Noncoding sequences from the slowly evolving chloroplast inverted repeat in addition to rbcL data do not support gnetalean affinities of angiosperms

Fleshy or dry: transcriptome analyses reveal the genetic mechanisms underlying bract development in Ephedra

BACKGROUND

Gnetales have a key phylogenetic position in the evolution of seed plants. Among the Gnetales, there is an extraordinary morphological diversity of seeds, the genus Ephedra, in particular, exhibits fleshy, coriaceous or winged (dry) seeds. Despite this striking diversity, its underlying genetic mechanisms remain poorly understood due to the limited studies in gymnosperms. Expanding the genomic and developmental data from gymnosperms contributes to a better understanding of seed evolution and development.

RESULTS

We performed transcriptome analyses on different plant tissues of two Ephedra species with different seed morphologies. Anatomical observations in early developing ovules, show that differences in the seed morphologies are established early in their development. The transcriptomic analyses in dry-seeded Ephedra californica and fleshy-seeded Ephedra antisyphilitica, allowed us to identify the major differences between the differentially expressed genes in these species. We detected several genes known to be involved in fruit ripening as upregulated in the fleshy seed of Ephedra antisyphilitica.

CONCLUSIONS

This study allowed us to determine the differentially expressed genes involved in seed development of two Ephedra species. Furthermore, the results of this study of seeds with the enigmatic morphology in Ephedra californica and Ephedra antisyphilitica, allowed us to corroborate the hypothesis which suggest that the extra envelopes covering the seeds of Gnetales are not genetically similar to integument. Our results highlight the importance of carrying out studies on less explored species such as gymnosperms, to gain a better understanding of the evolutionary history of plants.

Comprehensive study of the genes involved in chlorophyll synthesis and degradation pathways in some monocot and dicot plant species

Chlorophyll (Chl) biosynthesis is one of the most important cellular processes essential for plant photosynthesis. Chl degradation pathway is also important catabolic process occurs during leaf senescence, fruit ripening and under biotic or abiotic stress conditions. Here we have systematically investigated the molecular evolution, gene structure, compositional analysis along with ENc plot, correspondence analysis and codon usage bias of the proteins and encoded genes involved in Chl metabolism from monocots and dicots. The gene and species specific phylogenetic trees using amino acid sequences showed clear clustering formation of the selected species based on monocots and dicots but not supported by 18S rRNA. Nucleotide composition of the encoding genes showed that average GC%, GC1%, GC2% and GC3% were higher in monocots. RSCU analysis depicts that genes from monocots for both pathways and genes for synthesis pathway from dicots only biased to G/C-ending synonymous codons but in degradation pathway most optimal codons (except UUG) in dicots biased to A/U-ending synonymous codons. We found strong evidence of episodic diversifying selection at several amino acid sites in all genes investigated. Conserved domain and gene structures were observed for the genes with varying lengths of introns and exons, involved in Chl metabolism along with some intronless genes within synthesis pathway. ENc and correspondence analyses suggested the mutational or selection constraint on the genes to shape the codon usage. These comprehensive studies may be helpful in further research in molecular phylogenetics and genomics and to better understand the evolutionary dynamics of Chl metabolic pathway.Communicated by Ramaswamy H. Sarma.

Fossil record of Ephedra in the Lower Cretaceous (Aptian), Argentina

Fossil plants from the Lower Cretaceous (upper Aptian) of the La Cantera Formation, Argentina, are described. The fossils studied represent a leafy shooting system with several orders of articulated and striated axes and attached leaves with unequivocal ephedroid affinity. We also found associated remains of ovulate cones with four whorls of sterile bracts, which contain two female reproductive units (FRU). Ovulate cone characters fit well within the genus Ephedra. Special characters in the ovulate cones including an outer seed envelope with two types of trichomes, allowed us to consider our remains as a new Ephedra species. Abundant dispersed ephedroid pollen obtained from the macrofossil-bearing strata also confirms the abundance of Ephedraceae in the basin. The co-occurrence of abundant fossil of Ephedra (adapted to dry habitats) associated with thermophilic cheirolepideacean conifer pollen (Classopollis) in the unit would suggest marked seasonality at the locality during the Early Cretaceous. Furthermore, the floristic association is linked to dry sensitive rocks in the entire section. The macro- and microflora from San Luis Basin are similar in composition to several Early Cretaceous floras from the Northern Gondwana floristic province, but it may represent one of the southernmost records of an arid biome in South America.

HETEROCHRONY AND DEVELOPMENTAL INNOVATION: EVOLUTION OF FEMALE GAMETOPHYTE ONTOGENY IN GNETUM, A HIGHLY APOMORPHIC SEED PLANT

Seed plant female gametophytes are focal points for the evolutionary modification of development. From a structural perspective, the most divergent female gametophytes among all seed plants are found in Gnetum, a clade within Gnetales. Coenocytic organization at sexual maturity, absence of defined egg cells (free nuclei are fertilized), lack of centripetal cellularization, and postfertilization development of embryo-nourishing tissues are features of the female gametophytes of Gnetum unparalleled among seed plants. Although the female gametophyte of Gnetum retains the three basic phases of somatic development common to female gametophytes of plesiomorphic seed plants (free nuclear development, cellularization, cellular growth), the timing of fertilization has been accelerated relative to the rate of somatic development. As a consequence, the female gametophyte of Gnetum matures sexually (is fertilized) at a juvenile (compared with the ancestral somatic ontogeny) and free nuclear stage of somatic development, thereby precluding differentiation of egg cells. Unlike progenetic animals, where truncation of somatic ontogeny evolves in tandem with acceleration in the timing of sexual maturation, the female gametophyte of Gnetum completes the entire ancestral somatic ontogeny after precocious sexual maturation. This results in the evolution of postfertilization development of embryo-nourishing female gametophyte tissues, a phenomenon unique among seed plants. Nonheterochronic developmental innovations have also played important roles in the evolution of the female gametophyte of Gnetum. Centripetal cellularization, which is always associated with the phase change from coenocytic to cellular organization among plesiomorphic seed plant female gametophytes, is lacking in Gnetum. Instead, during early phases of development, apomorphic free nuclear organization is coupled with a highly anomalous pattern of cellularization. Stage-specific innovations during early development in the female gametophyte of Gnetum do not affect plesiomorphic aspects of later phases of development. Thus, a complex array of heterochronic and nonheterochronic developmental innovations have played critical roles in the ontogenetic evolution of the highly apomorphic female gametophyte of Gnetum.

A comparison of 16 DNA regions for use as phylogenetic markers in the pleurocarpous moss genus Plagiothecium (Hypnales)

PREMISE OF THE STUDY

Within the Hypnales-the most derived and species-rich order of pleurocarpous mosses - phylogenies at or below the family level often show poor resolution. In preparation for a phylogeny of the genus Plagiothecium, we wished to identify the DNA markers best suited for evolutionary reconstruction in this group of hypnalean pleurocarps.

