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The origin of plants and their colonization of land fundamentally transformed the terrestrial environment. Here we elucidate the basis of this formative episode in Earth history through patterns of lineage, gene and genome evolution. We use new fossil calibrations, a relative clade age calibration (informed by horizontal gene transfer) and new phylogenomic methods for mapping gene family origins. Distinct rooting strategies resolve tracheophytes (vascular plants) and bryophytes (non-vascular plants) as monophyletic sister groups that diverged during the Cambrian, 515–494 million years ago. The embryophyte stem is characterized by a burst of gene innovation, while bryophytes subsequently experienced an equally dramatic episode of reductive genome evolution in which they lost genes associated with the elaboration of vasculature and the stomatal complex. Overall, our analyses reveal that extant tracheophytes and bryophytes are both highly derived from a more complex ancestral land plant. Understanding the origin of land plants requires tracing character evolution across a diversity of modern lineages.

The relationships among the four major embryophyte lineages (mosses, liverworts, hornworts, vascular plants) and the timing of the origin of land plants are enigmatic problems in plant evolution. Here, we resolve the monophyly of bryophytes by improving taxon sampling of hornworts and eliminating the effect of synonymous substitutions. We then estimate the divergence time of crown embryophytes based on three fossil calibration strategies, and reveal that maximum calibration constraints have a major effect on estimating the time of origin of land plants. Moreover, comparison of priors and posteriors provides a guide for evaluating the optimal calibration strategy. By considering the reliability of fossil calibrations and the influences of molecular data, we estimate that land plants originated in the Precambrian (980–682 Ma), much older than widely recognized. Our study highlights the important contribution of molecular data when faced with contentious fossil evidence, and that fossil calibrations used in estimating the timescale of plant evolution require critical scrutiny.

Premise Phylogenetic trees of bryophytes provide important evolutionary context for land plants. However, published inferences of overall embryophyte relationships vary considerably. We performed phylogenomic analyses of bryophytes and relatives using both mitochondrial and plastid gene sets, and investigated bryophyte plastome evolution. Methods We employed diverse likelihood‐based analyses to infer large‐scale bryophyte phylogeny for mitochondrial and plastid data sets. We tested for changes in purifying selection in plastid genes of a mycoheterotrophic liverwort (Aneura mirabilis) and a putatively mycoheterotrophic moss (Buxbaumia), and compared 15 bryophyte plastomes for major structural rearrangements. Results Overall land‐plant relationships conflict across analyses, generally weakly. However, an underlying (unrooted) four‐taxon tree is consistent across most analyses and published studies. Despite gene coverage patchiness, relationships within mosses, liverworts, and hornworts are largely congruent with previous studies, with plastid results generally better supported. Exclusion of RNA edit sites restores cases of unexpected non‐monophyly to monophyly for Takakia and two hornwort genera. Relaxed purifying selection affects multiple plastid genes in mycoheterotrophic Aneura but not Buxbaumia. Plastid genome structure is nearly invariant across bryophytes, but the tufA locus, presumed lost in embryophytes, is unexpectedly retained in several mosses. Conclusions A common unrooted tree underlies embryophyte phylogeny, [(liverworts, mosses), (hornworts, vascular plants)]; rooting inconsistency across studies likely reflects substantial distance to algal outgroups. Analyses combining genomic and transcriptomic data may be misled locally for heavily RNA‐edited taxa. The Buxbaumia plastome lacks hallmarks of relaxed selection found in mycoheterotrophic Aneura. Autotrophic bryophyte plastomes, including Buxbaumia, hardly vary in overall structure.

— Separate cladistic analyses of the green algae, liverworts, and hornworts are presented. Classificatory and evolutionary implications of these analyses, in addition to our previously published cladistic analyses of mosses and the embryophytes as a whole, are discussed. The embryophytes are monophyletic, and are part of a larger monophyletic group that includes some of the green algae (the “charophytes”). Important evolutionary transformations in the early phylogeny of the land plants include: (1) retention of the zygote on the haploid plant (gametophyte), with the sporophyte generation arising de novo by delaying meiosis, (2) independent elaboration of an elongate sporophyte in some liverworts, some hornworts, and in the moss-tracheophyte clade, (3) independent origin of radial (axial) symmetry in the gametophyte in some liverworts and in the moss-tracheophyte clade, (4) independent origin of leaves on the gametophyte in some liverworts and in mosses, and (5) the unique development of a branching sporophyte with multiple sporangia in the tracheophytes.

