© 2006 Society of Systematic Biologists
Dating Dispersal and Radiation in the Gymnosperm Gnetum (Gnetales)—Clock Calibration When Outgroup Relationships Are Uncertain
Edited by Peter Linder: Associate Editor
1 University of Missouri-St. Louis, Department of Biology 8001 Natural Bridge Road, St. Louis, Missouri, 63121, USA The Missouri Botanical Garden St. Louis, Missouri, 63166, USA E-mail: wonhs{at}snu.ac.kr (H.W.) renner{at}umsl.edu (S.R.R.)
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Most implementations of molecular clocks require resolved topologies. However, one of the Bayesian relaxed clock approaches accepts input topologies that include polytomies. We explored the effects of resolved and polytomous input topologies in a rate-heterogeneous sequence data set for Gnetum, a member of the seed plant lineage Gnetales. Gnetum has 10 species in South America, 1 in tropical West Africa, and 20 to 25 in tropical Asia, and explanations for the ages of these disjunctions involve long-distance dispersal and/or the breakup of Gondwana. To resolve relationships within Gnetum, we sequenced most of its species for six loci from the chloroplast (rbcL, matK, and the trnT-trnF region), the nucleus (rITS/5.8S and the LEAFY gene second intron), and the mitochondrion (nad1 gene second intron). Because Gnetum has no fossil record, we relied on fossils from other Gnetales and from the seed plant lineages conifers, Ginkgo, cycads, and angiosperms to constrain a molecular clock and obtain absolute times for within-Gnetum divergence events. Relationships among Gnetales and the other seed plant lineages are still unresolved, and we therefore used differently resolved topologies, including one that contained a basal polytomy among gymnosperms. For a small set of Gnetales exemplars (n = 13) in which rbcL and matK satisfied the clock assumption, we also obtained time estimates from a strict clock, calibrated with one outgroup fossil. The changing hierarchical relationships among seed plants (and accordingly changing placements of distant fossils) resulted in small changes of within-Gnetum estimates because topologically closest constraints overrode more distant constraints. Regardless of the seed plant topology assumed, relaxed clock estimates suggest that the extant clades of Gnetum began diverging from each other during the Upper Oligocene. Strict clock estimates imply a mid-Miocene divergence. These estimates, together with the phylogeny for Gnetum from the six combined data sets, imply that the single African species of Gnetum is not a remnant of a once Gondwanan distribution. Miocene and Pliocene range expansions are inferred for the Asian subclades of Gnetum, which stem from an ancestor that arrived from Africa. These findings fit with seed dispersal by water in several species of Gnetum, morphological similarities among apparently young species, and incomplete concerted evolution in the nuclear ITS region.
Keywords: Bayesian relaxed clock; biogeography; Ephedra; Gnetum; long-distance water dispersal; polytomies in molecular clock dating
Received June 23, 2005; Revised September 2, 2005; Accepted March 13, 2006
"It is not at all clear—although often tacitly assumed—that an old lineage has occupied its current range for a long time. Gnetum in particular provides neat examples of the opposite." (Markgraf, 1929:429; translated from the German by SR)
Age estimation from molecular sequences has emerged as a powerful tool for inferring the time it took a plant lineage to radiate in a particular area. Analytical methods now try to model change in substitution rates along individual branches of a phylogeny by combining molecular data with multiple simultaneous time constraints, usually from fossils (Thorne et al., 1998; Rambaut and Bromham, 1998; Kishino et al., 2001; Thorne and Kishino, 2002; Aris-Brosou and Yang, 2002; Sanderson, 2002; Drummond and Rambaut, 2005). Simulations have shown that such "relaxed" clock approaches can recover known rates (and hence ages) only as long as several calibration points are accurate (Ho et al., 2005). In practice, uncertainties in calibrations due to misidentified or misdated fossils (Doyle and Donoghue, 1993; Sanderson and Doyle, 2001; Near et al., 2005), taxon-sampling effects (Linder et al., Rutschmann, 2005), and asymmetric tree shape often reduce the reliability of the temporal constraints employed. Given the difficulty of calibrating genetic distances, it is desirable to use multiple constraints wherever possible. Using multiple fossil constraints, however, usually requires knowing phylogenetic relationships outside the study group, with the corollary of having to use relatively conservative gene regions that are alignable across phylogenetically distant taxa. These conserved gene regions will often be uninformative in the group of interest. In the face of these difficulties, assuming a strict clock for a reduced (and then more or less clock-like) data set may still be the best way to improve the precision, and perhaps accuracy, of rate and date estimates (Sanderson, 2002; Ho et al., 2005). For data sets that behave in a less clock-like fashion, the safest approach may be to compare results from strict clocks with those from relaxed clocks, employing alternative input topologies and constrained with as many critical fossils as possible.
We here deal with the problems of rate heterogeneity and unclear outgroup relationships in the seed plant lineage Gnetales, focusing on Gnetum, for which we have near-complete species sampling. Many seed plant lineages, especially conifers, Ginkgo, and cycads, have excellent fossils that potentially can serve to constrain the timing of events within Gnetum. Gnetum itself has no fossil record. Using constraints from outgroup fossils in this group, however, is problematic for at least two reasons. First, Gnetum is highly divergent from its closest living relatives (below) and, second, the relationships of the Gnetales to the other four lineages of seed plants, cycads, Ginkgo, conifers, and flowering plants, are still unresolved. In what has been referred to as the single most surprising grouping discovered with molecular data (Palmer et al., 2004), Gnetales appear to be sister to Pinaceae, and both then sister to the remaining conifers. This is the favored topology in the most comprehensive analysis to date (Burleigh and Mathews, 2004). Other analyses place Gnetales as sister to conifers or to all other seed plants (Quandt et al., 2006). The so-called anthophyte hypothesis, which sees Gnetales as sister to flowering plants, is rarely recovered with molecular data (e.g., Chaw et al., 2000; Bowe et al., 2000; Magallón and Sanderson, 2002; Rydin et al., 2002; Schmidt and Schneider-Poetsch, 2002; Soltis et al., 2002; Rai et al., 2003; see Burleigh and Mathews, 2004, for a review).
Obtaining estimates for divergence events within Gnetum is of interest mainly because of the group's disjunct geographic distribution, but also because of a lateral gene transfer event in one subclade for which the time to nonfunctionalization (pseudogenization) can be estimated (Won and Renner, 2003). Gnetum consists of probably fewer than 33 species; most are large woody climbers, two are trees (Markgraf, 1929; HW, monograph in preparation). Ten species occur in tropical South America, one in West Africa, and the remainder in tropical and subtropical Asia. Species relationships within Asian Gnetum cannot be resolved with the highly conserved gene regions required for seed plant-wide analyses and dating. Instead, we relied on a six-locus data set that includes nuclear, mitochondrial, and chloroplast genes, spacers, and introns.
The accepted hypothesis has long been that the pantropical range of Gnetum reflects a Gondwanan history (Markgraf, 1929). As explained above, Gnetum has no fossils, but the Gondwanan hypothesis receives indirect support from the fossil record of Welwitschia, the sister lineage of Gnetum. Welwitschia mirabilis, today restricted to the Namib dessert, is known from a 110-My-old seedling from the Lower Cretaceous (Aptian) Crato Formation in northeastern Brazil (Rydin et al., 2003). With its famously weird morphology that includes a deep tap root and two strap-shaped leaves that can grow for hundreds of years (Henschel and Seely, 2000), Welwitschia differs remarkably from the canopy climbers that are typical of the genus Gnetum. Gnetum and Welwitschia together are the sister clade to Ephedra, which consists of 35 to 45 species of shrubby plants with photosynthetic stems and reduced leaves that are widely distributed in temperate to arid areas of Eurasia, northern Africa, southwestern North America, and western South America (Ickert-Bond and Wojciechowski, 2004; Huang et al., 2005). The monophyly of these three genera, which make up the Gnetales, is supported by numerous morphological and molecular phylogenetic analyses (Kubitzki, 1990; Price, 1996).
The Crato Formation has also yielded male strobili similar to those of Welwitschia and vegetative stems with joints, whorled branchlets, reduced leaves, and sessile male strobili resembling those of Ephedra (Mohr et al., 2004; Dilcher et al., 2005, the last reviews the Welwitschia fossil record). Early Cretaceous floras from Buarcos in Portugal, Virginia, USA and from the Yixian Formation in northeast China contain additional fossils that probably represent Ephedra (Rydin et al., 2004, 2006; Yang et al., 2005), including Chaoyangia liangii (Duan, 1998), which, however has winged diaspores that superficially resemble those of Welwitschia. Similar fossils combining Ephedra-like stems with winged diaspores have been described as Gurvanella dictyoptera from the Early Cretaceous Gurvan-Eren Formation of Mongolia (Krassilov, 1982, 1997) and as Gurvanella exquisita, again from the Yixian Formation (Sun et al., 2001). Further fossils associated with the Welwitschia lineage include Aptian Eastern North American male cones (Drewria; Crane and Upchurch, 1987) and a Barremian-Aptian female cone from the Lake Baikal area (Eoantha; Krassilov, 1986). The earliest Gnetales pollen is much older, from the Late Triassic and Early Jurassic, and could represent either Ephedra or Welwitschia (Crane, 1996; Dilcher et al., 2005); a recent study even describes Permian (270 my old) cones with such pollen (Wang, 2004). Gnetum pollen has a much lower fossilization potential because of its thin exine (Hesse et al., 2000).