METHODS

For each of 25 collections of Plagiothecium and associated taxa, 16 DNA regions were sequenced: nuclear ITS and 26S, and plastid rps4, rps4-trnL, trnL-F, trnK (matK)-psbA, psbA-trnH, trnM-V, trnD-T, rbcL, atpB-rbcL, psbT-H, rpoC1 exon 2 (partial), the trnG intron, the rpl16 intron and the plastid ribosomal spacer DNA (cpITS). Each region was evaluated on the basis of its ability to resolve clades, the amount of homoplasy present in the data set, and the relative ease of obtaining the data. Descriptive statistics for each region are given.

KEY RESULTS

Under-utilized plastid markers for bryophytes such as trnK-psbA, rps4-trnL, and trnD-T outperformed more traditional markers such as trnL-F and rps4. Individual plastid topologies were similar, suggesting that only a limited amount of plastid data are needed to recover a backbone phylogeny. Adding a small amount of nuclear ribosomal data to a large plastid matrix restructured the recovered topology, emphasizing the importance of sampling multiple genomes and the need for new low-copy nuclear markers in bryophyte systematics.

CONCLUSIONS

Future genus-level phylogenies of pleurocarpous mosses should target under-utilized plastid markers such as trnK-psbA and rps4-trnL in conjunction with low-copy nuclear markers.

Phylogenomics and coalescent analyses resolve extant seed plant relationships

The extant seed plants include more than 260,000 species that belong to five main lineages: angiosperms, conifers, cycads, Ginkgo, and gnetophytes. Despite tremendous effort using molecular data, phylogenetic relationships among these five lineages remain uncertain. Here, we provide the first broad coalescent-based species tree estimation of seed plants using genome-scale nuclear and plastid data By incorporating 305 nuclear genes and 47 plastid genes from 14 species, we identify that i) extant gymnosperms (i.e., conifers, cycads, Ginkgo, and gnetophytes) are monophyletic, ii) gnetophytes exhibit discordant placements within conifers between their nuclear and plastid genomes, and iii) cycads plus Ginkgo form a clade that is sister to all remaining extant gymnosperms. We additionally observe that the placement of Ginkgo inferred from coalescent analyses is congruent across different nucleotide rate partitions. In contrast, the standard concatenation method produces strongly supported, but incongruent placements of Ginkgo between slow- and fast-evolving sites. Specifically, fast-evolving sites yield relationships in conflict with coalescent analyses. We hypothesize that this incongruence may be related to the way in which concatenation methods treat sites with elevated nucleotide substitution rates. More empirical and simulation investigations are needed to understand this potential weakness of concatenation methods.

Chloroplast phylogenomics indicates that Ginkgo biloba is sister to cycads

Molecular phylogenetic studies have not yet reached a consensus on the placement of Ginkgoales, which is represented by the only living species, Ginkgo biloba (common name: ginkgo). At least six discrepant placements of ginkgo have been proposed. This study aimed to use the chloroplast phylogenomic approach to examine possible factors that lead to such disagreeing placements. We found the sequence types used in the analyses as the most critical factor in the conflicting placements of ginkgo. In addition, the placement of ginkgo varied in the trees inferred from nucleotide (NU) sequences, which notably depended on breadth of taxon sampling, tree-building methods, codon positions, positions of Gnetopsida (common name: gnetophytes), and including or excluding gnetophytes in data sets. In contrast, the trees inferred from amino acid (AA) sequences congruently supported the monophyly of a ginkgo and Cycadales (common name: cycads) clade, regardless of which factors were examined. Our site-stripping analysis further revealed that the high substitution saturation of NU sequences mainly derived from the third codon positions and contributed to the variable placements of ginkgo. In summary, the factors we surveyed did not affect results inferred from analyses of AA sequences. Congruent topologies in our AA trees give more confidence in supporting the ginkgo-cycad sister-group hypothesis.

Using multiple analytical methods to improve phylogenetic hypotheses in Minaria (Apocynaceae)

Metastelmatinae is a neotropical subtribe of Asclepiadoideae (Apocynaceae), comprising 13 genera and around 260 species whose phylogenetic relationships are often unresolved or incongruent between plastid and nuclear datasets. The genus Minaria is one of the first lineages to emerge in the Metastelmatinae and is highly supported based on plastid markers. It comprises 21 species, most of which are endemic to small areas with open vegetation in the Espinhaço Range, Brazil. In the work presented here, we use plastid (rps16, trnH-psbA, trnS-trnG, and trnD-trnT) and nuclear (ITS and ETS) datasets to investigate the relationships within Minaria. We show that the three methods mostly used in phylogenetic studies, namely, maximum parsimony, maximum likelihood, and Bayesian Inference, have different performances and that a pluralistic analytical approach combining results from them can increase tree resolution and clade confidence, providing valuable phylogenetic information.

A functional phylogenomic view of the seed plants

A novel result of the current research is the development and implementation of a unique functional phylogenomic approach that explores the genomic origins of seed plant diversification. We first use 22,833 sets of orthologs from the nuclear genomes of 101 genera across land plants to reconstruct their phylogenetic relationships. One of the more salient results is the resolution of some enigmatic relationships in seed plant phylogeny, such as the placement of Gnetales as sister to the rest of the gymnosperms. In using this novel phylogenomic approach, we were also able to identify overrepresented functional gene ontology categories in genes that provide positive branch support for major nodes prompting new hypotheses for genes associated with the diversification of angiosperms. For example, RNA interference (RNAi) has played a significant role in the divergence of monocots from other angiosperms, which has experimental support in Arabidopsis and rice. This analysis also implied that the second largest subunit of RNA polymerase IV and V (NRPD2) played a prominent role in the divergence of gymnosperms. This hypothesis is supported by the lack of 24nt siRNA in conifers, the maternal control of small RNA in the seeds of flowering plants, and the emergence of double fertilization in angiosperms. Our approach takes advantage of genomic data to define orthologs, reconstruct relationships, and narrow down candidate genes involved in plant evolution within a phylogenomic view of species' diversification.

