Horsetails and ferns are a monophyletic group and the closest living relatives to seed plants

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.

Tree ferns: monophyletic groups and their relationships as revealed by four protein-coding plastid loci

Tree ferns are a well-established clade within leptosporangiate ferns. Most of the 600 species (in seven families and 13 genera) are arborescent, but considerable morphological variability exists, spanning the giant scaly tree ferns (Cyatheaceae), the low, erect plants (Plagiogyriaceae), and the diminutive endemics of the Guayana Highlands (Hymenophyllopsidaceae). In this study, we investigate phylogenetic relationships within tree ferns based on analyses of four protein-coding, plastid loci (atpA, atpB, rbcL, and rps4). Our results reveal four well-supported clades, with genera of Dicksoniaceae (sensu ) interspersed among them: (A) (Loxomataceae, (Culcita, Plagiogyriaceae)), (B) (Calochlaena, (Dicksonia, Lophosoriaceae)), (C) Cibotium, and (D) Cyatheaceae, with Hymenophyllopsidaceae nested within. How these four groups are related to one other, to Thyrsopteris, or to Metaxyaceae is weakly supported. Our results show that Dicksoniaceae and Cyatheaceae, as currently recognised, are not monophyletic and new circumscriptions for these families are needed.

Mechanism of leaf-shape determination

Biodiversity of plant shape is mainly attributable to biodiversity of leaf shape and the shape of floral organs, the modified leaves. However, the exact mechanisms of leaf-shape determination remain unclear due to the complexity of flat-structure organogenesis that includes the simultaneous cell cycling and cell enlargement in primordia. Recent studies in developmental and molecular genetics have revealed several important aspects of leaf-shape control mechanisms. For example, understanding of polar control in leaf-blade expansion has advanced greatly. A curious phenomenon called "compensated cell enlargement" found in leaf organogenesis studies should also provide interesting clues regarding the mechanisms of multicellular organ development. This paper reviews recent research findings with a focus on leaf development in Arabidopsis thaliana.

Amplification of noncoding chloroplast DNA for phylogenetic studies in lycophytes and monilophytes with a comparative example of relative phylogenetic utility from Ophioglossaceae

Noncoding DNA sequences from numerous regions of the chloroplast genome have provided a significant source of characters for phylogenetic studies in seed plants. In lycophytes and monilophytes (leptosporangiate ferns, eusporangiate ferns, Psilotaceae, and Equisetaceae), on the other hand, relatively few noncoding chloroplast DNA regions have been explored. We screened 30 lycophyte and monilophyte species to determine the potential utility of PCR amplification primers for 18 noncoding chloroplast DNA regions that have previously been used in seed plant studies. Of these primer sets eight appear to be nearly universally capable of amplifying lycophyte and monilophyte DNAs, and an additional six are useful in at least some groups. To further explore the application of noncoding chloroplast DNA, we analyzed the relative phylogenetic utility of five cpDNA regions for resolving relationships in Botrychium s.l. (Ophioglossaceae). Previous studies have evaluated both the gene rbcL and the trnL(UAA)-trnF(GAA) intergenic spacer in this group. To these published data we added sequences of the trnS(GCU)-trnG(UUC) intergenic spacer + the trnG(UUC) intron region, the trnS(GGA)-rpS4 intergenic spacer+rpS4 gene, and the rpL16 intron. Both the trnS(GCU)-trnG(UUC) and rpL16 regions are highly variable in angiosperms and the trnS(GGA)-rpS4 region has been widely used in monilophyte phylogenetic studies. Phylogenetic resolution was equivalent across regions, but the strength of support for the phylogenies varied among regions. Of the five sampled regions the trnS(GCU)-trnG(UUC) spacer+trnG(UUC) intron region provided the strongest support for the inferred phylogeny.

Incongruence between primary sequence data and the distribution of a mitochondrial atp1 group II intron among ferns and horsetails

Using DNA sequence data from multiple genes (often from more than one genome compartment) to reconstruct phylogenetic relationships has become routine. Augmenting this approach with genomic structural characters (e.g., intron gain and loss, changes in gene order) as these data become available from comparative studies already has provided critical insight into some long-standing questions about the evolution of land plants. Here we report on the presence of a group II intron located in the mitochondrial atp1 gene of leptosporangiate and marattioid ferns. Primary sequence data for the atp1 gene are newly reported for 27 taxa, and results are presented from maximum likelihood-based phylogenetic analyses using Bayesian inference for 34 land plants in three data sets: (1) single-gene mitochondrial atp1 (exon+intron sequences); (2) five combined genes (mitochondrial atp1 [exon only]; plastid rbcL, atpB, rps4; nuclear SSU rDNA); and (3) same five combined genes plus morphology. All our phylogenetic analyses corroborate results from previous fern studies that used plastid and nuclear sequence data: the monophyly of euphyllophytes, as well as of monilophytes; whisk ferns (Psilotidae) sister to ophioglossoid ferns (Ophioglossidae); horsetails (Equisetopsida) sister to marattioid ferns (Marattiidae), which together are sister to the monophyletic leptosporangiate ferns. In contrast to the results from the primary sequence data, the genomic structural data (atp1 intron distribution pattern) would seem to suggest that leptosporangiate and marattioid ferns are monophyletic, and together they are the sister group to horsetails--a topology that is rarely reconstructed using primary sequence data.