These macro- and microfossils demonstrate the diversity of Gnetales in the Mesozoic (Late Triassic to Cretaceous) and provide an overall temporal context. However, their assignment to nodes in the tree of living species of Ephedra, Welwitschia, or Gnetum is problematic. Because Welwitschia consists of a single species, the above-mentioned fossil seedling, Cratonia cotyledon (belonging to the Welwitschia lineage), can only constrain the split between Gnetum and Welwitschia, possibly resulting in a considerable underestimate of the true age of that split. Similarly, the best preserved Ephedra fossils, 125-My-old seeds (Rydin et al., 2004; Yang et al., 2005), cannot confidently be assigned to the crown group of Ephedra, but do constrain the split between Ephedra and the other two genera. (We nevertheless carried out an experiment to test the effect of assigning them to the Ephedra crown group.)
To overcome these calibration problems, we decided to employ additional constraints from well-dated fossils of conifers, cycads, and flowering plants. This required a relaxed clock approach (i.e., modeling substitution rate change along branches) because the larger data matrix rejected the clock assumption and added the problem of the uncertain phylogenetic placement of Gnetales among seed plants (above). As a way out, we employed the current best estimate seed plant tree (Burleigh and Mathews, 2004), three alternative seed plant trees, and a topology with a basal polytomy in the gymnosperms. The latter implies a prior belief that Gnetales, conifers, cycads, and Ginkgo present a hard polytomy that cannot be resolved. In most current implementations of Bayesian clock approaches, prior beliefs about the topology cannot be overwritten by the data (they can in BEAST; Drummond and Rambaut, 2005), and workers have therefore generally preferred to use completely resolved topologies even for parts of the tree that are not supported by the underlying (or other) data (but see Renner and Zhang, 2004). Such a prior polytomy, however, does not prevent branch length information in the data from strongly affecting the posterior branch lengths assigned to branches above or below the polytomy. Where there is strong signal, substitutions will sort themselves out along the branches emanating from the multifurcating node. The situation is complicated by the specific position of temporal constraints employed in a particular study. While in strict clock approaches the effect of a calibration point is identical throughout the tree, in relaxed clocks, the effect of age constraints—whether minimal, maximal, or fixed—diminishes with each node further away from the constraint(s). Given that the behavior of relaxed clocks is still so poorly understood, we felt it worthwhile to explore the empirical effects of a multifurcation in the input topology.
Having determined the time horizon for the evolution of Gnetum with multiple approaches, we develop a hypothesis for the radiation of the climbing and tree forms of Gnetum that incorporates climatic, geological, and biological evidence and set out ways in which it might be tested.
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Taxon Sampling
Leaf samples with voucher information and GenBank accession numbers for the sequences obtained from them are listed in Appendices 1 and 2 (www.systematicbiology.org), which also give author names for all taxa. Most Gnetum samples were collected in the field by the first author; a few are from botanical gardens or herbarium material. Thirty-one accessions of Gnetum were sequenced for six loci, usually all from the same DNA aliquot (for exceptions see Appendix 2). The seed plant data set included representatives of all major clades of Gnetum, Welwitschia mirabilis, Ginkgo biloba, three species of Ephedra chosen to span the root of that genus (Ickert-Bond and Wojciechowski, 2004; Rydin et al., 2004; Huang et al., 2005), and representatives of conifers and cycads chosen based on the results of Gugerli et al. (2001), Quinn et al. (2002), and Rai et al. (2003). Seed plant-wide analyses were rooted with Psilotum because the matK sequence of Marchantia (liverwort) is much shorter than those of other vascular plants (1113 bp versus 1497–1662 bp in seed plants; it lacks the conserved domain X; see Hilu and Liang [1997]) and has a lower G+C content (18.1%; see Appendix 1), strongly suggesting pseudogenization.
Gene Sequencing
DNA extraction, cloning, and sequencing followed the methods described in Won and Renner (2005a, 2005b). Forward and reverse strands were sequenced. Figure S1 (www.systematicbiology.org) shows the approximate primer positions and organization of the six markers (cp rbcL, matK, and the tRNALeu intron/spacer region; nuclear (nu) rITS/5.8S and the second intron of the LEAFY gene; and mt nad1 second intron and partial exons) and Appendix 3 lists all primer sequences. To amplify rbcL, we used the rbcL-1352R primer, because the commonly used combination of rbcL-724F and 1460R failed to work in Gnetum. The matK regions of G. woodsonianum (= G. leyboldii var. woodsonianum) and G. gnemon Won 514 were cloned and provided by S.-M. Chaw (Institute of Botany, Academia Sinica, Taiwan). Gnetum-specific internal primers for matK were then designed, based on the sequences of G. gnemon, G. montanum, and G. woodsonianum. Except for these clones, the remaining matK sequences were obtained directly from PCR products.
Sequence Analyses and Phylogenetic Analyses
While rbcL sequences were constant in length (1428 base pairs [bp]), matK sequences showed large nucleotide composition and length variation. They were therefore translated into amino acid sequences to guide sequence alignment with Clustal X (Thompson et al., 1997). In addition, a combined six-marker data matrix (Appendix 2) was constructed by concatenating the data matrices of Won and Renner (2005a, 2005b: cp tRNALeu intron/spacer; nu rITS/5.8S; nu LEAFY second intron; and mt nad1 second intron/partial exons) with the rbcL and matK seed plant matrices generated here. Final alignments have been submitted to TreeBase (accession numbers S1493, M2681, M2682).
Length and G+C content of rbcL and matK were calculated from aligned sequences, and sequence divergences were obtained under the K-2-P model (Kimura, 1980). The number of substitutions at synonymous sites (Ks) and non-synonymous sites (Ka) was calculated using MEGA2 (Kumar et al., 2001). Analyses included full-length matK sequences and base positions 77 to 1324 of rbcL.
The concatenated matrix of six loci used to resolve intra-Gnetum relationships (Appendix 2) did not include outgroups because large length and nucleotide differences in several of the spacers and introns prevent alignment across Gnetum, Welwitschia, and Ephedra. (Separate studies have analyzed the phylogenetic signal contained in the secondary structure of these loci in Gnetales; Won and Renner, 2005a, 2005b.) Based on the results of the seed plant-wide analysis, within-Gnetum trees were rooted on the South American Gnetum clade.
Parsimony and maximum likelihood analyses were conduced using PAUP 4.0b10 (Swofford, 2002). Data matrices were analyzed separately under parsimony optimization and in the absence of statistically supported conflict were then combined. Parsimony analyses employed heuristic searches that used 100 random taxon-addition replicates, holding 100 trees at each step, tree bisection-reconnection (TBR) branch swapping, and the options MulTrees, Collapse, and Steepest Descent, without an upper limit for trees held in memory. Nonparametric bootstrap support was obtained by resampling the data 1000 times with the same search options and model, except using closest taxon addition.
Best-fitting substitution models for the combined matK/rbcL data sets, one comprising 13 taxa, the other 38 taxa, were found with ModelTest (Posada and Crandall, 1998), applying the Akaike information criterion. The best-fit model was the general time-reversible model with a gamma-shape parameter and a proportion of sites modeled as invariable; i.e., the GTR+G+I model. The best-fit model for the 6-locus-31-taxa data set also was the GTR+G+I model.
Bayesian analyses of the 6-locus-31-taxa data set relied on MrBayes 3.1 (Huelsenbeck and Ronquist, 2001) and were conducted under the GTR+G+I model, employing the flat prior beliefs that are the default in MrBayes and four Markov chain Monte Carlo (MCMC) chains, one of them heated (the default in MrBayes). Markov chains were run twice for 1 million generations, sampling every 100th generation for a total of 10,000 trees. The first 1000 trees were discarded as burn-in (data points sampled before the chain reaches stationarity), and the remaining 9000 samples were combined into a single file and analyzed using the "sumt" command in MrBayes. Both independent runs found essentially identical tree topologies and posterior probabilities, indicating that the sample number was sufficient to permit the algorithm to converge on a global solution.