A set of 100 chloroplast DNA primer pairs to study population genetics and phylogeny in monocotyledons

Chloroplast DNA sequences are of great interest for population genetics and phylogenetic studies. However, only a small set of markers are commonly used. Most of them have been designed for amplification in a large range of Angiosperms and are located in the Large Single Copy (LSC). Here we developed a new set of 100 primer pairs optimized for amplification in Monocotyledons. Primer pairs amplify coding (exon) and non-coding regions (intron and intergenic spacer). They span the different chloroplast regions: 72 are located in the LSC, 13 in the Small Single Copy (SSC) and 15 in the Inverted Repeat region (IR). Amplification and sequencing were tested in 13 species of Monocotyledons: Dioscorea abyssinica, D. praehensilis, D. rotundata, D. dumetorum, D. bulbifera, Trichopus sempervirens (Dioscoreaceae), Phoenix canariensis, P. dactylifera, Astrocaryum scopatum, A. murumuru, Ceroxylon echinulatum (Arecaceae), Digitaria excilis and Pennisetum glaucum (Poaceae). The diversity found in Dioscorea, Digitaria and Pennisetum mainly corresponded to Single Nucleotide Polymorphism (SNP) while the diversity found in Arecaceae also comprises Variable Number Tandem Repeat (VNTR). We observed that the most variable loci (rps15-ycf1, rpl32-ccsA, ndhF-rpl32, ndhG-ndhI and ccsA) are located in the SSC. Through the analysis of the genetic structure of a wild-cultivated species complex in Dioscorea, we demonstrated that this new set of primers is of great interest for population genetics and we anticipate that it will also be useful for phylogeny and bar-coding studies.

The impact of outgroup choice and missing data on major seed plant phylogenetics using genome-wide EST data

BACKGROUND

Genome level analyses have enhanced our view of phylogenetics in many areas of the tree of life. With the production of whole genome DNA sequences of hundreds of organisms and large-scale EST databases a large number of candidate genes for inclusion into phylogenetic analysis have become available. In this work, we exploit the burgeoning genomic data being generated for plant genomes to address one of the more important plant phylogenetic questions concerning the hierarchical relationships of the several major seed plant lineages (angiosperms, Cycadales, Gingkoales, Gnetales, and Coniferales), which continues to be a work in progress, despite numerous studies using single, few or several genes and morphology datasets. Although most recent studies support the notion that gymnosperms and angiosperms are monophyletic and sister groups, they differ on the topological arrangements within each major group.

METHODOLOGY

We exploited the EST database to construct a supermatrix of DNA sequences (over 1,200 concatenated orthologous gene partitions for 17 taxa) to examine non-flowering seed plant relationships. This analysis employed programs that offer rapid and robust orthology determination of novel, short sequences from plant ESTs based on reference seed plant genomes. Our phylogenetic analysis retrieved an unbiased (with respect to gene choice), well-resolved and highly supported phylogenetic hypothesis that was robust to various outgroup combinations.

CONCLUSIONS

We evaluated character support and the relative contribution of numerous variables (e.g. gene number, missing data, partitioning schemes, taxon sampling and outgroup choice) on tree topology, stability and support metrics. Our results indicate that while missing characters and order of addition of genes to an analysis do not influence branch support, inadequate taxon sampling and limited choice of outgroup(s) can lead to spurious inference of phylogeny when dealing with phylogenomic scale data sets. As expected, support and resolution increases significantly as more informative characters are added, until reaching a threshold, beyond which support metrics stabilize, and the effect of adding conflicting characters is minimized.

Chloroplast genome (cpDNA) of Cycas taitungensis and 56 cp protein-coding genes of Gnetum parvifolium: insights into cpDNA evolution and phylogeny of extant seed plants

Phylogenetic relationships among the 5 groups of extant seed plants are presently unsettled. To reexamine this long-standing debate, we determine the complete chloroplast genome (cpDNA) of Cycas taitungensis and 56 protein-coding genes encoded in the cpDNA of Gnetum parvifolium. The cpDNA of Cycas is a circular molecule of 163,403 bp with 2 typical large inverted repeats (IRs) of 25,074 bp each. We inferred phylogenetic relationships among major seed plant lineages using concatenated 56 protein-coding genes in 37 land plants. Phylogenies, generated by the use of 3 independent methods, provide concordant and robust support for the monophylies of extant seed plants, gymnosperms, and angiosperms. Within the modern gymnosperms are 2 highly supported sister clades: Cycas-Ginkgo and Gnetum-Pinus. This result agrees with both the "gnetifer" and "gnepines" hypotheses. The sister relationships in Cycas-Ginkgo and Gnetum-Pinus clades are further reinforced by cpDNA structural evidence. Branch lengths of Cycas-Ginkgo and Gnetum were consistently the shortest and the longest, respectively, in all separate analyses. However, the Gnetum relative rate test revealed this tendency only for the 3rd codon positions and the transversional sites of the first 2 codon positions. A PsitufA located between psbE and petL genes is here first detected in Anthoceros (a hornwort), cycads, and Ginkgo. We demonstrate that the PsitufA is a footprint descended from the chloroplast tufA of green algae. The duplication of ycf2 genes and their shift into IRs should have taken place at least in the common ancestor of seed plants more than 300 MYA, and the tRNAPro-GGG gene was lost from the angiosperm lineage at least 150 MYA. Additionally, from cpDNA structural comparison, we propose an alternative model for the loss of large IR regions in black pine. More cpDNA data from non-Pinaceae conifers are necessary to justify whether the gnetifer or gnepines hypothesis is valid and to generate solid structural evidence for the monophyly of extant gymnosperms.

A new test of phylogenetic model fitness addresses the issue of the basal angiosperm phylogeny

We readdress the issue of phylogeny of the basal extant angiosperms employing a source previously not systematically investigated, specifically, the non-coding sequences of cpDNA. Comparison of trees with and without grasses or the outgroup (Pinus) in our analyses revealed no rearrangements in tree topology that might be expected if LBA were distorting the position of the magnoliids. For each model applied, irrespective of whether monocots or ANITA members appeared basally divergent, the orchid Phalaenopsis assumed the same position on the trees with the reduced taxon set as did the branch bearing the orchid plus the grasses in the full alignment. However, our new test of model fitness revealed a different flaw influencing the placement of monocots, which is related to model mis-specification. This flaw similarly affects the full alignment and the alignment with grasses removed. In both cases the models favouring a relatively derived position for the monocots and basal placement of the branch of Amborella plus Nymphaea provide better overall prediction of the observed data structure. In the view of apparent unsuitability of the bootstrap method for large data sets, our novel test provides a new means of exploring conflicts caused by systematic errors in phylogenetic analyses.

Former diversity of Ephedra (Gnetales): evidence from Early Cretaceous seeds from Portugal and North America

BACKGROUND AND AIMS

The extant species of the seed plant group Gnetales (Ephedra, Gnetum and Welwitschia) have been considered a remnant of a much greater, now extinct, diversity due to the pronounced differences in form and ecology among the genera. Until recently, this hypothesis has not been supported by evidence from the fossil record. This paper adds to the expanding information on Gnetales from the Early Cretaceous and describes coalified seeds from Barremian-Albian localities in Portugal and USA.