Construction of a bacterial artificial chromosome library from the spikemoss Selaginella moellendorffii: a new resource for plant comparative genomics

BACKGROUND

The lycophytes are an ancient lineage of vascular plants that diverged from the seed plant lineage about 400 Myr ago. Although the lycophytes occupy an important phylogenetic position for understanding the evolution of plants and their genomes, no genomic resources exist for this group of plants.

RESULTS

Here we describe the construction of a large-insert bacterial artificial chromosome (BAC) library from the lycophyte Selaginella moellendorffii. Based on cell flow cytometry, this species has the smallest genome size among the different lycophytes tested, including Huperzia lucidula, Diphaiastrum digita, Isoetes engelmanii and S. kraussiana. The arrayed BAC library consists of 9126 clones; the average insert size is estimated to be 122 kb. Inserts of chloroplast origin account for 2.3% of the clones. The BAC library contains an estimated ten genome-equivalents based on DNA hybridizations using five single-copy and two duplicated S. moellendorffii genes as probes.

CONCLUSION

The S. moellenforffii BAC library, the first to be constructed from a lycophyte, will be useful to the scientific community as a resource for comparative plant genomics and evolution.

KNOX homeobox genes potentially have similar function in both diploid unicellular and multicellular meristems, but not in haploid meristems

Members of the class 1 knotted-like homeobox (KNOX) gene family are important regulators of shoot apical meristem development in angiosperms. To determine whether they function similarly in seedless plants, three KNOX genes (two class 1 genes and one class 2 gene) from the fern Ceratopteris richardii were characterized. Expression of both class 1 genes was detected in the shoot apical cell, leaf primordia, marginal part of the leaves, and vascular bundles by in situ hybridization, a pattern that closely resembles that of class 1 KNOX genes in angiosperms with compound leaves. The fern class 2 gene was expressed in all sporophyte tissues examined, which is characteristic of class 2 gene expression in angiosperms. All three CRKNOX genes were not detected in gametophyte tissues by RNA gel blot analysis. Arabidopsis plants overexpressing the fern class 1 genes resembled plants that overexpress seed plant class 1 KNOX genes in leaf morphology. Ectopic expression of the class 2 gene in Arabidopsis did not result in any unusual phenotypes. Taken together with phylogenetic analysis, our results suggest that (a) the class 1 and 2 KNOX genes diverged prior to the divergence of fern and seed plant lineages, (b) the class 1 KNOX genes function similarly in seed plant and fern sporophyte meristem development despite their differences in structure, (c) KNOX gene expression is not required for the development of the fern gametophyte, and (d) the sporophyte and gametophyte meristems of ferns are not regulated by the same developmental mechanisms at the molecular level.

Phylogenomics and the reconstruction of the tree of life

As more complete genomes are sequenced, phylogenetic analysis is entering a new era - that of phylogenomics. One branch of this expanding field aims to reconstruct the evolutionary history of organisms on the basis of the analysis of their genomes. Recent studies have demonstrated the power of this approach, which has the potential to provide answers to several fundamental evolutionary questions. However, challenges for the future have also been revealed. The very nature of the evolutionary history of organisms and the limitations of current phylogenetic reconstruction methods mean that part of the tree of life might prove difficult, if not impossible, to resolve with confidence.

Decoding the genomic tree of life

Genomes hold within them the record of the evolution of life on Earth. But genome fusions and horizontal gene transfer (HGT) seem to have obscured sufficiently the gene sequence record such that it is difficult to reconstruct the phylogenetic tree of life. HGT among prokaryotes is not random, however. Some genes (informational genes) are more difficult to transfer than others (operational genes). Furthermore, environmental, metabolic, and genetic differences among organisms restrict HGT, so that prokaryotes preferentially share genes with other prokaryotes having properties in common, including genome size, genome G+C composition, carbon utilization, oxygen utilization/sensitivity, and temperature optima, further complicating attempts to reconstruct the tree of life. A new method of phylogenetic reconstruction based on gene presence and absence, called conditioned reconstruction, has improved our prospects for reconstructing prokaryotic evolution. It is also able to detect past genome fusions, such as the fusion that appears to have created the first eukaryote. This genome fusion between a deep branching eubacterium, possibly an ancestor of the cyanobacterium and a proteobacterium, with an archaeal eocyte (crenarchaea), appears to be the result of an early symbiosis. Given new tools and new genes from relevant organisms, it should soon be possible to test current and future fusion theories for the origin of eukaryotes and to discover the general outlines of the prokaryotic tree of life.