Molecular Clock Divergence Time Estimation
For age estimation, most gapped positions were excluded from the matK data set, so that the gene matrix used for dating consisted of 2756 bp, 1428 bases of rbcL and 1328 bp of matK. Likelihood-ratio tests were used to assess rate heterogeneity in the concatenated rbcL + matK data sets of 38 seed plant exemplars and of 13 exemplars (each set including Psilotum for rooting purposes as explained under Taxon Sampling). When the 13-taxon data set justified the assumption of equal rates between sister groups, we used it to estimate divergence times from a strict clock by choosing the "enforce clock" option in PAUP. When the 38-taxon data rejected the assumption of equal rates in sister groups, we used a Bayesian approach that attempts to model variation in the rate of substitution along a tree. The software package used was that of Thorne and Kishino (2002; available at http://statgen.ncsu.edu/thorne/). Branch lengths were estimated with PAML's baseml component (ver. 3.14; Yang, 1997) under the F84+G model (with five rate categories), that being the only model implemented in Thorne's estbranches software, which calculates a variance/covariance matrix of branch length estimates, given sequence data and a specified rooted topology that may include polytomies. The five rooted topologies we used as input are described below. Output branch lengths from estbranches became priors for MCMC searches in multidivtime that sought to find the most likely model of rate change (with rate change assumed to be log-normally distributed), given the branch lengths, topology, time constraints on nodes, and a Brownian motion parameter nu that controls the magnitude of autocorrelation per million years along the descending branches of the tree. Prior gamma distributions on parameters of the relaxed clock model were as follows: The mean of the prior distribution for the root age was set to 3 time units (i.e., 300 My, based on seed plant fossils; below); the standard deviation of this prior was also set to 3. The mean and SD of the prior distribution for ingroup root rate were set to 0.0035 substitutions/site/My by dividing the median of the distances between the ingroup root and the tips by the time unit. The prior for nu was set to 0.4, following the manual's recommendation that the time units between root and tips multiplied by nu be about 1. The standard deviation on nu was also set to 0.4. Markov chains in multidivtime were run for 1 million generations, sampling every 100th generation for a total of 10,000 trees, with a burn-in of 1000 trees before the first sampling of the Markov chain. In the course of this study, 19 runs of 1 million generations were carried out on the matK/rbcL 38-taxon matrix, with consistent results that reflected the experimentally changed fossil constraints.
Because of the unresolved placement of Gnetales among seed plants, we used the following alternative input topologies for the 38-taxon data set: (1) The preferred topology of Burleigh and Mathews (2004; our Fig. 1), which has Gnetales embedded in conifers as sister to Pinaceae and is referred to as the Gnepine hypothesis; (2) Gnetales as sister to conifers, the Gnetifer hypothesis (Fig. S1A; www.systematicbiology.org); (3) Gnetales as sister to all other seed plants, the Gnetales sister hypothesis (Fig. S1B); (4) Gnetales as sister to angiosperms, the Anthophyte hypothesis (Fig. S1C); and (5) a topology with a basal polytomy in the gymnosperms (Fig. S1D).
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For absolute ages we relied on the geologic time scale of Gradstein et al. (2004) and the following calibrations (Fig. 1): The root node, i.e., the crown group of seed plants, was constrained to maximally 385 My old based on the oldest seed precursors (Gerrienne et al., 2004). This may be an overestimate because these early seeds, which have lobed integuments, probably reflecting their origin from fused sporangia or fertile telomes, are quite different from the seeds of modern seed plants. Modern seed types with completely fused integuments are not known until the late Early Carboniferous (ca. 325 My; J. Doyle, personal communication, July 2005). Crown group seed plants thus arose between 325 and 385 Mya. Node 2, the gymnosperm crown group, was constrained to 315 Mya, based on the appearance of stem relatives of living conifers in the middle Late Carboniferous (ca. 310 Mya) and the appearance of Cordaitales, which are probably still more basal stem relatives of conifers, in the earliest Late Carboniferous (ca. 318 Mya). Node 3 was constrained to minimally 125 My old based on earliest Ephedra-type seeds (Barrett, 2000; Rydin et al., 2004; Yang et al., 2005); the minimal age of 125 My for the appearance of Ephedra is further supported by Ephedra-like macrofossil from the Brazilian Crato Formation (Mohr et al., 2004). Node 4, the split between Gnetum and Welwitschia, was constrained to 110 My based on the Cratonia cotyledon fossil (Rydin et al., 2003). Node 5, crown conifers, was constrained to minimally 225 My old based on the oldest Pinaceae-type cones (Miller, 1999; however, most genera of Pinaceae first appear during the Early Tertiary; LePage, 2003a). The split of Pinaceae from other conifers is bracketed not only by these Triassic cones, but also by records of Taxaceae (Palaeotaxus) from the Late Triassic and probable stem relatives of Podocarpaceae (Rissikia) from the (mid?) Triassic (J. Doyle, personal communication, July, 2005). Node 6 was constrained to minimally 160 My based on Middle Jurassic (160 to 175 My) Araucariaceae cones from Argentina (Stockey, 1982). Node 7 was constrained to minimally 90 My old based on Late Cretaceous (Turonian) Cupressaceae Thuja-like fossils (LePage, 2003b). The node just below could also have been constrained to the Late Cretaceous based on Cunninghamia-like cones (Farjon and Ortiz Garcia, 2003). Node 8 was constrained to minimally 90 My based on Turonian cones that clearly belong to crown Pinaceae (Gandolfo et al., 2001). Node 9, crown cycads, was constrained to minimally 270 My old based on Crossozamia from the Early Permian Lower Shihhotse Formation (Gao and Thomas, 1989), which appears to be nested among crown group cycads (Brenner et al., 2003). The 270-My age was chosen because the age of the top of the Lower Shihhotse Formation, though poorly constrained, is probably between from 275 and 265 My old (J. Hill, School of Geography, Earth and Environmental Sciences, University of Birmingham, personal communication, 9 Nov. 2005). Node 10 was constrained to minimally 125 My old, based on oldest Nymphaeaceae flowers (Friis et al., 2001). Gandolfo et al. (2004) do not accept these flowers as Nymphaeaceae, but other stem relatives or crown group members of crown angiosperms, such as Chloranthaceae, Winteraceae, monocots, and even eudicots also are known from 120- to 125-My-old fossils.
To allow for the possibility that 125-My-old Ephedra seed fossils may represent living species (as implied by Rydin et al., 2004, and Yang et al., 2005), we used these fossils to constrain the Ephedra crown group to 125 My old; i.e., we moved the constraint at node 3 in Figure 1 up to the node where E. fragilis diverges from E. sinica and E. trifurca.
Calibration for the strict clock (in the 13-taxon data set) came from the Cratonia fossil, which was used to fix the split between Gnetum and Welwitschia as 110 My. This split may have occurred considerably earlier since Cratonia is almost as apomorphic as Welwitschia (J. Doyle, personal communication, 2005), and this was one of the reasons why we resorted to calibration with fossils from more distant outgroups.
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Characteristics of Gnetum rbcL and matK Sequences
We generated 47 rbcL sequences from Gnetum as well as one sequence each from Welwitschia mirabilis and Ephedra trifurca. None of the rbcL sequences contained insertions or deletions within the exon stretch (bp 1 to 1352). The length of rbcL in Gnetales as in other seed plants is 1428 bp. For matK, we generated 12 new sequences (Appendix 1). Because a GenBank matK sequence identified as G. parvifolium (accession number AF280995 [GenBank] ) was indistinguishable from sequences of G. gnemon, it was excluded from further analyses. Two other matK sequences with single-base deletions were also excluded (Appendices 1 and 2). The length of matK is 1554 to 1557 bp for Gnetum, 1575 bp for Welwitschia, and 1662 bp for Ephedra (Appendix 1; also Huang et al., 2005). The length variation in Gnetum matK sequences was caused by a three-base-pair insertion between positions 10 and 12 in African G. africanum sequences. The G+C contents of rbcL sequences ranged from 41.8% to 45.2% and those of matK sequences from 31.1% to 33.1%, fitting well with G+C contents of other vascular plants (40.8 to 45.8% for rbcL and 27.1% to 37.7% for matK; Appendix 1).