METHODS

The fossils were extracted from sediment samples by sieving in water. Adhering mineral matrix was removed by chemical treatment. Seeds were investigated using light and scanning electron microscopy. Morphology and anatomy of the seeds were documented and compared with those of extant species.

KEY RESULTS

The fossils share characters with extant Ephedra, for example papillae on the inner surface of the seed envelope and in situ polyplicate pollen grains that shed the exine during germination. They differ from extant Ephedra seeds in morphological and anatomical details as well as in their smaller size. Two new species of Ephedra are described together with one species assigned to a new genus of Gnetales. Other Ephedra-like seeds, for which pollen and critical morphological details are currently unknown, are also present in the samples.

CONCLUSIONS

These Cretaceous seeds document that key reproductive characters and pollen germination processes have remained unchanged within Ephedra for about 120 million years or more. There is sufficient variety in details of morphology to suggest that a diversity of Ephedra and Ephedra-like species were present in the Early Cretaceous flora. Their presence in Portugal and eastern North America indicates that they were widespread on the Laurasian continent. The fossil seeds are similar to seeds of Erdtmanithecales and this supports the previously suggested relationship between Erdtmanithecales and Gnetales.

ESTimating plant phylogeny: lessons from partitioning

BACKGROUND

While Expressed Sequence Tags (ESTs) have proven a viable and efficient way to sample genomes, particularly those for which whole-genome sequencing is impractical, phylogenetic analysis using ESTs remains difficult. Sequencing errors and orthology determination are the major problems when using ESTs as a source of characters for systematics. Here we develop methods to incorporate EST sequence information in a simultaneous analysis framework to address controversial phylogenetic questions regarding the relationships among the major groups of seed plants. We use an automated, phylogenetically derived approach to orthology determination called OrthologID generate a phylogeny based on 43 process partitions, many of which are derived from ESTs, and examine several measures of support to assess the utility of EST data for phylogenies.

RESULTS

A maximum parsimony (MP) analysis resulted in a single tree with relatively high support at all nodes in the tree despite rampant conflict among trees generated from the separate analysis of individual partitions. In a comparison of broader-scale groupings based on cellular compartment (ie: chloroplast, mitochondrial or nuclear) or function, only the nuclear partition tree (based largely on EST data) was found to be topologically identical to the tree based on the simultaneous analysis of all data. Despite topological conflict among the broader-scale groupings examined, only the tree based on morphological data showed statistically significant differences.

CONCLUSION

Based on the amount of character support contributed by EST data which make up a majority of the nuclear data set, and the lack of conflict of the nuclear data set with the simultaneous analysis tree, we conclude that the inclusion of EST data does provide a viable and efficient approach to address phylogenetic questions within a parsimony framework on a genomic scale, if problems of orthology determination and potential sequencing errors can be overcome. In addition, approaches that examine conflict and support in a simultaneous analysis framework allow for a more precise understanding of the evolutionary history of individual process partitions and may be a novel way to understand functional aspects of different kinds of cellular classes of gene products.

Seed plant phylogeny: gnetophytes are derived conifers and a sister group to Pinaceae

The phylogenetic position of gnetophytes has long been controversial. We sequenced parts of the genes coding for the largest subunit of nuclear RNA polymerase I, II, and III and combined these sequences with those of four chloroplast genes, two mitochondrial genes, and 18S rRNA genes to address this issue. Both maximum likelihood and maximum parsimony analyses of the sites not affected by high substitution levels strongly support a phylogeny where gymnosperms and angiosperms are monophyletic, where cycads are at the base of gymnosperm tree and are followed by ginkgos, and where gnetophytes are grouped within conifers as the sister group of pines. The evolution of several morphological and molecular characters of gnetophytes and conifers will therefore need to be reinterpreted.

Phylogenetic relationships in Ephedra (Ephedraceae) inferred from chloroplast and nuclear DNA sequences

Sequences of the nuclear ribosomal DNA internal transcribed spacer region 1 and the chloroplast-encoded genes maturase K and ribulose-1,5 biphosphate carboxylase large subunit were obtained from species of Ephedra (Ephedraceae) representing the geographic range and morphological diversity of the genus. Phylogenetic analyses of the DNA data indicate that relationships within the genus are better predicted by geographic region of origin than by ovulate cone characters. The sampled species with dry, winged (versus fleshy) ovulate cone bracts or single-seeded cones do not form monophyletic groups and therefore the previous classification systems of Ephedra based on these aspects of bract morphology appear to be largely unnatural. Three groups were identified among the Old World species studied, one comprising European and Mediterranean species and two including only Asian species. The sequence data suggest a possible early divergence of a New World clade of Ephedra from among the Old World groups. The South American species form a distinct clade apparently related to one of two groups of North American species, which accords with a frequent floristic pattern of close relationships between species groups in western South America and southwestern North America.

Identifying the basal angiosperm node in chloroplast genome phylogenies: sampling one's way out of the Felsenstein zone

While there has been strong support for Amborella and Nymphaeales (water lilies) as branching from basal-most nodes in the angiosperm phylogeny, this hypothesis has recently been challenged by phylogenetic analyses of 61 protein-coding genes extracted from the chloroplast genome sequences of Amborella, Nymphaea, and 12 other available land plant chloroplast genomes. These character-rich analyses placed the monocots, represented by three grasses (Poaceae), as sister to all other extant angiosperm lineages. We have extracted protein-coding regions from draft sequences for six additional chloroplast genomes to test whether this surprising result could be an artifact of long-branch attraction due to limited taxon sampling. The added taxa include three monocots (Acorus, Yucca, and Typha), a water lily (Nuphar), a ranunculid (Ranunculus), and a gymnosperm (Ginkgo). Phylogenetic analyses of the expanded DNA and protein data sets together with microstructural characters (indels) provided unambiguous support for Amborella and the Nymphaeales as branching from the basal-most nodes in the angiosperm phylogeny. However, their relative positions proved to be dependent on the method of analysis, with parsimony favoring Amborella as sister to all other angiosperms and maximum likelihood (ML) and neighbor-joining methods favoring an Amborella + Nymphaeales clade as sister. The ML phylogeny supported the later hypothesis, but the likelihood for the former hypothesis was not significantly different. Parametric bootstrap analysis, single-gene phylogenies, estimated divergence dates, and conflicting indel characters all help to illuminate the nature of the conflict in resolution of the most basal nodes in the angiosperm phylogeny. Molecular dating analyses provided median age estimates of 161 MYA for the most recent common ancestor (MRCA) of all extant angiosperms and 145 MYA for the MRCA of monocots, magnoliids, and eudicots. Whereas long sequences reduce variance in branch lengths and molecular dating estimates, the impact of improved taxon sampling on the rooting of the angiosperm phylogeny together with the results of parametric bootstrap analyses demonstrate how long-branch attraction might mislead genome-scale phylogenetic analyses.