A novel additional group II intron distinguishes the mitochondrial rps3 gene in gymnosperms

Comparative analysis of the ribosomal protein S3 gene (rps3) in the mitochondrial genome of Cycas with newly sequenced counterparts from Magnolia and Helianthus and available sequences from higher plants revealed that the positional clustering with the genes for ribosomal protein S19 (rps19) and L16 (rpl16) is preserved in gymnosperms. However, in contrast to the other land plant species, the rps3 gene in Cycas mitochondria is unique in possessing a second intron: rps3i2. Reverse transcription-polymerase chain reaction (RT-PCR) analysis of the transcripts generated from the rps19-rps3-rpl16 cluster in Cycas mitochondria demonstrated that the genes are cotranscribed and extensively modified by RNA editing and that both introns are efficiently spliced. Despite remarkable size heterogeneity, the Cycas rps3i1 can be shown to be homologous to the group IIA introns present within the rps3 gene of algae and land plants, including Magnolia and Helianthus. Conversely, sequences similar to the rps3i2 have not been reported previously. On the basis of conserved primary and secondary structure the second intervening sequence interrupting the Cycas rps3 gene has been classified as a group II intron. The close relationship of the rps3i2 to a group of different plant mitochondrial introns is intriguing and suggestive of a mitochondrial derivation for this novel intervening sequence. Interestingly, the rps3i2 appears to be conserved at the same gene location in other gymnosperms. Furthermore, the pattern of the rps3i2 distribution among algae and land plants provides evidence for the evolutionary acquisition of this novel intron in gymnosperms via intragenomic transposition or retrotransposition.

Many independent origins of trans splicing of a plant mitochondrial group II intron

We examined the cis- vs. trans-splicing status of the mitochondrial group II intron nad1i728 in 439 species (427 genera) of land plants, using both Southern hybridization results (for 416 species) and intron sequence data from the literature. A total of 164 species (157 genera), all angiosperms, was found to have a trans-spliced form of the intron. Using a multigene land plant phylogeny, we infer that the intron underwent a transition from cis to trans splicing 15 times among the sampled angiosperms. In 10 cases, the intron was fractured between its 5' end and the intron-encoded matR gene, while in the other 5 cases the fracture occurred between matR and the 3' end of the intron. The 15 intron fractures took place at different time depths during the evolution of angiosperms, with those in Nymphaeales, Austrobaileyales, Chloranthaceae, and eumonocots occurring early in angiosperm evolution and those in Syringodium filiforme, Hydrocharis morsus- ranae, Najas, and Erodium relatively recently. The trans-splicing events uncovered in Austrobaileyales, eumonocots, Polygonales, Caryophyllales, Sapindales, and core Rosales reinforce the naturalness of these major clades of angiosperms, some of which have been identified solely on the basis of recent DNA sequence analyses.

Distribution of introns in the mitochondrial gene nad1 in land plants: phylogenetic and molecular evolutionary implications

Forty-six species of diverse land plants were investigated by sequencing for their intron content in the mitochondrial gene nad1. A total of seven introns, all belonging to group II, were found, and two were newly discovered in this study. All 13 liverworts examined contain no intron, the same condition as in green algae. Mosses and hornworts, however, share one intron by themselves and another one with vascular plants. These intron distribution patterns are consistent with the hypothesis that liverworts represent the basal-most land plants and that the two introns were gained in the common ancestor of mosses-hornworts-vascular plants after liverworts had diverged. Hornworts also possess a unique intron of their own. A fourth intron was found only in Equisetum L., Marattiaceae, Ophioglossum L., Osmunda L., Asplenium L., and Adiantum L., and was likely acquired in their common ancestor, which supports the monophyly of moniliformopses. Three introns that were previously characterized in angiosperms and a few pteridophytes are now all extended to lycopods, and were likely gained in the common ancestor of vascular plants. Phylogenetic analyses of the intron sequences recovered topologies mirroring those of the plants, suggesting that the introns have all been vertically inherited. All seven nad1 group II introns show broad phylogenetic distribution patterns, with the narrowest being in moniliformopses and hornworts, lineages that date back to at least the Devonian (345 million years ago) and Silurian (435 million years ago), respectively. Hence, these introns must have invaded the genes via ancient transpositional events during the early stage of land plant evolution. Potentially heavy RNA editing was observed in nad1 of Haplomitrium Dedecek, Takakia Hatt. & Inoue, hornworts, Isoetes L., Ophioglossum, and Asplenium. A new nomenclature is proposed for group II introns.

