's treatment (1866). On the other hand, Lackey (1977a)
reluctantly assigned Mastersia to the Shuteria group within Glycininae because of strong resemblance between the reniform seeds with a long, thin funiculus of Mastersia and those of Shuteria. Dividing tribe Phaseoleae into three subtribes, Baudet (1978)
treated Mastersia in Glycininae. Subsequently, his system was supported by Welzen and Hengst (1994)
. However, the molecular phylogeny investigated here does not support a sister-group relationship between Mastersia and Shuteria except in the neighbor-joining tree, which shows relatively weak support between the two genera (32% bootstrap value). Both genera are near basal in Glycininae, but the relationships among them, Pueraria wallichii and the clade comprising other genera of Glycininae, are ambiguous. Mastersia differs from other genera of Glycininae in having indehiscent pods with vertical seeds.
In order to increase resolution among the basal nodes of Glycininae phylogeny and intergeneric relationships within the subtribe, it will be necessary to study representatives of tribe Phaseoleae and seek information from DNA sequences evolving more slowly than those of the rps16 intron. Rearrangement of tribe Phaseoleae, which is not monophyletic (Doyle and Doyle, 1993
; Bruneau, Doyle, and Doyle, 1994
) may be also needed to better understand phylogenetic relationships within the subtribe Glycininae. The results presented herein represent an initial attempt to find closely related genera (genus) to the soybean within Leguminosae subtribe Glycininae. Further investigation within Glycininae will need to be done to confirm the relationship between Teramnus and Glycine.
|
FOOTNOTES |
|---|
2 Author for reprint requests (Tel: 217-333-9454; Fax: 217-333-9817; soyui{at}uiuc.edu
).
|
LITERATURE CITED |
|---|
|
TOPABSTRACTINTRODUCTIONMATERIALS AND METHODSRESULTSDISCUSSIONLITERATURE CITED |
|---|
Baudet J. C. 1978 Prodrome d'une classification générique des Papilionaceae-Phaseoleae. Bulletin du Jardin Botanique National du Belgique 48: 183-220
Bentham G. 1837 Commentaiones de leguminosarum generibus. Sollingeri, Vienna, Austria
Bentham G. 1858 Synopsis of the genus Clitoria. Proceedings of the Linnean Society of London, Botany 2: 33-44
Bentham G. 1865 Genera Plantarum. In G. Bentham and J. D. Hooker [eds.], Leguminosae, 434–600. Reeve & Co., London, UK
Bentham G. 1866 IX. Description of some new genera and species of tropical Leguminosae. Transactions of the Linnean Society of London, Botany 25: 297-320
Bremer K. 1988 The limits of amino acid sequence data in angiosperm phylogenetic reconstruction. Evolution 42: 795-803[CrossRef][ISI]
Bruneau A. J. J. Doyle J. L. Doyle 1994 Phylogenetic relationships in Phaseoleae: evidence from chloroplast DNA restriction site characters. In M. Crisp and J. J. Doyle [eds.], Advances in legume systematics, 309–330. Royal Botanic Gardens, Kew, UK
Downie S. R. J. D. Palmer 1992 Use of chloroplast DNA rearrangements in reconstructing plant phylogeny. In P. S. Soltis, D. E. Soltis, and J. E. Doyle [eds.], Molecular systematics of plants, 14–35. Chapman and Hall, New York, New York, USA
Doyle J. J. J. L. Doyle 1987 A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochemical Bulletin 19: 11-15
Doyle J. J. J. L. Doyle 1993 Chloroplast DNA phylogeny of the Papilionoid legume tribe Phaseoleae. Systematic Botany 18: 309-327[CrossRef][ISI]
Doyle J. J. J. L. Doyle J. D. Palmer 1995 Multiple independent losses of two genes and one intron from legume chloroplast genomes. Systematic Botany 20: 272-294[CrossRef][ISI]
Farris J. S. 1989 The retention index and homoplasy excess. Systematic Zoology 38: 406-407[CrossRef]