Sequence divergences of rbcL and matK sequences within and among gnetalean genera are shown in Appendix 4 and neighbor-joining trees from these data are shown as Figure S3. Figure S4 plots the numbers of nucleotide substitution at synonymous (Ks) and nonsynonymous sites (Ka) in rbcL and matK across seed plants. Pairwise comparisons between nongnetalean vascular plants and comparisons between Gnetales and other vascular plants revealed no significant differences. Numbers of variable and parsimony-informative sites did not differ among codon positions (Appendix 5). The estimated number of nucleotide substitutions for Gnetum rbcL sequences was 0.058 (Ks) for synonymous sites and 0.031 (Ka) for nonsynonymous sites, on average. The averages and standard deviations of the observed Ka/Ks ratios were 0.057 ± 0.081 for rbcL and 0.524 ± 0.125 for matK. The Ka/Ks ratio in rbcL was thus about 1/10th that in matK, mainly because of much reduced substitutions at nonsynonymous sites (Fig. S4). Over all taxa, matK sequences showed about 1.5 times the maximum sequence divergence seen in rbcL, and in both genes, Gnetum had about six times the maximum divergence observed in Ephedra (in rbcL 0.048 versus 0.008; in matK 0.068 versus 0.012).
Phylogenetic Analyses and Divergence Time Estimation
Statistics for sequence variation, parsimony tree length, and consistency indices for the six data partitions are given in Appendix 6. The rbcL gene did not contain sufficient signal to reliably resolve relationships within Gnetum, but matK supported a sister-group relationship between Asian and African Gnetum and subdivision of Asian Gnetum into two clades (Fig. S5A). Bayesian analysis of the combined rbcL and matK data yielded a well-resolved and supported topology (Fig. S5B) in which Gnetales were sister to Pinaceae (with .86 posterior probability [PP]). However, matK alone placed Gnetales as sister to conifers (.96 PP), regardless of whether all positions, only 1st and 2nd positions, or only 3rd positions were included (trees not shown). It also weakly supported the monophyly of conifers (.80 PP).
A maximum likelihood tree obtained from the 6-locus-31-taxon data set shows well-resolved relationships within Gnetum (Fig. 2). Likelihood-ratio tests for this data set strongly rejected the clock assumption, and it was not used for dating purposes. The clock assumption was also rejected by just the rbcL and matK sequences (individually or combined) as long as data matrices included other seed plants besides Gnetales (P << 0.001). However, a matK/rbcL data set that included only 12 species of Gnetales plus Psilotum satisfied the clock (P > 0.05) and was analyzed under the assumption of a strict clock using the GTR+G+I model. Resulting genetic distances were calibrated by fixing the split between Gnetum and Welwitschia at 110 My based on the Cratonia fossil (see Materials and Methods).
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Because all larger rbcL/matK matrices rejected a strict clock, we applied a Bayesian relaxed clock, constrained with the fossil-based minimal ages specified in Materials and Methods and shown in Figure 1; the root node was constrained by a maximal age (Materials and Methods). Figure S6 shows a GTR+G+I ML phylogram from these data to provide a sense of branch length heterogeneity.
Table 1 lists the divergence times obtained for key nodes within Gnetum (labeled A, B, C, and D in all figures) under the Gnepine, Gnetifer, Gnetales-sister, Anthophyte, and Polytomy input topologies shown in Figures 1 and S1A–D. The different hierarchical relationships of seed plants, in particular whether conifers are monophyletic or paraphyletic and whether Gnetales are sister to all other seed plants or embedded in conifers, imply changes in the placements of two minimal constraints, namely the oldest gymnosperm (node 2) and the oldest conifer (node 5). This changed within-Gnetum time estimates by more or less 10 My (Table 1). For example, under the Gnepine seed plant topology, Gnetum first diverged at 26 My, under the Gnetifer topology it diverged at 29 My, under the Gnetales-sister hypothesis at 38 My, and under the Anthophyte hypothesis at 37 My. Estimates under the Polytomy input tree were closest to the estimates under the Gnetifer topology (Table 1). The experimental reassignment of the 125-My-old Ephedra seeds to the Ephedra crown instead of the stem (node 3 in Fig. 1), resulted in almost doubled within-Gnetum ages (Table 1).
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Estimates for major divergence events in Gnetum from the 13-taxon strict clock analysis were younger by about half compared to those from the 38-taxon relaxed clock analysis (Table 1). For example, the time estimated for the divergence of South American Gnetum from the remainder of the genus under a relaxed clock and the Gnepine topology (Fig. 1) was 26 My (13 to 47 my, 95% confidence interval), whereas under a strict clock, the same event was dated to 14 My.
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Effects of Tree Topologies, Constraints from Distant Outgroups, and Strict versus Relaxed Clock Inference
A polytomy in the input tree for a Bayesian analysis implies a prior belief that speciation events occurred at about the same time so that it cannot be estimated from substitutions in what order they occurred. This is hardly a well-founded hypothesis for the evolution of the four lineages of gymnospermous seed plants that make up the particular polytomy relevant to the present study. Empirically, however, this unconvincing prior hypothesis had little impact on the posterior distribution of within-Gnetum estimates, which under the polytomy input tree closely resembled estimates obtained under the Gnetifer input tree. The likely reason is that polytomies in dating trees might impact posteriors branch lengths only where there is branch length uncertainty throughout the tree (J. Thorne, personal communication, Oct. 2005), whereas there is strong branch length information in many parts of the seed plant tree, as evident in a phylogram of the underlying data (Fig. S6). Another caveat concerning current Bayesian relaxed clock implementations is that the impact of the other priors used, namely the root rate and the Brownian motion parameter (Materials and Methods), is poorly understood.
What is clear from our results is that the constraint(s) closest to the nodes being estimated exert(s) the strongest impact (also Wiegmann et al., 2003) and that clear signal in molecular branch lengths can push nodes far from their own minimal constraints. For example, node 7, crown Cupressaceae, and node 8, crown Pinaceae, are both constrained by fossils to minimally 90 My old, but inspection of Figure 1 and S1A–D shows that based on genetic distances and irrespective of the seed plant topology employed, crown Pinaceae are considerably older than crown Cupressaceae.
In terms of their likelihood scores, the unconstrained input topologies rank as follows: Gnepine seed plant topology (–ln = 27,964.2703), Gnetifer topology (–ln = 27,964.9216), Gnetales sister topology (–ln = 27,971.7141), and, worst, the Anthophyte topology (–ln = 27,976.5747). The most comprehensive seed plant analysis to date (Burleigh and Mathews, 2004) found that combined data from 13 loci (for 31 exemplar taxa) favored the Gnetales sister topology, whereas slower evolving data partitions favored the Gnepine tree. In the following section we concentrate on the estimates obtained under the Gnepine topology (Table 1, row 2). However, the within-Gnetum ages obtained under the alternative seed plant topologies, including the polytomy tree, differ by only 4 to 12 My, and our inferences concerning Gnetum therefore would change little if one of the other seed plant trees turned out to be true. Our conclusions further incorporate strict clock estimates, which do not depend on seed plants outside Gnetales. The strict clock (for 13 Gnetales) yielded an estimate of 14 My for the onset of diversification within Gnetum, about half that from the 38-taxon relaxed clock (26 My; 95% confidence range 13–47 My). This is probably due to the well-known taxon density effect in molecular dating (e.g., Linder et al., 2005); more densely sampled clades generally yield older ages. An earlier strict clock estimate for the onset of diversification of extant Gnetum was 11 to 6 My (Won and Renner, 2003); the difference between our earlier analysis and the present is that we here included two additional species of Ephedra and deleted a stretch of about 400 bp from the matK data because of gapped Ephedra sequences.
Biogeography and Evolution of Gnetum
The major divergence events among extant clades of Gnetum are estimated as dating to the Upper Oligocene, Miocene, and Pliocene (Table 1). Under the strict clock, the main South American, African, and Asian divergence events occurred sometime during the Miocene and Pliocene, whereas the Bayesian relaxed clock implies divergence during the Upper Oligocene and Miocene. These estimates in no way contradict the Mesozoic fossil record of Gnetales (Introduction), which includes over 100-My-old relatives of extant species of Ephedra and Welwitschia (e.g., Mohr and Friis, 2000; Yang, 2002; Rydin et al., 2003, 2004, 2006; Mohr et al., 2004; Wang, 2004; Yang et al., 2005; Dilcher et al., 2005). Rather, the molecular estimates concern the recent-most common ancestor of living clades, while the fossils may represent members of stem lineages or extinct sister species. Gnetales were diverse and widespread during the Cretaceous, and the almost worldwide occurrence of their fossils compared to their present range indicates that they have suffered major extinctions. A new insight from this study is that Gnetum has undergone a geologically recent radiation, especially in the Malesian region and that the genus's present disjunct range is not Gondwanan. It is possible that the Asian radiation coincided with times of low sea levels because of the opportunities for overland seed dispersal they would have afforded (Fig. 2). Temporally, although not geographically, our findings for Gnetum parallel those for Ephedra (Huang and Price, 2003; Ickert-Bond and Wojciechowski, 2004). In the case of Ephedra, the evolution of Mediterranean climates, the rise of the Rockies and the Andes, and seed dispersal by birds and rodents (e.g., Ridley, 1930; Holmgren et al., 2003) all seem to have contributed to relatively recent radiations (as well as contributing to species formation per se).