ANGIOSPERM DIVERGENCE TIMES: THE EFFECT OF GENES, CODON POSITIONS, AND TIME CONSTRAINTS

An understanding of the evolution of modern terrestrial ecosystems requires an understanding of the dynamics associated with angiosperm evolution, including the timing of their origin and diversification into their extraordinary present-day diversity. Molecular estimates of angiosperm age have varied widely, and many substantially predate the Early Cretaceous fossil appearance of the group. In this study, the effect of different genes, codon positions, and chronological constraints on node ages are examined on divergence time estimates across seed plants, with a special focus on angiosperms. Penalized likelihood was used to estimate divergence times on a phylogenetic hypothesis for seed plants derived from Bayesian analysis, with branch lengths estimated with maximum likelihood. The plastid genes atpB, psaA, psbB, and rbcL were used individually and in combination, using first and second, third, and the three codon positions, including and excluding age constraints on 20 nodes derived from a critical examination of the land-plant fossil record. The optimal level of rate smoothing according to each unconstrained and constrained dataset was obtained with penalized likelihood. Tests for a molecular clock revealed significantly unclocklike rates in all datasets. Addition of fossil constraints resulted in even greater departures from constancy. Consistently with significant deviations from a clock, estimated optimal smoothing values were low, but a strict correlation between rate heterogeneity and optimal smoothing value was not found. Age estimates for nodes across the phylogeny varied, sometimes substantially, with gene and codon position. Nevertheless, estimates based on the four concatenated genes are very similar to the mean of the four individual gene estimates. For any given node, unconstrained age estimates are more variable than constrained estimates and are frequently younger than well-substantiated fossil members of the clade. Constrained estimates of ages of clades are older than unconstrained estimates and oldest fossil representatives, sometimes substantially so. Angiosperm age estimates decreased as rate smoothing increased. Whereas the range of unconstrained angiosperm age estimates spans the fossil age of the clade, the range of constrained estimates is narrower (and older) than the earliest angiosperm fossils. Results unambiguously indicate the relevance of constraints in reducing the variability of ages derived from different partitions of the data and diminishing the effect of the smoothing parameter. Constrained optimizations of divergence times and substitution rates across the phylogeny suggest appreciably different evolutionary dynamics for angiosperms and for gymnosperms. Whereas the gymnosperm crown group originated shortly after the origin of seed plants, a long time elapsed before the origin of crown group angiosperms. Although absolute age estimates of angiosperms and angiosperm clades are older than their earliest fossils, the estimated pace of phylogenetic diversification largely agrees with the rapid appearance of angiosperm lineages in stratigraphic sequences.

Phylogeny and evolution of ferns (monilophytes) with a focus on the early leptosporangiate divergences

The phylogenetic structure of ferns (= monilophytes) is explored here, with a special focus on the early divergences among leptosporangiate lineages. Despite considerable progress in our understanding of fern relationships, a rigorous and comprehensive analysis of the early leptosporangiate divergences was lacking. Therefore, a data set was designed here to include critical taxa that were not included in earlier studies. More than 5000 bp from the plastid (rbcL, atpB, rps4) and the nuclear (18S rDNA) genomes were sequenced for 62 taxa. Phylogenetic analyses of these data (1) confirm that Osmundaceae are sister to the rest of the leptosporangiates, (2) resolve a diverse set of ferns formerly thought to be a subsequent grade as possibly monophyletic (((Dipteridaceae, Matoniaceae), Gleicheniaceae), Hymenophyllaceae), and (3) place schizaeoid ferns as sister to a large clade of "core leptosporangiates" that includes heterosporous ferns, tree ferns, and polypods. Divergence time estimates for ferns are reported from penalized likelihood analyses of our molecular data, with constraints from a reassessment of the fossil record.

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.

Monocot relationships: an overview

In 10 years, the monocots have gone from being one of the least studied and most phylogenetically misunderstood groups of the angiosperms to one of the best characterized. Based on analyses of seven genes representing all three genomes, the following clades have high bootstrap support: Acorales (with the single genus Acorus) is sister to the rest of the monocots, followed successively by Alismatales (including Araceae and Tofieldiaceae), Petrosaviales, Dioscoreales/Pandanales, Liliales, Asparagales, and finally a polytomy of Arecales, Commelinales/Zingiberales, Dasypogonaceae, and Poales. Many of these results also have support from at least some morphological data, but some are unique to the trees created from DNA sequence data. Monocots have been shown in molecular clock studies to be at least 140 million years old, and all major clades and most families date to well before the end of the Cretaceous. More data are required to clarify the positions of the remaining unclearly placed orders, Asparagles, Liliales, and Arecales, as well as Dasypogonaceae. More sequences from the nuclear and mitochondrial genomes are also needed to complement those from the plastid genome, which is the most sampled and thus far most pattern-rich.

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.

Primary cell wall composition of pteridophytes and spermatophytes

•  Primary cell walls (PCWs) of major vascular plant taxa were analysed as a contribution towards understanding wall evolution. •  Alcohol-insoluble residues from immature shoots were acid- or enzyme-hydrolysed and the products analysed chromatographically and electrophoretically. •  There were phylogenetic differences in abundance of mannose, galacturonate and glucuronate residues, mixed-linkage glucan (MLG) and tannins. Eusporangiate pteridophytes (lycopodiophytes, a psilotophyte, an equisetophyte and a eusporangiate fern) were richer in mannose than leptosporangiate ferns, gymnosperms and angiosperms. Galacturonate was always the most abundant uronate; glucuronate was not abundant in PCWs of vascular plants except angiosperms (especially monocots and some magnoliids). MLG was detected in the Poaceae and Flagellariaceae, but no other vascular plants. Proanthocyanidins were associated with PCWs from leptosporangiate ferns, gymnosperms and some angiosperms, but not eusporangiate pteridophytes. Xyloglucan was present in all vascular plants tested. •  The results imply that major evolutionary changes in the PCW occurred not only during the charophyte-bryophyte and bryophyte-lycopodiophyte transitions but also after plants attained the vascular condition and upright growth habit, particularly during the eusporangiate-leptosporangiate transition.

Fossils and plant phylogeny

Developing a detailed estimate of plant phylogeny is the key first step toward a more sophisticated and particularized understanding of plant evolution. At many levels in the hierarchy of plant life, it will be impossible to develop an adequate understanding of plant phylogeny without taking into account the additional diversity provided by fossil plants. This is especially the case for relatively deep divergences among extant lineages that have a long evolutionary history and in which much of the relevant diversity has been lost by extinction. In such circumstances, attempts to integrate data and interpretations from extant and fossil plants stand the best chance of success. For this to be possible, what will be required is meticulous and thorough descriptions of fossil material, thoughtful and rigorous analysis of characters, and careful comparison of extant and fossil taxa, as a basis for determining their systematic relationships.