Fearing O. S. 1959 A cytotaxonomic study of the genus Cologania and its relationship to Amphicarpaea (Leguminosae–Papilionoideae). Ph.D. dissertation, University of Texas, Austin, Texas, USA
Felsenstein J. 1985 Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39: 783-791[CrossRef][ISI]
Felsenstein J. 1993 PHYLIP (Phylogeny Inference Package), version 3.5s. Distributed by the author. Department of Genetics, University of Washington, Seattle, Washington, USA
Harms H. 1911 Über die Verbreitung der Leguminosen—Gattung Mastersia. Repertorium specierum novarum regni vegatabilis 9: 367-369
Hillis D. M. 1991 Discriminating between phylogenetic signal and random noise in DNA sequences. In M. M. Miyamoto and J. Cracraft [eds.], Phylogenetic analysis of DNA sequences, 278–294. Oxford University Press, New York, New York, USA
Hillis D. M. J. P. Huelsenbeck 1992 Signal, noise, and reliability in molecular phylogenetic analyses. Journal of Heredity 83: 189-195
Hiratsuka J. et al 1989 The complete sequence of the rice (Oryza sativa) chloroplast genome: intermolecular recombination between distant tRNA genes accounts for a major plastid DNA inversion during the evolution of the cereals. Molecular and General Genetics 217: 185-194
Ingham J. L. 1990 Systematic aspects of phytoalexin formation within tribe Phaseoleae of the Leguminosae (Subfamily Papilionoideae). Biochemical Systematics and Ecology 18: 329-343[CrossRef]
Kimura M. 1980 A simple method for estimating evolutionary rates of base substitution through comparative studies of nucleotide sequences. Journal of Molecular Evolution 16: 111-120[CrossRef][ISI][Medline]
Kluge A. G. J. S. Farris 1969 Quantitative phyletics and evolution of anurans. Systematics Zoology 18: 1-32
Krukoff B. A. R. C. Barneby 1981 Chromosomes. In R. M. Polhill and P. H. Raven [eds.], Advances in legume systematics, 307–310. Royal Botanic Gardens, Kew, UK
Lackey J. A. 1977a A synopsis of the Phaseoleae (Leguminosae, Papilionoideae). Ph.D. dissertation, Iowa State Universiy, Ames, Iowa, USA
Lackey J. A. 1977b A revised classification of the tribe Phaseoleae (Leguminosae: Papilionoideae), and its relation to canavanine distribution. Botanical Journal of the Linnean Society 74: 163-178
Lackey J. A. 1977c Neonotonia, a new generic name to include Glycine wightii (Arnott) Verdcourt (Leguminosae, Papilionoideae). Phytologia 37: 209-212
Lackey J. A. 1981 Tribe 19. Phaseoleae DC. (1825). In R. M. Polhill and P. H. Raven [eds.], Advances in legume systematics, 301–327. Royal Botanic Gardens, Kew, UK
Lee J. 2000 Molecular genetics on the genus Glycine: I. Phylogenetic study of the subtribe Glycininae. II. Development of a universal soybean genetic map. Ph.D. dissertation, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
Maddison W. P. D. R. Maddison 1992 MacClade, version 3.0: analysis of phylogeny and character evolution. Sinauer, Sunderland, Massachusetts, USA
Maréchal R. J. M. Mascherpa F. Stainier 1978 Étude taxonomique d'un groupe d'espèces des genres Phaseolus et Vigna (Papilionaceae) sur la base de données morphologiques et polliniques, traités par l'analyse informatique. Boissiera 28: 1-273
Neuhaus H. A. Scholz G. Link 1989 Structure and expression of a split chloroplast gene from mustard (Sinapis alba): ribosomal protein gene rps16 reveals unusual transcrptional features and complex RNA maturation. Current Genetics 15: 63-70[CrossRef][ISI][Medline]
Oxelman B. M. Liden D. Berglund 1997 Chloroplast rps16 intron phylogeny of the tribe Sileneae (Caryophyllaceae). Plant Systematics and Evolution 206: 393-410[CrossRef][ISI]