A relatively rich association of six species of embryophyte plants is known from the upper Silurian of the Prague Basin (Bohemian Massif, Czech Republic). All stratigraphically controlled specimens come from the Neocolonograptus parultimus-Neocolonograptus ultimus Zone of the Přidoli. A new genus and species, Tichavekia grandis Psenicka, Sakala et Kraft, is established. The new combination Aberlemnia bohemica (Schweitzer) Sakala, Psenicka et Kraft, comb. nov. illustrates its Lycophytina affinity. The distribution and taphonomy of these plants in the Prague Basin indicates the proximity of exposed land interpreted to be islands of volcanic origin. Two local associations show primary differences in vegetated areas of the islands and apparent ecological responses of the primitive vascular plants to their habitats. Suitable environments in the coastal zones of volcanic islands in the Prague Basin, which was situated at the outer periphery of a broad Gondwanan shelf, likely represent significant transfer points for an initial dispersion and a first expansion of land plants. Repeated vegetation of the islands is inferred from the discrete distribution of land plants at different stratigraphic levels. These changes are explained partly in context of local changes of the island relief, and partly as responses to global climatic and sea level fluctuations, and fit environmental dynamics of islands of volcanic origin in general. This Initial Plant Diversification and Dispersal Event (IPDDE) is of considerable significance in the evolution of plants documented from the Bohemian Massif.

ECERIFERUM1 (CER1) and ECERIFERUM3 (CER3) are key genes in synthesis of alkanes, a major component of cuticular waxes in land plants. The genes share extensive similarity, including the N-terminal (ERG3/FAH) and C-terminal (WAX2) domains. This study, traces the origin, evolutionary history, phylogenetic relationships and variation in copy number of the two genes within and beyond the Viridiplantae (green plants). Protein homologs of both CER1 and CER3 were identified across most Embryophyta (land plants), a single homolog (CER1/3) in charophytes and prasinophytes, and none in the other green, red or brown algae. Ancestral state reconstructions in 100 sequenced Archaeplastida using presence/absence of CER1/3 family genes revealed that the CER1/3 gene probably originated in the common ancestor of Viridiplantae. Phylogenetic analysis of CER1 and CER3 protein sequences from 146 plant species strongly suggests that the two genes originated by duplication of CER1/3 in the ancestral embryophyte. The evolution of CER1 and CER3 genes involved differential divergence of the two domains. Outside Embryophyta, CER1/3 similar sequences identified in diatoms and a cryptophyte, were the closest relatives of the CER1/3 family proteins. Proteins harbouring WAX2-wxAR (WAX2 associated region) similar regions were identified in proteins of bacteria, Archaea, cryptophytes, dinoflagellates and Stramenopiles. The independent existence of both ERG3/FAH and WAX2-wxAR domains in diverse lineages strongly points to the origin of CER1/3 gene in green plants by the fusion of pre-existing domains.

The interiors of plants are colonized by diverse microorganisms that are referred to as endophytes. Endophytes have received much attention over the past few decades, yet many questions remain unanswered regarding patterns in their biodiversity at local to global scales. To characterize research effort to date, we synthesized results from ∼600 published studies. Our survey revealed a global research interest and highlighted several gaps in knowledge. For instance, of the seventeen biomes encompassed by our survey, seven were understudied and together composed only 7% of the studies that we considered. We found that fungal endophyte diversity has been characterized in at least one host from 30% of embryophyte families, while bacterial endophytes have been surveyed in hosts from only 10.5% of families. We complimented our survey with a vote counting procedure to determine endophyte richness patterns among plant tissue types. We found that variation in endophyte assemblages in above-ground tissues varied with host growth habit. Stems were the richest tissue in woody plants, whereas roots were the richest tissue in graminoids. For forbs, we found no consistent differences in relative tissue richness among studies. We propose future directions to fill the gaps in knowledge we uncovered and inspire further research.Originality-Significance StatementMuch remains to be learned regarding the biodiversity and distribution of the microbes that colonize the interiors of plants. Here, we surveyed approximately 600 publications to characterize gaps in knowledge and provide a roadmap for future research. We compared biomes, plant families, and geographical regions in terms of the research interest that they have garnered. Additionally, we synthesized published results and report that variation in endophyte richness among plant tissue types is a function of host growth habit. Stems were the richest tissue in woody plants, whereas roots were the richest tissue in graminoids. We hope to inspire research to fill the gaps in knowledge that we uncovered.

Premise of research. Climatically favorable conditions correspond with fossil evidence for dramatic Ordovician marine biodiversification, but coeval terrestrial biodiversity is less well understood. Although diverse Middle and Late Ordovician microfossils are interpreted as reproductive remains of early bryophyte-like land plants (consistent with molecular data indicating pre-Ordovician embryophyte origin), the vegetative structure of Ordovician plants remains mysterious, as do relationships to modern groups. Because distinctive fungal microfossils indicating land plant presence were previously reported from Ordovician carbonate deposits in Wisconsin, we examined another nearby outcrop for additional evidence of terrestrial biodiversification.Methodology. Replicate collections were made from well-understood 455–454 Ma Platteville Formation carbonates of relatively low porosity and hydraulic conductivity. We employed measures to avoid contamination, and organic remains extracted by acid maceration were cha...