Biogeographic analyses of other plant families with ancient and relatively good fossil records, such as Calycanthaceae, Chloranthaceae, Nothofagus, and Nymphaeaceae, have obtained similar results, namely that in spite of their impressive fossil records, these clades apparently reached some parts of their range quite recently (Zhang and Renner, 2003: Chloranthaceae; Knapp et al., 2005: Nothofagus; Zhou et al., 2006: Calycanthaceae; Yoo et al., 2006: Nymphaeaceae). In other words, old lineages do not necessarily stop dispersing and diversifying, as pointed out by Markgraf (1929), the last monographer of Gnetum, in the quote at the beginning of this paper. Similarly, Ephedra seems to have diversified in its current habitat during Miocene times (Huang and Price, 2003; Ickert-Bond and Wojciechowski, 2004), in spite of morphological stasis in some morphological traits, such as the seed coat in fossil E. archaeorhytidosperma and living E. rhytidosperma (Yang et al., 2005). Such morphological stasis does not imply that the respective fossil represents a member of continuous ancestor-descendent chains of populations without intervening speciation events. When we nevertheless used the 125-My-old Ephedra seed fossils to constrain the minimal age of living species of Ephedra (the experiment reported in Table 1, row 7), divergences between South American, African, and Asian Gnetum were still estimated as dating to the Eocene and Oligocene, rather than being Gondwanan.
Gnetum currently comprises ten species in South America, one in West Africa, and 
25 in tropical and subtropical Asia. If an Oligocene/Miocene age is accepted for the extant lineages in South America and Asia (Fig. 2), then Gnetum must have reached its disjunct pantropical range either through transoceanic dispersal or through a Laurasian expansion followed by southwards spread. If one considers the upper error bracket of ± 50 My (under any of the different seed plant topologies; Table 1), rather than the point estimates, Gnetum would be old enough to have dispersed across the North Atlantic land bridge to Africa and Asia. An Eocene boreotropical range, with subsequent fragmentation during the Oligocene climate cooling, is difficult to reject with available data, but does not fit well with the occurrence of it sister group, Welwitschia, in Africa and Brazil (living and as fossils, respectively).
In terms of dispersal biology, water dispersal in seawater is a strong possibility. Some South American species, for example, G. venosum, have a special middle layer in the seed coat that gives buoyancy (Kubitzki, 1985), and others, such as G. gnemonoides, have large, corky diaspores (Markgraf, 1951). The smallest diaspores in the genus, those of G. africanum, measure 1.2–1.5 cm x 0.8 cm; the largest Gnetum seeds measure 7 cm x 3–4 cm. In most species, the mature seed envelope turns red or yellow, and seeds are then attractive to large birds, such as toucans, but also to rodents and monkeys (e.g., Ridley, 1930; Markgraf, 1951; Kubitzki, 1985; Van Roosmalen, 1985; Forget at al., 2002). Fish eat the seeds when they fall into streams, and Amazon catfish are known to regurgitate them because of sclerenchyma needles in the seed envelope (Goulding, 1980; Kubitzki, 1985). Fish dispersal therefore does not destroy the embryo. Gnetum species commonly grow along rivers, and there are also observations of Gnetum seeds from sea drift; for example, from beaches in Malaysia (Ridley, 1930; Hemsley in Markgraf, 1951). Several months are required for embryo maturation (Maheshwari and Vasil, 1961).
A review of molecular clock-dated instances of diaspore dispersal and how they relate to the direction of surface currents in the Atlantic (Renner, 2004) showed that there are several cases of likely water dispersal between South America and Africa. Dispersal between Africa, Madagascar, and India/Malaysia appears even more common (Thorne, 1973; additional references in Renner, 2005) and is more readily explained than that between South America and Africa because distances are shorter and there are regular monsoon wind systems as well as sea currents favorable for the transport of small objects between Africa, the Seychelles, the Comores, the Chagos archipelago (about half way between Africa and Indonesia), and India. Recently discovered examples of transmarine dispersal between Madagascar, Africa, and the Seychelles include multiple lineages of frogs, chameleons, rodents, Carnivora, and lemurs (De Queiroz, 2004; Renner, 2004).
With the likely time horizon for the evolution of Gnetum being the Upper Oligocene, Miocene, and Pliocene (Table 1), what were the main forces behind the radiation of the genus in South American and Southeast Asia? Entry into new kinds of habits appears to have played a limited role; the climbing species of Gnetum as well as the two tree species occur in the understory of upland forests and in riparian vegetation. The tree habit appears to have evolved once, in the ancestor of G. costatum and G. gnemon, rather than being an ancestral state as previously assumed (Markgraf, 1929; Fig. 2). Besides growth form, there are few other morphological differences that would readily suggest different habitat niches; instead, species differences in Gnetum concern details of strobilus branching, and seed and leaf size.
Apparently, geographic isolation played the main role in species formation in Gnetum. Thus, in South America, the uplift of the northern Andes led to at least one species pair: Gnetum woodsonianum (= G. leyboldii var. woodsonianum) occurs from Costa Rica to Colombia and is sister to G. schwackeanum from Venezuela and the Guianas to northern Brazil (Stevenson and Zanoni, 1991; Fig. 2). The Colombian Andes were formed by rapid uplift of the Eastern Cordillera between 5 and 2 Mya (Gregory-Wodzicki, 2000), and Central and South America were not connected until about 3 Mya (Haug and Tiedemann, 1998). The ancestor of G. woodsonianum likely became separated by the uplift of the Colombian Andes and then expanded its distribution across the Panamanian land bridge into Costa Rica. The remaining eight South American species are distributed east of the Andes, mainly in the Amazonian lowland below 600 m altitude; only G. camporum occurs in the Guiana highland at up to 1800 m altitude.
The Asian subclades of Gnetum are between 4 and 22 My old (Table 1, Fig. 2) and result from multiple cycles of colonization, judging from the overlapping distributions of the largest subclades, G. hainanense s.l., G. latifolium s.l., and G. cuspidatum. All three subclades range from the Malay Peninsula to New Guinea across Borneo, Sulawesi, and the Philippines. Each subclade contains widely distributed and endemic species. Such pairs (Fig. 2) are G. gnemon with a wide distribution and its sister species G. costatum, endemic in New Guinea; G. gnemonoides with a wide distribution and its sister G. raya, endemic to Borneo; and G. latifolium s.l. with a wide distribution and its sister clade G. neglectum, endemic to Borneo, and G. sp. nov. Takeuchi et al. 7049, endemic in New Guinea. The Gnetum cuspidatum clade includes further pairs of wide-ranging species and narrow endemics (Fig. 2: G. klossii endemic to Borneo; G. tenuifolium endemic to the Malay Peninsula; G. microcarpum, G. diminutum, and G. acutum endemic to the Malay Peninsula and Borneo, G. macrostachyum ranging all the way from southern Indochina through the Malay Peninsula to Sumatra). These overlaid patterns of wide-ranging species related to local endemics suggest waves of expansion, local isolation or extinction, and reexpansion. Fluctuation in sea level (Haq et al., 1987; our Fig. 2) may have facilitated the dispersal of Gnetum over to the Malesian islands, while at other times acting as barriers to dispersal. To date, only one case of introgression has been detected among species of Gnetum: analyses of nuclear ribosomal internal transcribed spacer (ITS) sequences and of the second intron of the nuclear LEAFY gene suggest that G. klossii, a member of the G. cuspidatum clade in terms of its ITS sequences (as well as its chloroplast sequences), falls in the G. latifolium s.l. clade in terms of its LEAFY second intron sequences (Won and Renner, 2005a).
Dense sampling of population-level genetic variation in several of the suspected young species pairs would allow testing our scenario of recent waves of expansion and extinction in Indonesian and Malesian clades of Gnetum. A complicating aspect deserving further study in this context is the impact humans may have had on the distribution of Gnetum; G. gnemon is commonly cultivated for food in Indonesia and New Guinea, where the migrations of human populations have greatly influenced the distribution patterns of important tropical crop plants (Barrau, 1963). Currently, G. gnemon has the widest distribution of all Asian Gnetum, even having reached Fiji, either via over water dispersal or with the help of Homo sapiens sapiens.