Polhill R. M. 1994 Classification of the Leguminosae. In F. A. Bisby, J. Buckingham, and J. B. Harborne [eds.], Phytochemical dictionary of the Leguminosae, xxxv–xlvii. Chapman & Hall, New York, New York, USA
Saitou N. M. Nei 1987 The neighbor-joining method: a new method for reconstructing evolutionary trees. Molecular Biology and Evolution 4: 406-425[Abstract]
Sexton T. B. J. T. Jones J. E. Mullet 1990 Sequence and transcriptional analysis of the barley ctDNA region upstream of psbD-psbC encoding trnK (UUU), rps16, trnQ (UUG), psbK, psbI, and trnS (GCU). Current Genetics 17: 445-454[CrossRef][ISI][Medline]
Shinozaki K. H. Deno M. Sugita S. Kuramitsu M. Sugiura 1986a Intron in the gene for the ribosomal protein S16 of tobacco chloroplast and its conserved boundary sequences. Molecular and General Genetics 202: 1-5[CrossRef]
Shinozaki K. et al 1986b The complete nucleotide sequence of the tobacco chloroplast genome: its gene organization and expression. European Molecular Biology Organization Journal 5: 2043-2049
SØrensen M. 1988 A taxonomic revision of the genus Pachyrhizus (Fabaceae-Phaseoleae). Nordic Journal of Botany 8: 167-192
Swofford D. L. 1998 Phylogenetic analysis using parsimony, v.4.01 beta. Sinauer, Sunderland, Massaachusetts, USA
Taubert P. 1894 Leguminosae. In A. Engler and K. Prantl [eds.], Die natürlichen Pflanzenfamilien, 70–396. Wilhelm Englemann, Leipzig, Germany
Turner B. L. O. S. Fearing 1964 A taxonomic study of the genus Amphicarpaea (Leguminosae). Southwestern Naturalist 9: 207-218[CrossRef]
Van der Maesen L. J. G. 1985 Revision of the genus Pueraria DC. with some notes on Teyleria Backer (Leguminosae). Agricultural University, Wageningen, The Netherlands
Verdcourt B. 1970 Studies in the Leguminosae-Papilionoideae for the Flora of Tropical East Africa: III. Kew Bulletin 24: 380-399
Viviani T. L. Conte G. Cristofolini M. Speranza 1991 Sero-systematic and taximetric studies on the Phaseoleae (Fabaceae) and related tribes. Botanical Journal of the Linnean Society 105: 113-136
Walbot V. 1988 Preparation of DNA from single rice seedlings. Rice Genetics Newsletter 5: 149-151
Welzen P. C. V. S. D. Hengst 1994 The genus Mastersia (Papilionaceae: Phaseoleae). Blumea 30: 77-87
This article has been cited by other articles:
|
|
 |
|
  E. M. Haston, G. P. Lewis, and J. A. Hawkins A phylogenetic reappraisal of the Peltophorum group (Caesalpinieae: Leguminosae) based on the chloroplast trnL-F, rbcL and rps16 sequence data Am. J. Botany, August 1, 2005; 92(8): 1359 - 1371. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Shaw, E. B. Lickey, J. T. Beck, S. B. Farmer, W. Liu, J. Miller, K. C. Siripun, C. T. Winder, E. E. Schilling, and R. L. Small The tortoise and the hare II: relative utility of 21 noncoding chloroplast DNA sequences for phylogenetic analysis Am. J. Botany, January 1, 2005; 92(1): 142 - 166. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. F. Wojciechowski, M. Lavin, and M. J. Sanderson A phylogeny of legumes (Leguminosae) based on analysis of the plastid matK gene resolves many well-supported subclades within the family Am. J. Botany, November 1, 2004; 91(11): 1846 - 1862. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. J. Doyle and M. A. Luckow The Rest of the Iceberg. Legume Diversity and Evolution in a Phylogenetic Context Plant Physiology, March 1, 2003; 131(3): 900 - 910. [Full Text] [PDF]
|
|
|
|
|
|
S. A. Kelchner Group II introns as phylogenetic tools: structure, function, and evolutionary constraints Am. J. Botany, October 1, 2002; 89(10): 1651 - 1669. [Abstract] [Full Text] [PDF]
|
|
| ||||||||||||||||||||||||||||||||||||
4 steps longer than the most parsimonious trees could not be performed owing to the computational constraints. Glycine groups of Lackey (1981)
