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2Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Caixa Postal 15053, 91501-970 Porto Alegre, RS, Brazil; 3Departamento de Botânica, Universidade Federal do Paraná, Caixa Postal 19031, 81531-970 Curitiba, PR, Brazil; 4Centro de Biologia Genômica e Molecular, Faculdade de Biociências, Pontifícia Universidade Católica do Rio Grande do Sul, Ipiranga 6681, 90610-001 Porto Alegre, RS, Brazil; 5Departamento de Botânica, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Av. Bento Gonçalves, 9500, Prédio 43433, 90509-900 Porto Alegre, RS, Brazil
Received for publication September 12, 2002. Accepted for publication March 28, 2003.
| ABSTRACT |
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1000 bp), and the rps4 plastid gene (
570 bp). Three major clades were highly supported, independent of the marker and phylogenetic method used; one included the subgenera Distephana, Dysosmia, Dysosmioides, Passiflora, and Tacsonioides, a second, the subgenera Adopogyne, Decaloba, Murucuja, and Pseudomurucuja, and a third, the subgenus Astrophea. We call these the Passiflora, Decaloba, and Astrophea clades, respectively. The position of subgenus Deidamioides is undefined. The monophyly of Passiflora could not be statistically corroborated, and the relationships among the major clades and of these clades with the related genera remain unresolved. Our results indicate that a reevaluation of the monophyly of Passiflora and its infrageneric classification is necessary.
Key Words: ITS Passiflora Passifloraceae phylogenetic analysis rps4 trnL-trnF
| INTRODUCTION |
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According to Killip (1938)
, the genus should be subdivided into 22 subgenera and the Decaloba and Astrophea subgenera into 13 sections. Escobar (1989)
described one additional subgenus. Killip's (1938)
classification was entirely based on morphological characters, especially those of the floral structure. Only two other studies deal with the infrageneric relationships in Passiflora (Sánchez et al., 1999
; de Melo et al., 2001
), but none employed modern phylogenetic methods, DNA sequence data, or suggested any infrageneric grouping.
In the present investigation we analyzed the relationships of 61 species of Passiflora, formally classified in 11 subgenera, and representatives of four other genera, using two noncoding DNA segments, the nuclear ribosomal internal transcribed spacers (ITS), and the plastid trnL-trnF spacers. These regions have been widely used in plant phylogenetics because of their high rate of nucleotide substitutions (Taberlet et al., 1991
; Baldwin, 1992
; Baldwin et al., 1995
; Rauscher, 2002
) and their power in elucidating infrageneric relationships (Gielly and Taberlet, 1996
; Bakker et al., 1998
; Molvray et al., 1999
; Nishikawa et al., 1999
; Hardig et al., 2000
). The rps4 gene (encoding protein 4 of the small plastid ribosomal subunit) was also studied in a smaller number of species to broadly access the major phylogenetic relationships within Passiflora. This gene was chosen mainly because of its slower evolutionary rate when compared with the other two regions studied here and its previously successful use in the phylogenetic reconstruction of Poaceae (Nadot et al., 1994
) and Iridaceae (Souza-Chies et al., 1997
). The data were evaluated using several phylogenetic reconstruction methods. Specific objectives were (a) to examine the nature of the variation in these two differently positioned spacer regions and in a coding region, assessing their phylogenetic utility in Passiflora; (b) to investigate the monophyly of the genus; and (c) to clarify the infrageneric phylogenetic relationships.