Analysis of Acorus calamus chloroplast genome and its phylogenetic implications

Determining the phylogenetic relationships among the major lines of angiosperms is a long-standing problem, yet the uncertainty as to the phylogenetic affinity of these lines persists. While a number of studies have suggested that the ANITA (Amborella-Nymphaeales-Illiciales-Trimeniales-Aristolochiales) grade is basal within angiosperms, studies of complete chloroplast genome sequences also suggested an alternative tree, wherein the line leading to the grasses branches first among the angiosperms. To improve taxon sampling in the existing chloroplast genome data, we sequenced the chloroplast genome of the monocot Acorus calamus. We generated a concatenated alignment (89,436 positions for 15 taxa), encompassing almost all sequences usable for phylogeny reconstruction within spermatophytes. The data still contain support for both the ANITA-basal and grasses-basal hypotheses. Using simulations we can show that were the ANITA-basal hypothesis true, parsimony (and distance-based methods with many models) would be expected to fail to recover it. The self-evident explanation for this failure appears to be a long-branch attraction (LBA) between the clade of grasses and the out-group. However, this LBA cannot explain the discrepancies observed between tree topology recovered using the maximum likelihood (ML) method and the topologies recovered using the parsimony and distance-based methods when grasses are deleted. Furthermore, the fact that neither maximum parsimony nor distance methods consistently recover the ML tree, when according to the simulations they would be expected to, when the out-group (Pinus) is deleted, suggests that either the generating tree is not correct or the best symmetric model is misspecified (or both). We demonstrate that the tree recovered under ML is extremely sensitive to model specification and that the best symmetric model is misspecified. Hence, we remain agnostic regarding phylogenetic relationships among basal angiosperm lineages.

Form, function and environments of the early angiosperms: merging extant phylogeny and ecophysiology with fossils

The flowering plants--angiosperms--appeared during the Early Cretaceous period and within 10-30 Myr dominated the species composition of many floras worldwide. Emerging insights into the phylogenetics of development and discoveries of early angiosperm fossils are shedding increased light on the patterns and processes of early angiosperm evolution. However, we also need to integrate ecology, in particular how early angiosperms established a roothold in pre-existing Mesozoic plant communities. These events were critical in guiding subsequent waves of angiosperm diversification during the Aptian-Albian. Previous pictures of the early flowering plant ecology have been diverse, ranging from large tropical rainforest trees, weedy drought-adapted and colonizing shrubs, disturbance- and sun-loving rhizomatous herbs, and, more recently, aquatic herbs; however, none of these images were tethered to a robust hypothesis of angiosperm phylogeny. Here, we synthesize our current understanding of early angiosperm ecology, focusing on patterns of functional ecology, by merging recent molecular phylogenetic studies and functional studies on extant 'basal angiosperms' with the picture of early angiosperm evolution drawn by the fossil record.

A phylogeny of cycads (Cycadales) inferred from chloroplast matK gene, trnK intron, and nuclear rDNA ITS region

Phylogenetic relationships among the three families and 12 living genera of cycads were reconstructed by distance and parsimony criteria using three markers: the chloroplast matK gene, the chloroplast trnK intron and the nuclear ITS/5.8S rDNA sequence. All datasets indicate that Cycadaceae (including only the genus Cycas) is remotely related to other cycads, in which Dioon was resolved as the basal-most clade, followed by Bowenia and a clade containing the remaining nine genera. Encephalartos and Lepidozamia are closer to each other than to Macrozamia. The African genus Stangeria is embedded within the New World subfamily Zamiodeae. Therefore, Bowenia is an unlikely sister to Stangeria, contrary to the view that they form the Stangeriaceae. The generic status of Dyerocycas and Chigua is unsupportable as they are paraphyletic with Cycas and the Zamia, respectively. Nonsense mutations in the matK gene and indels in the other two datasets lend evidence to reinforce the above conclusions. According to the phylogenies, the past geography of the genera of cycads and the evolution of character states are hypothesized and discussed. Within the suborder Zamiieae, Stangeria, and the tribe Zamieae evolved significantly faster than other genera. The matK gene and ITS/5.8S region contain more useful information than the trnK intron in addressing phylogeny. Redelimitations of Zamiaceae, Stangeriaceae, subfamily Encephalartoideae and subtribe Macrozamiineae are necessary.

Phylogenetic signal in nucleotide data from seed plants: implications for resolving the seed plant tree of life

Effects of taxonomic sampling and conflicting signal on the inference of seed plant trees supported in previous molecular analyses were explored using 13 single-locus data sets. Changing the number of taxa in single-locus analyses had limited effects on log likelihood differences between the gnepine (Gnetales plus Pinaceae) and gnetifer (Gnetales plus conifers) trees. Distinguishing among these trees also was little affected by the use of different substitution parameters. The 13-locus combined data set was partitioned into nine classes based on substitution rates. Sites evolving at intermediate rates had the best likelihood and parsimony scores on gnepine trees, and those evolving at the fastest rates had the best parsimony scores on Gnetales-sister trees (Gnetales plus other seed plants). When the fastest evolving sites were excluded from parsimony analyses, well-supported gnepine trees were inferred from the combined data and from each genomic partition. When all sites were included, Gnetales-sister trees were inferred from the combined data, whereas a different tree was inferred from each genomic partition. Maximum likelihood trees from the combined data and from each genomic partition were well-supported gnepine trees. A preliminary stratigraphic test highlights the poor fit of Gnetales-sister trees to the fossil data.

The evolution of plant development

The last decade has witnessed a resurgence in the study of the evolution of plant development, combining investigations in systematics, developmental morphology, molecular developmental genetics, and molecular evolution. The integration of phylogenetic studies, structural analyses of fossil and extant taxa, and molecular developmental genetic information allows the formulation of explicit and testable hypotheses for the evolution of morphological characters. These comprehensive approaches provide opportunities to dissect the evolution of major developmental transitions among land plants, including those associated with apical meristems, the origins of the root/shoot dichotomy, diversification of leaves, and origin and subsequent modification of flower structure. The evolution of these major developmental innovations is discussed within both phylogenetic and molecular genetic contexts. We conclude that it is the combination of these approaches that will lead to the greatest understanding of the evolution of plant development.

The mitochondrial DNA of land plants: peculiarities in phylogenetic perspective

Land plants exhibit a significant evolutionary plasticity in their mitochondrial DNA (mtDNA), which contrasts with the more conservative evolution of their chloroplast genomes. Frequent genomic rearrangements, the incorporation of foreign DNA from the nuclear and chloroplast genomes, an ongoing transfer of genes to the nucleus in recent evolutionary times and the disruption of gene continuity in introns or exons are the hallmarks of plant mtDNA, at least in flowering plants. Peculiarities of gene expression, most notably RNA editing and trans-splicing, are significantly more pronounced in land plant mitochondria than in chloroplasts. At the same time, mtDNA is generally the most slowly evolving of the three plant cell genomes on the sequence level, with unique exceptions in only some plant lineages. The slow sequence evolution and a variable occurrence of introns in plant mtDNA provide an attractive reservoir of phylogenetic information to trace the phylogeny of older land plant clades, which is as yet not fully resolved. This review attempts to summarize the unique aspects of land plant mitochondrial evolution from a phylogenetic perspective.