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.

Chloroplast phylogeny indicates that bryophytes are monophyletic

Opinions on the basal relationship of land plants vary considerably and no phylogenetic tree with significant statistical support has been obtained. Here, we report phylogenetic analyses using 51 genes from the entire chloroplast genome sequences of 20 representative green plant species. The analyses, using translated amino acid sequences, indicated that extant bryophytes (mosses, liverworts, and hornworts) form a monophyletic group with high statistical confidence and that extant bryophytes are likely sisters to extant vascular plants, although the support for monophyletic vascular plants was not strong. Analyses at the nucleotide level could not resolve the basal relationship with statistical confidence. Bryophyte monophyly inferred using amino acid sequences has a good statistical foundation and is not rejected statistically by other data sets. We propose bryophyte monophyly as the currently best hypothesis.

Dating the monocot-dicot divergence and the origin of core eudicots using whole chloroplast genomes

We estimated the dates of the monocot-dicot split and the origin of core eudicots using a large chloroplast (cp) genomic dataset. Sixty-one protein-coding genes common to the 12 completely sequenced cp genomes of land plants were concatenated and analyzed. Three reliable split events were used as calibration points and for cross references. Both the method based on the assumption of a constant rate and the Li-Tanimura unequal-rate method were used to estimate divergence times. The phylogenetic analyses indicated that nonsynonymous substitution rates of cp genomes are unequal among tracheophyte lineages. For this reason, the constant-rate method gave overestimates of the monocot-dicot divergence and the age of core eudicots, especially when fast-evolving monocots were included in the analysis. In contrast, the Li-Tanimura method gave estimates consistent with the known evolutionary sequence of seed plant lineages and with known fossil records. Combining estimates calibrated by two known fossil nodes and the Li-Tanimura method, we propose that monocots branched off from dicots 140-150 Myr ago (late Jurassic-early Cretaceous), at least 50 Myr younger than previous estimates based on the molecular clock hypothesis, and that the core eudicots diverged 100-115 Myr ago (Albian-Aptian of the Cretaceous). These estimates indicate that both the monocot-dicot divergence and the core eudicot's age are older than their respective fossil records.

Unraveling the phylogeny of polygrammoid ferns (Polypodiaceae and Grammitidaceae): exploring aspects of the diversification of epiphytic plants

We explore the phylogeny of the polygrammoid ferns using nucleotide sequences derived from three plastid loci for each of 98 selected species. Our analyses recovered four major monophyletic lineages: the loxogrammoids, two clades consisting of taxa restricted to the Old World, and a largely neotropical clade that also includes the pantropical Grammitidaceae. The loxogrammoid lineage diverges first and is sister to a large clade comprising the three remaining species-rich lineages. One paleotropical clade includes the drynarioid and selligueoid ferns, whereas the second paleotropical clade includes the platycerioids, lepisoroids, microsoroids, and their relatives. The grammitids nest within the neotropical clade, although the sister taxon of this circum-tropic, epiphytic group remains ambiguous. Microsorum and Polypodium, as traditionally defined, were recovered as polyphyletic. The relatively short branch lengths of the deepest clades contrast with the long branch lengths leading to the terminal groups. This suggests that the polygrammoid ferns arose through an old, rapid radiation. Our analysis also reveals that the rate of substitution in the grammitids is remarkably higher relative to other polygrammoids. Disparities in substitution rate may be correlated with one or more features characterizing grammitids, including species richness, chlorophyllous spores, and an extended gametophytic phase.

Amborella not a "basal angiosperm"? Not so fast

The sequence of the plastid genome of Amborella trichopoda, the putative sister to all other extant angiosperms, was recently reported (Molecular Biology and Evolution 20: 1499-1505). Goremykin et al. used sequence data for 61 plastid genes from Amborella and 12 other embryophytes in phylogenetic analyses and concluded that Amborella is not the sister to the remaining flowering plants; the monocots instead occupy this position. The authors attributed their results, which differ substantially from all recent phylogenetic analyses of angiosperms, to the increased character sampling (30 017 nucleotides in their aligned matrix) in their analysis relative to published studies that included fewer genes but more taxa. We hypothesized that the difference in topology is not due to limited character sampling in previous studies but to limited taxon sampling in the analysis by Goremykin et al. To test this, we conducted a series of phylogenetic analyses using a three-gene, 12 (or more)-taxon data set to evaluate the topological effects of (i) including three vs. 61 genes for (nearly) the same set of taxa, (ii) analyzing different codon positions, (iii) substituting representatives of other basal lineages for Amborella, (iv) replacing the grasses used to represent the monocots with other monocots, selected either for their phylogenetic position or randomly, and (v) adding other basal taxa-Nymphaea, Austrobaileya, magnoliids, and monocots-to the 12-taxon data set. Our results demonstrate that the "monocots basal" topology obtained by Goremykin et al. is not due to increased character sampling of the plastid genome; their topology was obtained using only two plastid genes or two plastid genes and one nuclear gene. This topology was also retained when either Nymphaea or Austrobaileya was substituted for Amborella, demonstrating that any of the three basal lineages will attach to Calycanthus for lack of any other close branch. Furthermore, the "monocots basal" topology is not robust to changes in sampling of monocots. Simply adding Oncidium, for example, places Amborella sister to the other angiosperms. Thus, limited taxon sampling, focusing on organisms with complete genome sequences, can lead to artifactual results.