| MATERIALS AND METHODS |
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DNA was extracted from fresh leaves (collected directly from nature or derived from seeds grown in the laboratory) or from herbarium material, using the cetyltrimethyl ammonium bromide (CTAB) method (Doyle and Doyle, 1987
). Amplification was done by polymerase chain reaction (PCR), using the primers described by Desfeux and Lejeune (1996)
for ITS and the primers e and f of Taberlet et al. (1991)
for trnL-trnF. The rps4 gene was amplified with primers rps5 and trnS described by Souza-Chies et al. (1997)
. The amplified material was purified with shrimp alkaline phosphatase and exonuclease I (Amersham Biosciences, Piscataway, New Jersey, USA), and the two strands were directly sequenced, using the internal primers ITS3 and ITS3-reverse (Desfeux and Lejeune, 1996
) for ITS. Sequencing was done using the BigDye Terminator Sequencing Kit (PE Applied Biosystems, Foster City, Michigan, USA) on an ABI Prism 310 (PE Applied Biosystems). Sequences were deposited with GENBANK (see Appendix 1 in the Supplementary Data accompanying the online version of this article).
Data analysis
Sequences were aligned using the ClustalX 1.81 program (Thompson et al., 1994
, 2001
) and manually refined. Phylogenetic analyses were performed in PAUP*, version 4.0b10 (Swofford, 1998
). All the analyses described later were done with each spacer considered as a different data set (ITS or trnL-trnF) and also with both markers combined in a single alignment. ITS1 and ITS2 were considered together. Because of technical problems, we could not obtain usable sequences for some species for some markers, so that only 55 species were studied for ITS and 60 for trnL-trnF. For rps4, we sequenced material from 32 species, in order to obtain representatives of the major clades of Passiflora, which were compared with three of the four outgroups.
Equally weighted parsimony (maximum parsimony [MP]) analyses were performed by a heuristic search with tree bisection-reconnection (TBR) branch swapping, the MULPARS option, and 1000 random-addition replicates. Bootstrap statistical support (Felsenstein, 1985
) was carried out with 1000 replications of heuristic search and simple taxon addition, with the all trees saved option. Topological congruence between the trees obtained by the different data sets was evaluated with Templeton's test (1983)
, and heterogeneity among markers was assessed using the partition homogeneity test or incongruence length difference test (IDL) developed by Farris et al. (1994)
with 1000 iterations. The g1 statistic (Hillis, 1991
) of skewed tree-length distribution was calculated from 10 000 random trees, to measure the phylogenetic information content of the two spacer regions independently and for the combined data.
The appropriate model of nucleotide substitution for maximum-likelihood (ML) analysis was determined using the MODELTEST 3.06 program (Posada and Crandall, 1998
). This procedure implements a hierarchical likelihood-ratio test to determine the model that best fits the data. For ML tree estimation, heuristic searches with as-is, TBR branch swapping, and MULPARS option, were conducted with PAUP*. Because obtaining support estimates for the ML trees' branches by bootstrap analysis is computationally too intensive with a data set of this size, we conducted a bootstrap analysis using the neighbor-joining method under a maximum-likelihood model, with parameters settings estimated by the MODELTEST, as described by Xiang et al. (2002)
. Topology comparisons between the trees obtained with the two spacers were done with the KH (Kishino and Hasegawa, 1989
) and SH (Shimodaira and Hasegawa, 1999
) tests.
The new MetaPIGA 1.02 software was used for phylogenetic inference under the ML criterion using a metapopulation genetic algorithm (Lemmon and Milinkovitch, 2002
). This method was developed to supply better and faster estimates of ML trees with large data sets. The program was run using the following relevant settings: HKY85 (Hasegawa et al., 1985
) nucleotide substitution model, four populations, and 10 replications. Lemmon and Milinkovitch (2002)
suggest that four population metaPIGA runs seem to give the best compromise between computing speed and accuracy of topology inference. All other settings were used as suggested in the program manual (Lemmon and Milinkovitch, 2002
). The 50% majority-rule consensus tree was constructed in PAUP*.