Inference of higher-order relationships in the cycads from a large chloroplast data set

We investigated higher-order relationships in the cycads, an ancient group of seed-bearing plants, by examining a large portion of the chloroplast genome from seven species chosen to exemplify our current understanding of taxonomic diversity in the order. The regions considered span approximately 13.5 kb of unaligned data per taxon, and comprise a diverse range of coding sequences, introns and intergenic spacers dispersed throughout the plastid genome. Our results provide substantial support for most of the inferred backbone of cycad phylogeny, and weak evidence that the sister-group of the cycads among living seed plants is Ginkgo biloba. Cycas (representing Cycadaceae) is the sister-group of the remaining cycads; Dioon is part of the next most basal split. Two of the three commonly recognized families of cycads (Zamiaceae and Stangeriaceae) are not monophyletic; Stangeria is embedded within Zamiaceae, close to Zamia and Ceratozamia, and not closely allied to the other genus of Stangeriaceae, Bowenia. In contrast to the other seed plants, cycad chloroplast genomes share two features with Ginkgo: a reduced rate of evolution and an elevated transition:transversion ratio. We demonstrate that the latter aspect of their molecular evolution is unlikely to have affected inference of cycad relationships in the context of seed-plant wide analyses.

Noncoding plastid trnT-trnF sequences reveal a well resolved phylogeny of basal angiosperms

Recent contributions from DNA sequences have revolutionized our concept of systematic relationships in angiosperms. However, parts of the angiosperm tree remain unclear. Previous studies have been based on coding or rDNA regions of relatively conserved genes. A phylogeny for basal angiosperms based on noncoding, fast-evolving sequences of the chloroplast genome region trnT-trnF is presented. The recognition of simple direct repeats allowed a robust alignment. Mutational hot spots appear to be confined to certain sectors, as in two stem-loop regions of the trnL intron secondary structure. Our highly resolved and well-supported phylogeny depicts the New Caledonian Amborella as the sister to all other angiosperms, followed by Nymphaeaceae and an Austrobaileya-Illicium-Schisandra clade. Ceratophyllum is substantiated as a close relative of monocots, as is a monophyletic eumagnoliid clade consisting of Piperales plus Winterales sister to Laurales plus Magnoliales. Possible reasons for the striking congruence between the trnT-trnF based phylogeny and phylogenies generated from combined multi-gene, multi-genome data are discussed.

A decade of progress in plant molecular phylogenetics

Over the past decade, botanists have produced several thousand phylogenetic analyses based on molecular data, with particular emphasis on sequencing rbcL, the plastid gene encoding the large subunit of Rubisco (ribulose bisphosphate carboxylase). Because phylogenetic trees retrieved from the three plant genomes (plastid, nuclear and mitochondrial) have been highly congruent, the "Angiosperm Phylogeny Group" has used these DNA-based phylogenetic trees to reclassify all families of flowering plants. However, in addition to taxonomy, these major phylogenetic efforts have also helped to define strategies to reconstruct the "tree of life", and have revealed the size of the ancestral plant genome, uncovered potential candidates for the ancestral flower, identified molecular living fossils, and linked the rate of neutral substitutions with species diversity. With an increased interest in DNA sequencing programmes in non-model organisms, the next decade will hopefully see these phylogenetic findings integrated into new genetic syntheses, from genomes to taxa.

Relationships among seed plants inferred from highly conserved genes: sorting conflicting phylogenetic signals among ancient lineages

Phylogenetic studies based on different types and treatment of data provide substantially conflicting hypotheses of relationships among seed plants. We conducted phylogenetic analyses of sequences of two highly conserved chloroplast genes, psaA and psbB, for a comprehensive taxonomic sample of seed plants and land plants. Parsimony analyses of two different codon position partitions resulted in well-supported, but significantly conflicting, phylogenetic trees. First and second codon positions place angiosperms and gymnosperms as sister clades and Gnetales as sister to Pinaceae. Third positions place Gnetales as sister to all other seed plants. Maximum likelihood trees for the two partitions are also in conflict. Relationships among the main seed plant clades according to first and second positions are similar to those found in parsimony analysis for the same data, but the third position maximum likelihood tree is substantially different from the corresponding parsimony tree, although it agrees partially with the first and second position trees in placing Gnetales as the sister group of Pinaceae. Our results document high rate heterogeneity among lineages, which, together with the greater average rate of substitution for third positions, may reduce phylogenetic signal due to long-branch attraction in parsimony reconstructions. Whereas resolution of relationships among major seed plant clades remains pending, this study provides increased support for relationships within major seed plant clades.

The evolution of embryo size in angiosperms and other seed plants: implications for the evolution of seed dormancy

Seed dormancy plays an important role in germination ecology and seed plant evolution. Morphological seed dormancy is caused by an underdeveloped embryo that must mature prior to germination. It has been suggested that the presence of an underdeveloped embryo is plesiomorphic among seed plants and that parallel directional change in embryo morphology has occurred separately in gymnosperms and in angiosperms. We test these hypotheses using original data on embryo morphology of key basal taxa, a published dataset, and the generalized least squares (GLS) method of ancestral character state reconstruction. Reconstructions for embryo to seed ratio (E:S) using family means for 179 families showed that E:S has increased between the ancestral angiosperm and almost all extant angiosperm taxa. Species in the rosid clade have particularly large embryos relative to the angiosperm ancestor. Results for the gymnosperms show a similar but smaller increase. There were no statistically significant differences in E:S between basal taxa and any derived group due to extremely large standard errors produced by GLS models. However, differences between reconstructed values for the angiosperm ancestor and more highly nested nodes are large and these results are robust to topological and branch-length manipulations. Our analysis supports the idea that the underdeveloped embryo is primitive among seed plants and that there has been a directional change in E:S within both angiosperms and gymnosperms. Our analysis suggests that dormancy enforced by an underdeveloped embryo is plesiomorphic among angiosperms and that nondormancy and other dormancy types probably evolved within the angiosperms. The shift in E:S was likely a heterochronic change, and has important implications for the life history of seed plants.