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We thank Jim Doyle, an anonymous reviewer, and the associate editor, Peter Linder, for constructive criticism; Y.-C. Chan, N. V. Dzu, H. Gang, A. Hussein, Z. bin Mat Said, J. F. Maxwell, M. Postar, R. Wang, and K.-M. Wong for help with fieldwork; L. Gillespie, D. K. Harder, M. F. Prévost, S. Shi, P. Suksathan, W. Takeuchi, and the botanical gardens of Bogor, Mainz, New York, Edinburgh, and the University of California–Berkeley for plant material; S.-M. Chaw for Gnetum matK cloning; S. Ickert-Bond, C. Rydin, and J. Huang for Ephedra aliquots and pre-publication sequences; B. Mohr and Y. Yang for information about Welwitschia and Ephedra fossils; and M. Krings, J. Hill, and E. Hermsen for discussion of seed plant fossils. This paper represents part of a dissertation submitted by the first author in partial fulfillment of the requirements for a Ph.D. from University of Missouri–St. Louis. The American Society of Plant Taxonomy, the International Association of Plant Taxonomy, and the International Center for Tropical Ecology at the University of Missouri–St. Louis supported our work financially.
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2 Present Address: Seoul National University, College of Natural Sciences, School of Biological Sciences, Seoul, Korea 151-742
3 Present Address: Department of Biology, Ludwig Maximilians University, D-80638, Munich, Germany E-mail: renner{at}lrz.uni-muenchen.de
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-
Aris-Brosou S., Yang Z. Effects of models of rate evolution on estimation of divergence dates with special reference to the metazoan 18S rRNA phylogeny. Syst. Biol. (2002) 51:703–714.
Barrau J. Plants and the migration of Pacific peoples (1963) Honolulu, Hawaii: Bishop Museum Press.
Barrett P. M. Evolutionary consequences of dating the Yixian Formation. Trends Ecol. Evol. (2000) 15:99–103.[CrossRef][Medline]
Bowe L. M., Coat G., dePamphilis C. W. Phylogeny of seed plants based on all three genomic compartments: extant gymnosperms are monophyletic and Gnetales' closest relatives are conifers. Proc. Natl. Acad. Sci. USA. (2000) 97:4092–4097.
Brenner E. D., Stevenson D. W., Twigg R. W. Cycads: evolutionary innovations and the role of plant-derived neurotoxins. Trends Plant Sci. (2003) 8:446–452.[CrossRef][Web of Science][Medline]
Brunsfeld S. J., Soltis P. S., Soltis D. E., Gadek P. A., Quinn C. J., Strenge D. D., Ranker T. A. Phylogenetic relationships among the genera of Taxodiaceae and Cupressaceae: evidence from rbcL sequences. Syst. Bot. (1994) 19:253–262.[CrossRef]
Burleigh J. G., Mathews S. Phylogenetic signal in nucleotide data from seed plants: implications for resolving the seed plant tree of life. Am J. Bot. (2004) 91:1599–1613.
Chaw S. -M., Parkinson C. L., Cheng Y., Vincent T. M., Palmer J. D. Seed plant phylogeny inferred from all three plant genomes: monophyly of extant gymnosperms and origin of Gnetales from conifers. Proc. Natl. Acad. Sci. USA. (2000) 97:4086–4091.
Cheng Y., Nicolson R. G., Tripp K., Chaw S. -M. Phylogeny of Taxaceae and Cephalotaxaceae genera inferred from chloroplast matK gene and nuclear rDNA ITS region. Mol. Phylogenet. Evol. (2000) 14:353–365.[CrossRef][Web of Science][Medline]
Conran J. G., Wood G. A., Martin P. G., Dowd J. M., Quinn C. J., Gadek P. A., Price R. A. Generic relationships within and between the gymnosperm families Podocarpaceae and Phyllocladaceae based on an analysis of the chloroplast gene rbcL. Aust. Syst. Bot. (2000) 48:715–724.
Crane P. R. The fossil history of the Gnetales. Int. J. Plant Sci. (1996) 157(6 Suppl.):S50–S57.[CrossRef][Web of Science]
Crane P. R., Upchurch G. R. Drewria potomacensis gen. et sp. nov. an early Cretaceous member of Gnetales from the Potomac group of Virginia. Am. J. Bot. (1987) 74:1722–1776.[CrossRef][Web of Science]
De Queiroz A. The resurrection of oceanic dispersal in historical biogeography. Trends Ecol. Evol. (2004) 20:68–73.[CrossRef]
Dilcher D. L., Bernardes-de-Oliveira M. E., Pons D., Lott T. A. Welwitschiaceae from the Lower Cretaceous of Northeastern Brazil. Am. J. Bot. (2005) 92:1294–1310.
Doyle J. A., Donoghue M. J. Phylogenies and angiosperm diversification. Paleobiol. (1993) 19:141–167.[Abstract]
Drummond A. J., Rambaut A. (2005) BEAST v1.3, Available from http://evolve.zoo.ox.ac.uk/beast/.
Duan S. -Y. The oldest angiosperm—a tricarpous female reproductive fossil from western Liaoning Province, NE China. Sci. China Ser. D (1998) 41:14–20.[CrossRef]
Farjon A., Ortiz Garcia S. Cone and ovule development in Cunninghamia and Taiwania (Cupressaceae sensu lato) and its significance for conifer evolution. Am. J. Bot. (2003) 90:8–16.
Forget P. -M., Hammond D. S., Milleron T., Thomas R. Seasonality of fruiting and food hoarding by rodents in neotropical forests: consequences for seed dispersal and seedling recruitment. In: Seed dispersal and frugivory: Ecology, evolution and conservation—Levey D. J., Silva W. R., Galetti M., eds. (2002) U.K.: CABI Publishing. 241–256.
Friis E. M., Pedersen K. R., Crane P. R. Fossil evidence of water lilies (Nymphaeales) in the Early Cretaceous. Nature (2001) 410:357–360.[CrossRef]
Gadek P. A., Alpers D. L., Heslewood M. M., Quinn C. J. Relationships within Cupressaceae sensu lato: a combined morphological and molecular approach. Am. J. Bot. (2000) 87:1044–1057.
Gandolfo M. A., Nixon K. C., Crepet W. L. Turonian Pinaceae of New Jersey. Plant Syst. Evol. (2001) 226:187–203.[CrossRef]
Gandolfo M. A., Nixon K. C., Crepet W. L. Cretaceous flowers of Nymphaeaceae and implications for complex insect entrapment pollination mechanisms in early angiosperms. Proc. Natl. Acad. Sci. USA. (2004) 101:8056–8060.
Gao Z., Thomas B. A. A review of cycad megasporophylls, with new evidence of Crossozamia Pomel and its associated leaves from the Lower Permian of Taiyuan, China. Rev. Palaeobot. Palynol. (1989) 60:205–233.[CrossRef][Web of Science]
Germano J., Klein A. S. Species-specific nuclear and chloroplast single nucleotide polymorphisms to distinguish Picea glauca, P. mariana and P. rubens. Theor. Appl. Genet. (1999) 99:37–49.[CrossRef][Web of Science]
Gerrienne P., Meyer-Berthaud B., Fairon-Demaret M., Streel M., Steemans P. Runcaria, a Middle Devonian seed plant precursor. Science (2004) 306:856–858.
Goulding M. The fishes and the forest (1980) Berkeley: University of California Press.
Gradstein F. M., Ogg J. G., Smith A. G., eds. A geologic time scale 2004 (2004) Cambridge, UK: Cambridge University Press.
Gregory-Wodzicki K. M. Uplift history of Central and Northern Andes: a review. GSA Bulletin (2000) 112:1091–1105.
Gugerli F., Sperisen C., Büchler U., Brunner I., Brodbeck S., Palmer J. D., Qiu Y. -L. The evolutionary split of Pinaceae from other conifers: evidence from an intron loss and a multigene phylogeny. Mol. Phylogenet. Evol. (2001) 21:167–175.[CrossRef][Web of Science][Medline]
Haq B. U., Hardenbol J., Vail P. R. Chronology of fluctuating sea levels since the Triassic. Science (1987) 235:1156–1167.
Hasebe M., Kofuji R., Ito M., Kato M., Iwatsuki K., Ueda K. Phylogeny of gymnosperms inferred from rbcL gene sequences. Bot. Mag. Tokyo (1992) 105:673–679.[CrossRef]
Hasebe M., Wolf P. G., Pryer K. M., Ueda K., Ito M., Sano R., Gastony G. J., Yokoyama J., Manhart J. R., Murakami N., Crane E. H., Haufler C. H., Hauk W. D. A global analysis of fern phylogeny based on rbcL nucleotide sequences. Am. Fern J. (1995) 35:134–181.
Haug G. H., Tiedemann R. Effect of the formation of the Isthmus of Panama on Atlantic Ocean thermohaline circulation. Nature (1998) 393:673–676.[CrossRef]
Henschel J. R., Seely M. K. Long-term growth patterns of Welwitschia mirabilis, a long-lived plant of the Namib Desert (including a bibliography). Plant Ecology (2000) 150:7–26.[CrossRef][Web of Science]
Hesse M., Weber M., Halbritter H. A comparative study of the polyplicate pollen types in Arales, Laurales, Zingiberales, and Gnetales. In: Pollen and spores: morphology and biology—Harley M. M., Morton C. M., Blackmore S., eds. (2000) Kew, UK: Royal Botanic Gardens. 227–239.