Bayesian analyses of the data were performed using MrBayes 2.01 (Huelsenbeck and Ronquist, 2001
) to generate a posterior probability distribution using Markov chain Monte Carlo (MCMC) methods. No a priori assumptions about the topology of the tree were made and all searches were provided with a uniform prior. The models of DNA substitution used were those estimated by MODELTEST and used in the standard ML analyses. The MCMC processes were set so that four chains were run simultaneously for 500 000 generations, with trees being sampled every 100 generations for a total of 5000 trees. Burn-in, or the time for each parameter to reach a stationary state, was determined when visual inspection indicated that the log-likelihood values achieved an asymptote over a large number of generations. To calculate the posterior probability of each bipartition, a 50% majority-rule consensus tree was constructed from the remaining trees using PAUP*.
For the distance analyses, trees were constructed using the neighbor-joining method (NJ; Saitou and Nei, 1987
) using proportional (p), Kimura two parameter, and logDet (Steel, 1994
; Lockhart et al., 1994
) distances. LogDet or paralinear distances were calculated to test the possible influence of the nucleotide composition difference in the phylogeny (Nei and Kumar, 2000
). Reliability of the trees was tested using 1000 bootstrap replications (Hedges, 1992
). Topology comparisons between the ITS and trnL-trnF data sets were performed using the KH and SH tests. Relative rate evaluations, based on the two-cluster test of Takezaki et al. (1995)
, were performed using the PHYLTEST program (Kumar, 1996
). Average nucleotide diversities and their standard errors within each subgenus were calculated by the SendBS program (Takezaki, 2001
) with the p distance option and 2000 bootstrap replications.
The results of the different inference phylogenetic methods within each data set were quite similar, so only selected results are presented here. (All other trees are presented in the Supplementary Data accompanying the online version of this article.) All trees were rooted with Paropsia because it is representative of Paropsieae and was shown to be more basal than Adenia by Chase et al. (2002)
.
A possible substitution saturation in the ITS region was investigated by plotting the ITS pairwise sequence p distances against the more conserved trnL-trnF pairwise distances. The minimum sizes of the flowers (using the descriptions of Killip [1938
], MacDougal [1994
], and Cervi [1997
]) of different clades (see Results) were compared using the Wilcoxon-Mann-Whitney test to determine if their averages were significantly different.
| RESULTS |
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2 = 34.8; 1 df; P < 0.0001). The pairwise p distances, including the outgroups, ranged from 1.9% to 38%, with an average value of 20%. The trnL-trnF intergenic region had a total aligned length of 416 bp (individual sequences ranged from 239 to 313 bp), 61 being parsimony-informative. The pairwise p distances, including the outgroups, ranged from 1.8% to 10%, with an average value of 4.4%. The GC content is low in this region (36%), and no marked differences were found among the subgenera. The alignment of the rps4 gene is 576 bp in length (unaligned sequences ranged from 542 to 560 bp), 58 being parsimony-informative. The GC content is very low in this region (27%), and again, no marked differences were found among the subgenera. The pairwise p distances, including the outgroups, ranged from 0.2% to 8.1%, with an average value of 3.5%.
Phylogenetic analysis
The selected model for the maximum-likelihood analysis using MODELTEST was TrN+I+G (lnL = 8227.1035) for ITS, HKY + G (lnL = 2131.0359) for trnL-trnF, and TVM + G (lnL = 2164.3538) for rps4 (see Posada and Crandall [1998
] for details of the models). The gamma shape parameters estimated for the three DNA regions were also different (ITS, 1.839; trnL-trnF, 0.5640; rps4, 0.7806). For the combined data of the spacer regions, the model selected was TrNef+I+G (lnL = 10 381.6836) with a gamma shape parameter of 1.078. Figures 13 present the phylogenetic trees obtained using the standard ML method on the ITS, trnL-trnF, and combined data sets, respectively. In the great majority of the trees we can observe three major clades within Passiflora, which are generally supported by high bootstrap values: one composed of all studied species of subgenera Distephana, Dysosmia, Dysosmioides, Passiflora, and Tacsonioides; another comprising all species of sugenera Adopogyne, Decaloba, Murucuja, and Pseudomurucuja; and a third composed of the four species of subgenus Astrophea. We call these the Passiflora, Decaloba, and Astrophea clades, respectively.