Phylogeny of seed plants based on evidence from eight genes

Relationships among the five groups of extant seed plants (cycads, Ginkgo, conifers, Gnetales, and angiosperms) remain uncertain. To explore relationships among groups of extant seed plants further and to attempt to explain the conflict among molecular data sets, we assembled a data set of four plastid (cpDNA) genes (rbcL, atpB, psaA, and psbB), three mitochondrial (mtDNA) genes (mtSSU, coxI, and atpA), and one nuclear gene (18S rDNA) for 19 exemplars representing the five groups of living seed plants. Analyses of the combined eight-gene data set (15 772 base pairs/taxon) with maximum parsimony (MP), maximum likelihood (ML), and Bayesian approaches reveal a gymnosperm clade that is sister to angiosperms. Within the gymnosperms, a conifer clade includes Gnetales as sister to Pinaceae. Cycads and Ginkgo are either successive sisters to this conifer clade (including Gnetales) or a clade that is sister to conifers and Gnetales. All analyses of the mtDNA partition and ML analyses of the nuclear partition yield very similar topologies. However, MP analyses of the combined cpDNA genes place Gnetales as sister to all other seed plants with strong bootstrap support, whereas ML and Bayesian analyses of the cpDNA data set place Gnetales as sister to Pinaceae. Maximum parsimony and ML analyses of first and second codon positions of the cpDNA partiation also place Gnetales as sister to Pinaceae. In contrast, MP analyses of third codon positions place Gnetales as sister to other seed plants, although ML analyses of third codon positions place Gnetales with Pinaceae. Thus, most of the discrepancies in seed plant topologies involve third codon positions of cpDNA genes. The likelihood ratio (LR) and Shimodaira-Hasegasa (SH) tests were applied to the cpDNA data. The preferred topology based on the LR test is that Gnetales are sister to Pseudotsuga. The SH test based on first and second codon and all three codon positions indicated that there is no significant difference between the best topology (Gnetales sister to Pseudotsuga) and Gnetales sister to a conifer clade. However, there is a significant difference between the best topology and topologies in which Gnetales are sister to the rest of the seed plants or Gnetales sister to angiosperms.

On the origin of class B floral homeotic genes: functional substitution and dominant inhibition in Arabidopsis by expression of an orthologue from the gymnosperm Gnetum

Class B floral homeotic genes are involved in specifying stamen and petal identity in angiosperms (flowering plants). Here we report that gymnosperms, the closest relatives of the angiosperms, contain at least two different clades representing putative orthologues of class B genes, termed GGM2-like and DAL12-like genes. To obtain information about the functional conservation of the class B genes in seed plants, the representative of one of these clades from Gnetum, termed GGM2, was expressed under the control of the CaMV 35S promoter in Arabidopsis wild-type plants and in different class B mutants. In wild-type plants and in a conditional mutant grown at a permissive temperature, gain-of-function phenotypes were obtained in whorls 1 and 4, where class B genes are usually not expressed. In contrast, loss-of-function phenotypes were observed in whorls 2 and 3, where class B genes are expressed. In different class B gene null mutants of Arabidopsis, and in the conditional B mutant grown at the non-permissive temperature, a partial complementation of the mutant phenotype was obtained. In situ hybridization studies and class B gene promoter test fusion experiments demonstrated that the gain-of-function phenotypes are not due to an upregulation of the endogenous B genes from Arabidopsis, and hence probably involve interactions between GGM2 protein homodimers and class B protein target genes other than the Arabidopsis class B genes itself. To our knowledge, this is the first time that partial complementation of a homeotic mutant by an orthologous gene from a distantly related species has been reported. These data suggest that GGM2 has a function in the gymnosperm Gnetum which is related to that of class B floral organ identity genes of angiosperms. That function may be in the specification of male reproductive organ identity, and in distinguishing male from female reproductive organs.

Pleiotropy, redundancy and the evolution of flowers

Most angiosperm flowers are tightly integrated, functionally bisexual shoots that have carpels with enclosed ovules. Flowering plants evolved from within the gymnosperms, which lack this combination of innovations. Paradoxically, phylogenetic reconstructions suggest that the flowering plant lineage substantially pre-dates the evolution of flowers themselves. We provide a model based on known gene regulatory networks whereby positive selection on a single, partially redundant gene duplicate 'trapped' the ancestors of flower-bearing plants into the condensed, bisexual state approximately 130 million years ago. The LEAFY (LFY) gene of Arabidopsis encodes a master regulator that functions as the main conduit of environmental signals to the reproductive developmental program. We directly link the elimination of one LFY paralog, pleiotropically maintained in gymnosperms, to the sudden appearance of flowers in the fossil record.

The evolutionary split of Pinaceae from other conifers: evidence from an intron loss and a multigene phylogeny

The second intron in the mitochondrial gene nad1 was surveyed using PCR, DNA sequencing, or Southern hybridization in 323 species (313 genera, 212 families) of seed plants. The intron was absent in all 22 species (22 genera, 8 families) of non-Pinaceae conifers studied, in Welwitschia mirabilis, and in seven angiosperms. Whereas absence of the intron in seven angiosperms and Welwitschia is likely due to seven independent losses when evaluated against the recently published multigene phylogenies, the lack of the intron in all non-Pinaceae conifers can be best explained by a single loss. These data suggest that the non-Pinaceae conifers represent a monophyletic group. We also conducted a phylogenetic analysis of seed plants using a combined data set of the partial exon and intron sequences of nad1 generated from this study and published sequences of mitochondrial cox1 and small subunit (SSU) rDNA, chloroplast rbcL, and nuclear 18S rDNA. The results supported the split of conifers into two groups: Pinaceae and non-Pinaceae conifers. The Gnetales were sister to Pinaceae, in agreement with the conclusion from other recent molecular phylogenetic studies that refute the anthophyte hypothesis.

Was the ANITA rooting of the angiosperm phylogeny affected by long-branch attraction? Amborella, Nymphaeales, Illiciales, Trimeniaceae, and Austrobaileya

Five groups of basal angiosperms, Amborella, Nymphaeales, Illiciales, Trimeniaceae, and Austrobaileya (ANITA), were identified in several recent studies as representing a series of the earliest-diverging lineages of the angiosperm phylogeny. All of these studies except one employed a multigene analysis approach and used gymnosperms as the outgroup to determine the ingroup topology. The high level of divergence between gymnosperms and angiosperms, however, has long been implicated in the difficulty of reconstructing relationships at the base of angiosperm phylogeny using DNA sequences, for fear of long-branch attraction (LBA). In this study, we replaced the gymnosperm sequences from the five-gene matrix (mitochondrial atp1 and matR, plastid atpB and rbcL, and nuclear 18S rDNA) used in our earlier study with four categories of divergent sequences--random sequences with equal base frequencies or equally AT- and GC-rich contents, homopolymers and heteropolymers, misaligned gymnosperm sequences, and aligned lycopod and bryophyte sequences--to evaluate whether the gymnosperms were an appropriate outgroup to angiosperms in our earlier study that identified the ANITA rooting. All 24 analyses performed rooted the angiosperm phylogeny at either Acorus or Alisma (or Alisma-Triglochin-Potamogeton in one case due to use of a slightly different alignment) and placed the monocots as a basal grade, producing genuine LBA results. These analyses demonstrate that the identification of ANITA as the basalmost extant angiosperms was based on historical signals preserved in the gymnosperm sequences and that the gymnosperms were an appropriate outgroup with which to root the angiosperm phylogeny in the multigene sequence analysis. This strategy of evaluating the appropriateness of an outgroup using artificial sequences and a series of outgroups with increments of divergence levels can be applied to investigations of phylogenetic patterns at the bases of other major clades, such as land plants, animals, and eukaryotes.