Hilu K. W., Borsch T., Müller K., Soltis D. E., Soltis P. S., Savolainen V., Chase M. W., Powell M. P., Alice L. A., Evans R., Sauquet H., Neinhuis C., Slotta T. A. B., Rohwer J. G., Slotta T. A. B., Rohwer J. G., Campbell C. S., Chatrou L. W. Angiosperm phylogeny based on matK sequence information. Am. J. Bot. (2003) 90:1758–1776.
Hilu K. W., Liang H. The matK gene: sequence variation and application in plant systematics. Am. J. Bot. (1997) 84:830–839.[Abstract]
Hipkins V. D., Tsai C. J., Strauss S. H. Sequence of the gene for the large subunit of ribulose 1,5-bisphosphate carboxylase from a gymnosperm, Douglas fir. Plant Mol. Biol. (1990) 15:505–507.[CrossRef][Web of Science][Medline]
Ho S. Y. W., Phillips M. J., Drummond A. J., Cooper A. Accuracy of rate estimation using relaxed-clock models with a critical focus on the early metazoan radiation. Mol. Biol. Evol. (2005) 22:1355–1363.
Holmgren C. A., Peñalba M. C., Rylander K. A., Betancourt J. L. A 16,000 14C yr B.P. packrat midden series from the USA–Mexico borderlands. Quatern. Res. (2003) 60:319–329.[CrossRef]
Huang J., Giannasi D. E., Price R. A. Phylogenetic relationships in Ephedra (Ephedraceae) inferred from chloroplast and nuclear DNA sequences. Mol. Phylogenet. Evol. (2005) 35:48–59.[CrossRef][Web of Science][Medline]
Huang J., Price R. A. Estimation of the age of extant Ephedra using chloroplast rbcL sequence data. Mol. Biol. Evol. (2003) 20:435–440.
Huelsenbeck J. P., Ronquist F. R. MrBayes: Bayesian inference of phylogenetic trees. Bioinformatics (2001) 17:754–755.
Ickert-Bond S. M., Wojciechowski M. F. Phylogenetic relationships in Ephedra (Gnetales): Evidence from nuclear and chloroplast DNA sequence data. Syst. Bot. (2004) 29:834–849.[CrossRef]
Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol. (1980) 16:111–120.[CrossRef][Web of Science][Medline]
Kishino H., Thorne J. L., Bruno W. J. Performance of a divergence time estimation method under a probabilistic model of rate evolution. Mol. Biol. Evol. (2001) 18:352–361.
Knapp M., Stöckler K., Havell D., Delsuc F., Sebastiani F., Lockhart P. J. Relaxed molecular clock provides evidence for long-distance dispersal of Nothofagus (Southern Beech). PLoS Bio. (2005) 3:38–43.[CrossRef]
Korall P., Kenrick P. Phylogenetic relationships in Selaginellaceae based on rbcL sequences. Am. J. Bot. (2002) 89:506–517.
Krassilov V. A. Early Cretaceous flora of Mongolia. Palaeontographica Abt. B. (1982) 181:1–43.
Krassilov V. A. New floral structure from the Lower Cretaceous of Lake Baikal area. Rev. Palaeobot. Palynol. (1986) 47:9–16.[CrossRef][Web of Science]
Krassilov V. A. Angiosperm origins: Morphological and ecological aspects (1997) Sofia, Bulgaria: PENSOFT Publishers. 50–52.
Kubitzki K. Ichthyochory in Gnetum venosum. An. Acad. Barsil. Ciênc. (1985) 57:513–516.
Kubitzki K. Gnetatae. In: The families and genera of vascular plants I: Pteridophytes and Gymnosperms—Kramer K. U., Green P. S., eds. (1990) Berlin, Heidelberg: Springer-Verlag. 378–391.
Kumar S., Tamura K., Jakobsen I. B., Nei M. MEGA2: molecular evolutionary genetics analysis software. Bioinformatics (2001) 17:1244–1245. http://www.megasoftware.net.
LePage B. A. A new species of Thuja (Cupressaceae) from the Late Cretaceous of Alaska: implications of being evergreen in a polar environment. Am. J. Bot. (2003a) 90:167–174.
LePage B. A. The evolution, biogeography and palaeoecology of the Pinaceae based on fossil and extant representatives. Acta Hort. (2003b) 615:29–52. IV Int. Conifer Conf.
Les D. H., Garvin D. K., Wimpee C. F. Molecular evolutionary history of ancient aquatic angiosperms. Proc. Natl. Acad. Sci. USA. (1991) 88:10119–10123.
Les D. H., Schneider E. L., Padgett D. J., Soltis P. S., Soltis D. E., Zanis M. Phylogeny, classification and floral evolution of water lilies (Nymphaeales): a synthesis of non-molecular, rbcL, matK and 18S rDNA data. Syst. Bot. (1999) 24:28–46.[CrossRef]
Lidholm J., Gustafsson P. A three-step model for the rearrangement of the chloroplast trnK-psbA region of the gymnosperm Pinus contorta. Nucleic Acids Res. (1991) 19:2881–2887.
Linder H. P., Hardy C. R., Rutschmann F. Taxon sampling effects in molecular clock dating: an example from the African Restionaceae. Mol. Phyl. Evol. (2005) 35:569–582.[CrossRef][Web of Science][Medline]
Magallón S., Sanderson M. J. Relationships among seed plants inferred from highly conserved genes: sorting conflicting phylogenetic signals among ancient lineages. Am. J. Bot. (2002) 89:1991–2006.
Maheshwari P., Vasil V. Gnetum (1961) New Delhi, India: Council of Scientific & Industrial Research.
Manhart J. R. Phylogenetic analysis of green plant rbcL sequences. Mol. Phylogenet. Evol. (1994) 3:114–127.[CrossRef][Medline]
Markgraf F. Monographie der Gattung Gnetum. Bull. Jard. Bot. Buitenzorg (1929) 10:407–511. Ser. 3.
Markgraf F. Gnetaceae. Flora Malesiana I (1951) 336–347. 4.
Miller C. N. Jr. Implications of fossil conifers for the phylogenetic relationships of living families. Bot. Rev. (1999) 65:239–277.[CrossRef]
Mohr B. A., Bernardes-de-Oliveira M. E., Barreto A. M. F., Castro-Fernandes M. C. Gnetophyte preservation and diversity in the Early Cretaceous Crato Formation (Brazil). VII. (2004) International Organization of Paleobotany Conference: BarilocheArgentina.
Mohr B. A., Friis E. M. Early angiosperms from the Lower Cretaceous Crato Formation (Brazil), a preliminary report. Int. J. Plant Sci. (2000) 161(6 Suppl.):S155–S167.[CrossRef][Web of Science]
Near T. J., Meylan P. A., Shaffer H. B. Assessing concordance of fossil calibration points in molecular clock studies: an example using turtles. Am. Nat. (2005) 165:137–146.[CrossRef][Web of Science][Medline]
Ohyama K., Fukuzawa H., Kohchi T., Shirai H., Sano T., Sano S., Umesono K., Shiki Y., Takeuchi M., Chang Z., Aota S., Inokuchi H., Ozeki H. Chloroplast gene organization deduced from complete sequence of liverwort Marchantia polymorpha chloroplast DNA. Nature (1986) 322:572–574.[CrossRef][Web of Science]
Palmer J. D., Soltis D. E., Chase M. W. The plant tree of life: an overview and some points of view Am. J. Bot. (2004) 91:1437–1445.[CrossRef]
Posada D., Crandall K. A. ModelTest: testing the model of DNA substitution. Bioinformatics (1998) 14:817–818.
Price R. A. Systematics of the Gnetales: a review of morphological and molecular evidence. Int. J. Plant Sci. (1996) 157(6 Suppl.):S40–S49.[CrossRef][Web of Science]
Pryer K. M., Schneider H., Smith A. R., Cranfill R., Wolf P. G., Hunt J. S., Sipes S. D. Horsetails and ferns are a monophyletic group and the closest living relatives to seed plants. Nature (2001) 409:618–622.[CrossRef][Medline]
Quandt D., Borsch T., Wicke S., Won H., Renner S. S., Hilu K. W. Land plant evolution: a perspective from fast-evolving chloroplast regions (2006) BAS abstract 835, http://2006.botanyconference.org/engine/search/index.php?func=detail&aid=835.