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There are some differences among the trees on the positioning of a few Passiflora species within the major clades that are worth noting. Passiflora lancetillensis and P. microstipula, from subgenus Deidamioides, form a sister group to the Decaloba clade in the trnL-trnF tree (Fig. 2) with a high divergence and therefore could possibly be considered a fourth main clade. But in the ITS tree (Fig. 1), P. lancetillensis is placed within the Decaloba clade. Passiflora rubra is also placed as a highly divergent sister to the remaining species of the Decaloba clade in the trnL-trnF trees (Fig. 2) but not in the ITS trees. Also noteworthy is the position of P. foetida in the ITS tree (Fig. 1), as sister to all other taxa in the Passiflora clade, a placement not seen in the trnL-trnF trees (Fig. 2).
By contrast with the high support among markers and phylogenetic methods for the major Passiflora clades, the relationships among the outgroups and clades received very low support (bootstrap and posterior probabilities values) in each tree and with many disagreements among them. For example, in the ITS maximum-likelihood tree (Fig. 1), the outgroups are not phylogenetically adjacent, because Tetrastilys ovalis and Adenia keramanthus are positioned as sister to the Passiflora clade (with a support value of 97%), while Mitostemma brevifilis is placed as a sister to the Decaloba + Astrophea clades (with support of <50%). In the trnL-trnF tree (Fig. 2), T. ovalis was included within the Passiflora clade as sister to P. speciosa, but here the other three outgroup species did group together, although with medium (73%) bootstrap support. The combined ML tree (Fig. 3) presents a topology that has components found in both single marker trees, with T. ovalis positioned as sister of the Passiflora clade (bootstrap support = 100%), Adenia keramanthus positioned among the three clades, and Mitostemma brevifilis appearing as the most basal species, but both with support values below 50%.
All trees of the rps4 data set, despite its much smaller size, corroborate the existence of three major Passiflora clades, but there is disagreement on the relationship among the clades and their relationship with the outgroups when comparing the different methods. For example, in the ML tree the higher-order relationships are statistically unresolved (Fig. 5), but in the NJ and Bayesian analyses (see Supplementary Data) there is moderate support for the non-monophyly of Passiflora. Therefore, the monophyly of the genus Passiflora was not statistically supported by any data set or phylogenetic method, and in several trees there was even statistical support for a non-monophyletic Passiflora.
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One interesting difference that can be observed visually is the higher divergence among the species of the Decaloba clade (implied by the usually longer branch lengths) as compared to those of the Passiflora clade, especially marked for the trnL-trnF region (Fig. 2). Also noteworthy is the usually longer branch leading to the Decaloba clade, as contrasted to that leading to the Passiflora clade. Nucleotide diversity (
) for the ITS region is significantly higher in the Decaloba clade (0.102 ± 0.013) as compared to the Passiflora clade (0.043 ± 0.078). The relative rate Z statistic (Z = 3.549) calculated with the PHYLTEST package rejects rate constancy (P < 0.05) between the two. A similar result was found for the trnL-trnF intergenic region (Z = 2.399, P < 0.05) and for the rps4 gene (Z = 2.976, P < 0.05), suggesting that these different evolutionary rates are not locus specific but characteristic of the clades. To test if these differences were not due to the different number of species sampled in them, new analyses were performed consisting of 10 random subsamples of species with an identical number of species in both clades. The results corroborated the significant differences between the two clades. Because of its much smaller sample size, we did not test the Astrophea clade for these divergence differences.