The sequence of the largest subunit of RNA polymerase II is a useful marker for inferring seed plant phylogeny

We used RT-PCR to sequence approximately 3 kb of the gene coding for the largest subunit of RNA polymerase II (rpb1) from nine land plants. Our results show that plant rpb1 genes all have a similar GC-content and that their amino acid sequences evolve at a similar rate in most species we examined, except for the Arabidopsis thaliana and rice sequences which evolve faster. This gene also exists as a single copy in most species and contains enough phylogenetically informative sites to resolve the evolutionary relationships among seed plants. Protein maximum parsimony, as well as neighbor-joining and maximum likelihood analyses of DNA and protein sequences, all generated identical tree topologies with similar strong support values at each node. The angiosperms are a clade comprising Amborella as a sister group to all other angiosperms, followed by Nymphaea, Magnolia, Arabidopsis, and a monocot clade containing maize and rice. The gymnosperms also form a monophyletic clade with Welwitschia and pine grouped together and sister to a Cycas and Zamia clade. These findings concur with recent studies that refute the Anthophyte Hypothesis and place Amborella at the base of the angiosperm tree. These rpb1 sequences also give a more consistent picture of seed plant relationships than similar analyses performed on data sets made of 18S rDNA, atpB, and rbcL sequences from the same species. These sequences therefore show great promise to help further resolve the phylogenetic relationships of seed plants.

Dating the monocot-dicot divergence and the origin of core eudicots using whole chloroplast genomes

We estimated the dates of the monocot-dicot split and the origin of core eudicots using a large chloroplast (cp) genomic dataset. Sixty-one protein-coding genes common to the 12 completely sequenced cp genomes of land plants were concatenated and analyzed. Three reliable split events were used as calibration points and for cross references. Both the method based on the assumption of a constant rate and the Li-Tanimura unequal-rate method were used to estimate divergence times. The phylogenetic analyses indicated that nonsynonymous substitution rates of cp genomes are unequal among tracheophyte lineages. For this reason, the constant-rate method gave overestimates of the monocot-dicot divergence and the age of core eudicots, especially when fast-evolving monocots were included in the analysis. In contrast, the Li-Tanimura method gave estimates consistent with the known evolutionary sequence of seed plant lineages and with known fossil records. Combining estimates calibrated by two known fossil nodes and the Li-Tanimura method, we propose that monocots branched off from dicots 140-150 Myr ago (late Jurassic-early Cretaceous), at least 50 Myr younger than previous estimates based on the molecular clock hypothesis, and that the core eudicots diverged 100-115 Myr ago (Albian-Aptian of the Cretaceous). These estimates indicate that both the monocot-dicot divergence and the core eudicot's age are older than their respective fossil records.

Genome-scale phylogeny and the detection of systematic biases

Phylogenetic inference from sequences can be misled by both sampling (stochastic) error and systematic error (nonhistorical signals where reality differs from our simplified models). A recent study of eight yeast species using 106 concatenated genes from complete genomes showed that even small internal edges of a tree received 100% bootstrap support. This effective negation of stochastic error from large data sets is important, but longer sequences exacerbate the potential for biases (systematic error) to be positively misleading. Indeed, when we analyzed the same data set using minimum evolution optimality criteria, an alternative tree received 100% bootstrap support. We identified a compositional bias as responsible for this inconsistency and showed that it is reduced effectively by coding the nucleotides as purines and pyrimidines (RY-coding), reinforcing the original tree. Thus, a comprehensive exploration of potential systematic biases is still required, even though genome-scale data sets greatly reduce sampling error.

Ferns diversified in the shadow of angiosperms

The rise of angiosperms during the Cretaceous period is often portrayed as coincident with a dramatic drop in the diversity and abundance of many seed-free vascular plant lineages, including ferns. This has led to the widespread belief that ferns, once a principal component of terrestrial ecosystems, succumbed to the ecological predominance of angiosperms and are mostly evolutionary holdovers from the late Palaeozoic/early Mesozoic era. The first appearance of many modern fern genera in the early Tertiary fossil record implies another evolutionary scenario; that is, that the majority of living ferns resulted from a more recent diversification. But a full understanding of trends in fern diversification and evolution using only palaeobotanical evidence is hindered by the poor taxonomic resolution of the fern fossil record in the Cretaceous. Here we report divergence time estimates for ferns and angiosperms based on molecular data, with constraints from a reassessment of the fossil record. We show that polypod ferns (> 80% of living fern species) diversified in the Cretaceous, after angiosperms, suggesting perhaps an ecological opportunistic response to the diversification of angiosperms, as angiosperms came to dominate terrestrial ecosystems.

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.