Developmental and evolutionary hypotheses for the origin of double fertilization and endosperm

The discovery of a second fertilization event that initiates endosperm in flowering plants, just over a century ago, stimulated intense interest in the evolutionary history and homology of endosperm, the genetically biparental embryo-nourishing tissue that is found only in angiosperms. Two alternative hypotheses for the origin of double fertilization and endosperm have been invoked to explain the origin of the angiosperm reproductive syndrome from a typical non-flowering seed plant reproductive syndrome. Endosperm may have arisen from a developmental transformation of a supernumerary embryo derived from a rudimentary second fertilization event that first evolved in the ancestors of angiosperms (endosperm homologous with an embryo). Conversely, endosperm may represent the developmental transformation of the cellular phase of non-flowering seed plant female gametophyte ontogeny that was later sexualized by the addition of a second fertilization event in a strongly progenetic female gametophyte (endosperm homologous with a female gametophyte). For the first time, explicit developmental and evolutionary transitions for both of these hypotheses are examined and compared. In addition, current data that may be congruent with either of these hypotheses are discussed. It is clear that much remains to be accomplished if the evolutionary significance of the process of double fertilization and the formation of endosperm is to be fully understood.

Perspective: the origin of flowering plants and their reproductive biology--a tale of two phylogenies

Recently, two areas of plant phylogeny have developed in ways that could not have been anticipated, even a few years ago. Among extant seed plants, new phylogenetic hypotheses suggest that Gnetales, a group of nonflowering seed plants widely hypothesized to be the closest extant relatives of angiosperms, may be less closely related to angiosperms than was believed. In addition, recent phylogenetic analyses of angiosperms have, for the first time, clearly identified the earliest lineages of flowering plants: Amborella, Nymphaeales, and a clade that includes Illiciales/ Trimeniaceae/Austrobaileyaceae. Together, the new seed plant and angiosperm phylogenetic hypotheses have major implications for interpretation of homology and character evolution associated with the origin and early history of flowering plants. As an example of the complex and often unpredictable interplay of phylogenetic and comparative biology, we analyze the evolution of double fertilization, a process that forms a diploid embryo and a triploid endosperm, the embryo-nourishing tissue unique to flowering plants. We demonstrate how the new phylogenetic hypotheses for seed plants and angiosperms can significantly alter previous interpretations of evolutionary homology and firmly entrenched assumptions about what is synapomorphic of flowering plants. In the case of endosperm, a solution to the century-old question of its potential homology with an embryo or a female gametophyte (the haploid egg-producing generation within the life cycle of a seed plant) remains complex and elusive. Too little is known of the comparative reproductive biology of extant nonflowering seed plants (Gnetales, conifers, cycads, and Ginkgo) to analyze definitively the potential homology of endosperm with antecedent structures. Remarkably, the new angiosperm phylogenies reveal that a second fertilization event to yield a biparental endosperm, long assumed to be an important synapomorphy of flowering plants, cannot be conclusively resolved as ancestral for flowering plants. Although substantive progress has been made in the analysis of phylogenetic relationships of seed plants and angiosperms, these efforts have not been matched by comparable levels of activity in comparative biology. The consequence of inadequate comparative biological information in an age of phylogenetic biology is a severe limitation on the potential to reconstruct key evolutionary historical events.

Multigene phylogeny of land plants with special reference to bryophytes and the earliest land plants

A widely held view of land plant relationships places liverworts as the first branch of the land plant tree, whereas some molecular analyses and a cladistic study of morphological characters indicate that hornworts are the earliest land plants. To help resolve this conflict, we used parsimony and likelihood methods to analyze a 6, 095-character data set composed of four genes (chloroplast rbcL and small-subunit rDNA from all three plant genomes) from all major land plant lineages. In all analyses, significant support was obtained for the monophyly of vascular plants, lycophytes, ferns (including PSILOTUM: and EQUISETUM:), seed plants, and angiosperms. Relationships among the three bryophyte lineages were unresolved in parsimony analyses in which all positions were included and weighted equally. However, in parsimony and likelihood analyses in which rbcL third-codon-position transitions were either excluded or downweighted (due to apparent saturation), hornworts were placed as sister to all other land plants, with mosses and liverworts jointly forming the second deepest lineage. Decay analyses and Kishino-Hasegawa tests of the third-position-excluded data set showed significant support for the hornwort-basal topology over several alternative topologies, including the commonly cited liverwort-basal topology. Among the four genes used, mitochondrial small-subunit rDNA showed the lowest homoplasy and alone recovered essentially the same topology as the multigene tree. This molecular phylogeny presents new opportunities to assess paleontological evidence and morphological innovations that occurred during the early evolution of terrestrial plants.

Utility of 17 chloroplast genes for inferring the phylogeny of the basal angiosperms

Sequences from 14 slowly evolving chloroplast genes (including three highly conserved introns) were obtained for representative basal angiosperm and seed-plant taxa, using novel primers described here. These data were combined with published sequences from atpB, rbcL, and newly obtained sequences from ndhF. Combined data from these 17 genes permit sturdy, well-resolved inference of major aspects of basal angiosperm relationships, demonstrating that the new primers are valuable tools for sorting out the deepest events in flowering plant phylogeny. Sequences from the inverted repeat (IR) proved to be particularly reliable (low homoplasy, high retention index). Representatives of Cabomba and Illicium were the first two successive branches of the angiosperms in an initial sampling of 19 exemplar taxa. This result was strongly supported by bootstrap analysis and by two small insertion/deletion events in the slowly evolving introns. Several paleoherb groups (representatives of Piperales) formed a strongly supported clade with taxa representing core woody magnoliids (Laurales, Magnoliales, and Winteraceae). The monophyly of the sampled eudicots and monocots was also well supported. Analyses of three major partitions of the data showed many of the same clades and supported the rooting seen with all the data combined. While Amborella trichopoda was supported as the sister group of the remaining angiosperms when we added Amborella and Nymphaea odorata to the analysis, a strongly conflicting rooting was observed when Amborella alone was added.