Qiu Y. -L., Chase M. W., Les D. H., Hills H. G., Parks C. R. Molecular phylogenetics of the Magnoliidae: A cladistic analysis of nucleotide sequences of the plastid gene rbcL. Ann. Mo. Bot. Gard. (1993) 80:587–606.[CrossRef]
Qiu Y. -L., Lee J., Bernasconi-Quadroni F., Soltis D. E., Soltis P. S., Zanis M., Zimmer E. A., Chen Z., Savolainen V., Chase M. W. The earliest angiosperms: evidence from mitochondrial, plastid and nuclear genomes. Nature (1999) 402:404–407.[CrossRef]
Quinn C. J., Price R. A., Gadek P. A. Familial concepts and relationships in the conifers based on rbcL and matK sequence comparisons. Kew Bull. (2002) 57:513–531.[CrossRef]
Rai H. S., O'Brien H. E., Reeves P. A., Olmstead R. G., Graham S. W. Inference of higher-order relationships in the cycads from a large chloroplast data set. Mol. Phylogenet. Evol. (2003) 29:350–359.[CrossRef][Web of Science][Medline]
Rambaut A., Bromham L. Estimating divergence dates from molecular sequences. Mol. Biol. Evol. (1998) 15:442–448.[Abstract]
Renner S. S. Circumscription and phylogeny of the Laurales: evidence from molecular and morphological data. Am. J. Bot. (1999) 86:1301–1315.
Renner S. S. Plant dispersal across the tropical Atlantic by wind and sea currents. Int. J. Plant Sciences (2004) 165(4 Suppl.):S23–S33.[CrossRef]
Renner S. S. Relaxed molecular clocks for dating historical plant dispersal events. Trends Plant Sci. (2005) 10:550–558.[CrossRef][Web of Science][Medline]
Renner S. S., Zhang L. -B. Biogeography of the Pistia clade (Araceae): Based on Chloroplast and mitochondrial DNA sequences and Bayesian divergence time inference. Syst. Biol. (2004) 53:422–432.
Ridley H. N. The dispersal of plants throughout the world (1930) Ashford: L. Reeve & Co. Ltd.
Rydin C., Källersjö M., Friis E. M. Seed plant relationships and the systematic position of Gnetales based on nuclear and chloroplast DNA: conflicting data, rooting problems and the monophyly of conifers. Int. J. Plant Sci. (2002) 163:197–214.[CrossRef][Web of Science]
Rydin C., Mohr B. A., Friis E. M. Cratonia cotyledon gen. et sp. nov.: a unique Cretaceous seedling related to Welwitschia. Proc. R. Soc. London Ser. B. (2003) 270(Suppl.):29–32.[CrossRef][Medline]
Rydin C., Pedersen K. R., Friis E. M. On the evolutionary history of Ephedra: Cretaceous fossils and extant molecules. Proc. Natl. Acad. Sci. USA. (2004) 101:16571–16576.
Rydin C., Wikström N. Phylogeny of Isoetes (Lycopsida): resolving basal relationships using rbcL sequences. Taxon (2002) 51:83–89.[CrossRef][Web of Science]
Rydin C., Pederson K. R., Crane P. R., Friis E. M. Former diversity of Ephedra (Gnetales): Evidence from Early cretaceous seed from Portugal and North America. Ann. Bot. (2006) 98:123–140.
Sanderson M. J. Estimating absolute rates of molecular evolution and divergence times: A penalized likelihood approach. Mol. Biol. Evol. (2002) 19:101–109.
Sanderson M. J., Doyle J. A. Source of error and confidence intervals in estimating the age of angiosperms from rbcL and 18S rDNA data. Am. J. Bot. (2001) 88:1499–1516.
Schmidt M., Schneider-Poetsch H. A. W. The evolution of gymnosperms redrawn by phytochrome genes: the Gnetatae appear at the base of the gymnosperms. J. Mol. Evol. (2002) 54:715–724.[CrossRef][Web of Science][Medline]
Setoguchi H., Osawa T. A., Pintaud J. -C., Jaffre T., Veillon J. -M. Phylogenetic relationships within Araucariaceae based on rbcL gene sequences. Am. J. Bot. (1998) 85:1507–1516.
Shi S., Jin H., Zhong Y., He X., Huang Y., Tan F., Boufford D. E. Phylogenetic relationships of the Magnoliaceae inferred from cpDNA matK sequences. Theor. Appl. Genet. (2000) 101:925–930.[CrossRef][Web of Science]
Soltis D. E., Soltis P. S., Zanis M. J. Phylogeny of seed plants based on evidence from eight genes. Am. J. Bot. (2002) 89:1670–1681.
Stevenson D., Zanoni T. Gnetaceae. In: Flora of the Guianas—Gorts-van Rijn A. R. A., ed. (1991) vol. 9:12–18. series A.
Stockey R. A. The Araucariaceae: an evolutionary perspective. Rev. Palaeobot. Palynol. (1982) 37:133–154.[CrossRef][Web of Science]
Sun G., Zheng S. -L., Dilcher D. L., Wang Y. -D., Mei S. -W. Early angiosperms and their associated plants from western Liaoning, China (2001) Shanghai, China: Shanghai Scientific and Technological Education Publishing House.
Swofford D. L. Phylogenetic analysis using parsimony (2002) Sunderland, Massachusetts: Sinauer Associates. PAUP*. (*and other methods), version 4.
Thompson J. D., Gibson T. J., Plewniak F., Jeanmougin F., Higgins D. G. The ClustalX Windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. (1997) 24:4876–4882.
Thorne J. L., Kishino H. Divergence time estimation and rate evolution with multilocus data sets. Syst. Biol. (2002) 51:689–702.
Thorne J. L., Kishino H., Painter I. S. Estimating the rate of evolution of the rate of molecular evolution. Mol. Biol. Evol. (1998) 15:1647–1657.[Abstract]
Treutlein J., Wink M. Molecular phylogeny of cycads inferred from rbcL sequences. Naturwissenschaften (2002) 89:221–225.[CrossRef][Web of Science][Medline]
Tsumura Y., Suyama Y. Differentiation of mitochondrial DNA polymorphisms in populations of five Japanese Abies species. Evolution (1998) 52:1031–1042.[CrossRef][Web of Science]
Van Roosmalen M. G. M. Fruits of the Guianan Flora (1985) Institute of Systematic Botany, Utrecht University.
Wang X. Q., Tank D. C., Sang T. Phylogeny and divergence times in Pinaceae: evidence from three genomes. Mol. Biol. Evol. (2000) 17:773–781.
Wang Z. -Q. A new Permian gnetalean cone as fossil evidence for supporting current molecular phylogeny. Ann. Bot. (2004) 94:281–288.
Wiegmann B. M., Yeates D. K., Thorne J. L., Kishino H. Time flies, a new molecular time-scale for brachyceran flye evolution without a clock. Syst. Biol. (2003) 52:745–756.
Wikström N., Kenrick P. Phylogeny of epiphytic Huperzia (Lycopodiaceae): paleotropical and neotropical clades corroborated by rbcL sequences. Nord. J. Bot. (2000) 20:165–171.[CrossRef]
Won H., Renner S. S. Horizontal gene transfer from flowering plants to Gnetum. Proc. Natl. Acad. Sci. USA. (2003) 100:10824–10829.
Won H., Renner S. S. The internal transcribed spacer of nuclear ribosomal DNA in the gymnosperm Gnetum. Mol. Phylogenet. Evol. (2005a) 36:581–597.[CrossRef][Web of Science][Medline]
Won H., Renner S. S. The chloroplast trnT-trnF region in the seed plant lineage Gnetales. J. Mol. Evol. (2005b) 60:1–12.[CrossRef][Web of Science][Medline]
Yang Y., Geng B. -Y., Dilcher D. L., Chen Z. -D., Lott T. A. Morphology and affinities of an Early Cretaceous Ephedra (Ephedraceae) from China. Am. J. Bot. (2005) 922:231–241.
Yang Z. PAML: A program package for phylogenetic analysis by maximum likelihood Computer Appl. Biosci. (1997) 13:555–556. http://abacus.gene.ucl.ac.uk/software/paml.html.
Yoo M. -J., Bell C. D., Soltis P. S., Soltis D. E. Divergence times and biogeography of Nymphaeales. Syst. Bot. (2005) 30:693–704.[CrossRef]
Zhang L -B., Renner S. S. The deepest splits in Chloranthaceae as resolved by chloroplast sequences. Int. J. Plant Sci. (2003) 164(5 Suppl.):S383–S392.[CrossRef][Web of Science]
Zhou S., Renner S. S., Wen J. Molecular phylogeny and inter- and intracontinental biogeography of Calycanthaceae. Molecular Phylogenetics and Evolution (2006) 39:1–15.[CrossRef][Web of Science][Medline]
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