Phylogenetic relationships within the fern genus Hymenophyllum s.l. (Hymenophyllaceae, Filicopsida): contribution of morphology and cytology

The phylogenetic relationships of Hymenophyllum and its segregate genera Cardiomanes, Hymenoglossum, Rosenstockia, Serpyllopsis and Microtrichomanes are addressed, using 31 morphological characters of the sporophyte and one cytological character. As expected, this study reveals considerable morphological heterogeneity within the genus sensu lato, but several apomorphic changes allow support for some clades. Four unresolved taxa, Cardiomanes, Hymenoglossum, Diplophyllum and Mecodium pro parte are probably the most basal elements in Hymenophyllum. The analysis also suggests the polyphyly of Mecodium, and two unexpected associations: Sphaerocionium together with Microtrichomanes; and a broad clade composed of subg. Hymenophyllum, Hemicyatheon and Craspedophyllum, genera Rosenstockia and Serpyllopsis, and subsect. Leptocionium and Amphipterum. These associations appear justified by morphological, cytological or geographical data, and most of them are in agreement with preliminary molecular results.

Phylogenetic studies of Ophioglossaceae: evidence from rbcL and trnL-F plastid DNA sequences and morphology

Ophioglossaceae are a putatively ancient lineage of ferns in which the aerial portion of the plant is composed of a single leaf. The simplicity of foliar morphology has limited the number of characters available for constructing classifications and contributed to taxonomic difficulties at nearly every level of classification within the family. Analysis of plastid DNA rbcL sequences from 36 species representing the diversity of Ophioglossaceae supported the monophyly of the family. Intrafamilial relationships were examined using rbcL and trnL-F plastid DNA sequences and morphological data. Individual and combined analyses of the three data sets revealed two main clades within the family, here termed ophioglossoid and botrychioid. In the botrychioid clade, Helminthostachys was sister to a broadly defined Botrychium, within which Botrychium in the narrow sense of some authors and Sceptridium were sister. Botrypus was paraphyletic, with Botrypus virginianus sister to Botrychium plus Sceptridium, and with Botrypus strictus sister to all other botrychioid species except Helminthostachys. In the ophioglossoid clade, Ophioglossum in the narrow sense was sister to Cheiroglossa plus Ophioderma, but relationships within Ophioglossum were not well supported.

Characterization of the Selaginella remotifolia MADS-box gene

Recent progress in plant molecular genetics has revealed that floral organ development is regulated by several homeotic selector genes, most of which belong to the MADS-box gene family. Here we report on SrMADS1,a MIKC(c)-type MADS-box gene from Selaginella, a spikemoss belonging to the lycophytes. SrMADS1 phylogenetically forms a monophyletic clade with genes of the LAMB2 group, which are MIKC(c) genes of the clubmoss Lycopodium, and is expressed in whole sporophytic tissues except roots and rhizophores. Our results and the previous report on Lycopodium MIKC(c) genes suggest that the ancestral MIKC(c )gene of primitive dichotomous plants in the early Devonian was involved in the development of basic sporophytic tissues such as shoot, stem, and sporangium.

Inhibition of plastid division by ampicillin in the pteridophyte Selaginella nipponica Fr. et Sav

We investigated the effect of the beta-lactam antibiotic, ampicillin, on plastid division in the pteridophyte Selaginella nipponica. Guard cells of plantlets treated with 1 mM ampicillin only often had one plastid, whereas guard cells of untreated plantlets had two to four plastids. We generated a S. nipponica cell culture system and used it to investigate the effects of ampicillin. Treatment with 1 mM ampicillin had no effect on cell division in culture. We classified cultured cells into four types based on the number of plastids they contained: one (Type I), two (Type II), three or four (Type III) and more than five (Type IV). After 3 d in culture, the percentage of each cell type (I-IV) was 29.5, 46.7, 20.9, and 1.9%, respectively. Subsequently, the percentage of Types III and IV increased gradually, reaching 61.9 and 11.4%, respectively, after 15 d in culture in the absence of ampicillin. When 1 mM ampicillin was added, there was a minimal increase in the number of Type III and IV cells, with high percentages of Type I and II cells (32.4 and 45.7%, respectively) after 15 d. These results suggest that ampicillin inhibits plastid division in S. nipponica.

Azolla--a model organism for plant genomic studies

The aquatic ferns of the genus Azolla are nitrogen-fixing plants that have great potentials in agricultural production and environmental conservation. Azolla in many aspects is qualified to serve as a model organism for genomic studies because of its importance in agriculture, its unique position in plant evolution, its symbiotic relationship with the N2-fixing cyanobacterium, Anabaena azollae, and its moderate-sized genome. The goals of this genome project are not only to understand the biology of the Azolla genome to promote its applications in biological research and agriculture practice but also to gain critical insights about evolution of plant genomes. Together with the strategic and technical improvement as well as cost reduction of DNA sequencing, the deciphering of their genetic code is imminent.

Deciding among green plants for whole genome studies

Recent comparative DNA-sequencing studies of chloroplast, mitochondrial and ribosomal genes have produced an evolutionary tree relating the diversity of green-plant lineages. By coupling this phylogenetic framework to the explosion of information on genome content, plant-genomic efforts can and should be extended beyond angiosperm crop and model systems. Including plant species representative of other crucial evolutionary nodes would produce the comparative information necessary to understand fully the organization, function and evolution of plant genomes. The simultaneous development of genomic tools for green algae, bryophytes, 'seed-free' vascular plants and gymnosperms should provide insights into the bases of the complex morphological, physiological, reproductive and biochemical innovations that have characterized the successful transition of green plants to land.