Anyone acquainted with Passiflora could intuitively perceive that the different subgenera could also have dissimilar flower sizes. Indeed, a Wilcoxon-Mann-Whitney test showed that the flowers of the Passiflora clade have a significantly larger (P < 0.001) minimum size than the flowers of the Decaloba and Astrophea clades (median values: 19 mm vs. 6.5 mm, respectively).
| DISCUSSION |
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By contrast, all phylogenetic results presented here suggest the existence of three well-defined clades in Passiflora. The largest comprise all representatives of Killip's (1938)
subgenera Distephana, Dysosmia, Dysosmioides, Passiflora, and Tacsonioides. Because the subgenus Passiflora is by far the most diverse of all, we named this set as the Passiflora clade. A second major clade comprises all species of Killip's (1938)
and MacDougal's (1994)
subgenus Decaloba, as well P. tulae of subgenus Murucuja, P. cuprea of subgenus Pseudomurucuja, and P. multiflora of subgenus Adopogyne. Using the same reasoning stated above, we called this the Decaloba clade. The third clade proposed here comprises the four species of the subgenus Astrophea (P. haematostigma, P. mansoi, P. citrifolia, and P. macrophylla), which has very high support values in most of the trees presented here.
The subgenus Deidamioides (represented here by P. lancetillensis and P. microstipula) presents ambiguous positions in the trees derived from the different markers. In the more conserved trnL-trnF spacer and rps4 gene, this subgenus is very divergent from the other subgenera, and it was placed in some trnL-trnF trees (e.g., the MP tree available in the supplementary data) as a very basal independent clade, suggesting that it could be considered as a fourth major clade of Passiflora. However, in the ITS trees (e.g., Fig. 1), P. lancetillensis is placed within the Decaloba clade, with a high bootstrap value. These ambiguities, and the low number of species sampled, determine that the status of this subgenus should remain undefined until further data are analyzed.
Though we could not find any published evidence that explicitly corroborates the existence of these three clades in Passiflora, two papers seem to agree with our results. De Melo et al. (2001)
described the basic chromosome number of several subgenera of Passiflora and some related genera. From the interpretation of their tree (their Fig. 6) in a phylogenetic context, a grouping of subgenera was suggested that is consistent with the three clades described here. On the other hand, Downie et al. (1996)
studied the rpoC1 chloroplast intron in several families and found that it was absent in four species of the subgenus Decaloba, but present in six species of the Passiflora clade (three subgenera). It should also be remembered (see Results) that the five subgenera that form the Passiflora clade all have statistically significant larger and more conspicuous flowers than those of the Decaloba and Astrophea clades.
Although there are some consistent species groupings within the Passiflora and Decaloba clades, only a few of them have high levels of statistical support and are consistent among markers and phylogenetic methods, such as the P. actinia + P. elegans + P. sidaefolia and the P. quadrangularis + P. alata subgroups. Most of these subgroups, however, are not consistent with Killip's (1938)
subgenera or sections.
One question that can be considered is the taxon sampling of our study and its bearing on the reliability of the major clades found. We are aware that a larger sample of species could result in more reliable trees. However, we suggest that our results and phylogenetic conclusions are presently adequate. Thus, our sampling represents about 15% and 49% of Passiflora's species and subgenera, respectively. These sample sizes are by no means unusual or small in phylogenetic studies of large and diversified taxa. For example, Miller et al. (2002)
investigated the monophyly of Ipomoea (Convolvulaceae) using just 35 (5.8%) of about 600 species of this genus; Bortiri et al. (2002)
studied just 22 (11%) of over 200 species of Prunus; and Cuénoud et al. (2002)
studied just one species of each genus for the phylogenetic analyses of Caryophyllales. Perhaps the clearest example of the utility of a limited taxonomic sampling is the most recent work that tries to infer ordinal and familial classification for angiosperms (such as that of the Angiosperm Phylogeny Group, 1998
) with a relatively limited sample of the angiosperm species. Rosenberg and Kumar (2001)
also suggested that incomplete sampling might not be a problem for phylogenetic inferences (but see Zwickl and Hillis [2002
] for a different position). Our results with 11 (49%) of the 23 putative subgenera suggest that at least the subgenera studied here should be grouped in three major clades: Passiflora, Decaloba, and Astrophea.