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.

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.

Two ancient classes of MIKC-type MADS-box genes are present in the moss Physcomitrella patens

Characterization of seven MADS-box genes, termed PPM1-PPM4 and PpMADS1-PpMADS3, from the moss model species Physcomitrella patens is reported. Phylogeny reconstructions and comparison of exon-intron structures revealed that the genes described here represent two different classes of homologous, yet distinct, MIKC-type MADS-box genes, termed MIKC(c)-type genes-"(c)" stands for "classic"-(PPM1, PPM2, PpMADS1) and MIKC(*)-type genes (PPM3, PPM4, PpMADS2, PpMADS3). The two gene classes deviate from each other in a characteristic way, especially in a sequence stretch termed intervening region. MIKC(c)-type genes are abundantly present in all land plants which have been investigated in this respect, and give rise to well-known gene types such as floral meristem and organ identity genes. In contrast, LAMB1 from the clubmoss Lycopodium annotinum was identified as the only other MIKC(*)-type gene published so far. Our findings strongly suggest that the most recent common ancestor of mosses and vascular plants contained at least one MIKC(c)-type and one MIKC(*)-type gene. Our studies thus reveal an ancient duplication of an MIKC-type gene that occurred before the separation of the lineages that led to extant mosses and vascular plants more than about 450 MYA. The identification of bona fide K-domains in both MIKC(*)-type and MIKC(c)-type proteins suggests that the K-domain is more ancient than is suggested by a recent alternative hypothesis. MIKC(*)-type genes may have escaped identification in ferns and seed plants so far. It seems more likely, however, that they represent a class of genes which has been lost in the lineage which led to extant ferns and seed plants. The high number of P. patens MADS-box genes and the presence of a K-box in the coding region and of some potential binding sites for MADS-domain proteins and other transcription factors in the putative promoter regions of these genes suggest that MADS-box genes in mosses are involved in complex gene regulatory networks similar to those in flowering plants.

Coevolution of roots and mycorrhizas of land plants

Here, the coevolution of mycorrhizal fungi and roots is assessed in the light of evidence now available, from palaeobotanical and morphological studies and the analysis of DNA-based phylogenies. The first bryophyte-like land plants, in the early Devonian (400 million years ago), had endophytic associations resembling vesicular-arbuscular mycorrhizas (VAM) even before roots evolved. Mycorrhizal evolution would have progressed from endophytic hyphae towards balanced associations where partners were interdependent due to the exchange of limiting energy and nutrient resources. Most mycorrhizas are mutualistic, but in some cases the trend for increasing plant control of fungi culminates in the exploitative mycorrhizas of achlorophyllous, mycoheterotrophic plants. Ectomycorrhizal, ericoid and orchid mycorrhizas, as well as nonmycorrhizal roots, evolved during the period of rapid angiosperm radiation in the Cretaceous. It is hypothesised that roots gradually evolved from rhizomes to provide more suitable habitats for mycorrhizal fungi and provide plants with complex branching and leaves with water and nutrients. Selection pressures have caused the morphological divergence of roots with different types of mycorrizas. Root cortex thickness and exodermis suberization are greatest in obllgately mycorrhizal plants, while nonmycorrhizal plants tend to have fine roots, with more roots hairs and relatively advanced chemical defences. Major coevolutionary trends and the relative success of plants with different root types are discussed. Contents Summary 275 I. Introduction 276 II. Mycorrhizal Fungi 276 III. The Dawn of Mycorrhizas 279 IV. Mycorrhizal Associations of Living and Extinct Plants 282 V. Evolution of Roots 288 VI. The Root as a Habitat for Fungi 290 VII. Mycorrhizal Evolution Trends 295 Acknowledgements 298 References 298.

Rate heterogeneity among lineages of tracheophytes: integration of molecular and fossil data and evidence for molecular living fossils

Many efforts to date evolutionary divergences by using a molecular clock have yielded age estimates that are grossly inconsistent with the paleontological evidence. Such discrepancies often are attributed to the inadequacy of the fossil record, but many potential sources of error can affect molecular-based estimates. In this study, we minimize the potential error caused by inaccurate topology and uncertain calibration times by using a well-supported tree, multiple genes, and multiple well-substantiated dates to explore the correspondence between the fossil record and molecular-based age estimates for major clades of tracheophytes. Age estimates varied because of gene effects, codon position, lineage effects, method of inferring branch lengths, and whether or not rate constancy was assumed. However, even methods designed to ameliorate the effects of rate heterogeneity among lineages could not accommodate the substantially slower rates observed in Marattia + Angiopteris and in the tree ferns. Both of these clades of ferns have undergone dramatic decelerations in their rates of molecular evolution and are "molecular living fossils," consistent with their relative morphological stasis for the past 165-200 million years. Similar discrepancies between the fossil record and molecular-based age estimates noted in other studies may also be explained in part by violations of rate constancy among lineages.