Sequence variation
The GC content in the ITS region varied from 47% to 67% in the different species of Passiflora, a variability that has also been observed in other groups of plants (e.g., Nishikawa et al., 1999
; Gaut et al., 2000
). Interestingly, the GC content differs significantly between the Decaloba and non-Decaloba clades, and although this may be a bias factor for most phylogenetic methods, the use of the logDet distance (Lockhart et al., 1994
; Steel, 1994
) should correct for it. The use of this distance with a subsample of our data yielded the same main clades presented here, suggesting that the ITS phylogeny was not biased by the heterogeneity in nucleotide content (see Supplementary Data).
Heterogeneity in the rates of DNA change such as that observed in the Decaloba/non-Decaloba clades has also been documented at several taxonomic levels in plants (Bousquet et al., 1992
; Gaut et al., 1993
; Suh et al., 1993
; Gielly and Taberlet, 1996
; Eyre-Walker and Gaut, 1997
; Aïnouche and Bayer, 1999
; Bortiri et al., 2002
). Many factors supposedly influence the rate of molecular evolution, such as generation time, selection, DNA replication or repair, and metabolic rates (Wu and Li, 1985
; Britten, 1986
; Bousquet et al., 1992
; Li, 1993
; Martin and Palumbi, 1993
; Eyre-Walker and Gaut, 1997
; Gaut et al., 1997
). Unfortunately, little is known about such factors in Passiflora, although Benson at al. (1975)
asserted that members of the subgenus Decaloba have shorter generation times than species of the subgenus Passiflora, a factor that may have accelerated its evolutionary rate. Another possible explanation for the very short branches within the Passiflora clade is a rapid radiation of the species of this clade, an explanatory factor that was attributed to similar results described in other groups of angiosperms (e.g., Bortiri et al., 2002
).
Comparison among markers
The discrepancies between the trees obtained with ITS and trnL-trnF are mainly due to the position of a few species (e.g., P. rubra and P. foetida) and the outgroup relationships. Some of these discrepancies could be due to the different forms of inheritance of nuclear and chloroplast markers. The majority of the angiosperms have maternal chloroplast inheritance, but Turnera ulmifolia, a closely related member of the Malpighiales, has mixed, paternally biased inheritance (Shore and Triassi, 1998
). (Note that Chase et al. [2002
] placed the Turneraceae within the Passifloraceae.) Courriveau and Coleman (1988)
found chloroplast paternal inheritance in P. edulis; and similar results were obtained by A. P. Lorenz et al. (Federal University of Rio Grande do Sul, unpublished data) in P. elegans and P. actinia. In accordance with this reasoning, the trees based on the two chloroplast markers, trnL-trnF and rps4, generally had fewer discrepancies among themselves than when they were compared with trees based on ITS sequences.
Another factor that may have contributed to these discrepancies, mainly at the higher level relationships, is the observed saturation in the ITS region, when contrasted to the trnL-trnF data (Fig. 5). The phylogenetic utility of the ITS spacers within the Passifloraceae seems to be restricted to the interspecific comparisons, and they should be used with caution at the intergeneric level.
Future considerations
We recommend, and it is in our plans, that future work should concentrate on certain critical areas, such as increased taxon sampling, mainly of the subgenera not yet studied and of the larger subgenera, such as Decaloba, that were underrepresented here. Furthermore, considering the lack of adequate resolution found in our trees at the higher order relationships, it is necessary to increase the amount of sequence data to clarify issues such as the monophyly of Passiflora and its relationship with its major clades and with the other genera of the Passifloraceae. Also of interest is an understanding of the causes underlying the different evolutionary dynamics found here among the major Passiflora clades.
| FOOTNOTES |
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6 Author for correspondence (e-mail: loreta.freitas{at}ufrgs.br
) ![]()
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