Understanding how plant species respond to climate change is one of the great challenges in biodiversity conservation and sustainable ecosystem planning. Current studies of the impact of climate change on plants are biased to tracheophytes, i.e. vascular-plants. Only a few studies have been carried out on bryophytes despite the fact that they are ecologically equally important groups of embryophytes with their origins predating contemporary vascular-plants. Bryophytes fundamentally differ from vascular-plants in their small size and utilization of a poikilohydric strategy for water and nutrients; their survival and reproduction are highly dependent on their external environment. Thus, the results from studies of tracheophytes cannot be generalized on bryophytes. In this review, we synthesize information about the influence of environmental factors on bryophytes to understand their relation to climate, especially to temperature on a global scale. We discuss a range of critical topics, including the responses of photosynthetic activities to temperature changes, and the consequences of temperature change on the interactions between bryophytes and vascular-plants, as well as on peatland ecosystems. As many species thrive in relatively low temperatures, with a low potential for short-term thermal acclimation to higher temperature in a hydrated state, elevated temperatures may shorten the time of metabolic activity, and increase desiccation intensity. This can bring significant physiological pressure on the survival of poikilohydric bryophytes. As a consequence of global warming, significant losses in bryophyte diversity can be expected, particularly in areas harbouring large number of species such as boreal forests of higher latitudes, alpine biomes and higher altitudes on tropical mountains. Furthermore, the decline of bryophyte diversity will ultimately lead to an alteration of ecosystem structure and function, nutrient cycling, and carbon balance. Further exploration of bryophyte ecophysiology in the changing environment, particularly the acclimation potential of photosynthesis and its biochemical and enzyme level basis to predicted changes in temperature will provide new knowledge that will assist bryophyte conservation.

International audience; This study aims to approximate an illustrative vision of the apparent temporal dynamics of land plant diversity during the terrestrialization process (i.e., the invasion of the land by plants). This problem has often been addressed through studying the Silurian–Devonian megafossil-based diversity patterns of land plants (embryophytes). However, the inclusion of the dispersed spore fossil record is essential for characterizing the first steps of this process (i.e., Eoembryophytic flora). Consequently, this new study includes both spore taxa and plant megafossils in order to discern the diversity trajectories from the first phases of early land plant diversification until the stabilization of early Carboniferous forests (i.e., Palaeophytic flora). The diversity patterns of the primary recognized plant lineages (i.e., Lycophyta and Euphyllophyta) have been also traced in order to discern the origin of the major fluctuations of plant megafossil-based diversity. Results reveal that while the dispersed spore diversity curve shows a sustained increase towards the end of the Devonian Period – with a first maximum towards the late Silurian – the megafossil embryophyte diversity curve is characterized by a set of sequential ascending peaks at the Pragian (Early Devonian), Givetian (Mid-Devonian), and Visean (Mississippian), with a single significant depletion in the Eifelian (Mid-Devonian). The comparative analysis of the lycophyte and euphyllophyte diversity patterns suggests that the substantial embryophytic diversity changes are driven by diversification within lineages rather than by the rhythm of the appearance of key morphological traits. This evidence (1) advocates for an intrinsic ecological control on the apparent changes in taxic richness and (2) implies that the observed plant diversity dynamics respond to the overlapping of the various expansion phases of the plant lineages involved.

Terrestrialization probably began more than one billion years ago and irreversibly altered biogeochemical processes at planetary scale. In this paper, we focus on the terrestrialization process of the Streptophyta, the division that includes charophytes and land plants (embryophytes) and whose members are today ecologically dominant in all terrestrial environments. The timing and the phylogenetic context of the early evolution of land plants are reviewed. The available information on the relationships within embryophytes and related organisms is compiled in two informal consensus trees based either on morphological/anatomical or on molecular data. We also consider the algal/embryophyte transition through the analysis of the evidence provided by microfossils (cryptospores and spores). The ongoing debate about the definition of the term cryptospores, but more importantly about the biological affinities of these microfossils that are possibly derived from early land plants, is discussed. All important clades of embryophytes, with a focus on their Palaeozoic representatives, are described; the significance of several embryophyte key characters is evaluated. The terrestrialization of land plants evolved in different steps. The new term “proembryophytic phase” is introduced to define the very long period of time during which the green algae ancestor of land plants acquired all the evolutionary characters that ultimately allowed their terrestrialization since the late Precambrian. An “eoembryophytic phase”, spanning the Middle-Upper Ordovician, is defined based on the occurrence of the earliest evidence of liverwort-like plants. The inception of the trilete spores in Late Ordovician times is then taken to define the start of the eo/eutracheophytic phase, which lasts until the first occurrence of vascular plant macrofossils in the Silurian.

Compression fossils from the Silurian and Devonian of southern Britain, composed of cuticles and tubes, were described by W. H. Lang as the genus Nematothallus and placed, with Prototaxites, in Nematophytales, related neither to algae nor tracheophytes. Dispersed cuticles of Nematothallus and perforated forms assigned to Cosmochlaina were frequently recovered in macerates, their affinities being unresolved. New collections from a Lochkovian locality in the Welsh Borderland permitted the reconstruction of the stratified thalli of these nematophytes; they comprise a superficial cortex (which produced the cuticles) overlying a palisade zone composed of septate, parallel tubes, presumed to be hyphae, and a basal zone comprising wefts of randomly interwoven hyphae. Excellent three dimensional preservation allows the erection of a new species of Nematothallus, N. williamii. A similar anatomy is seen in a new group of fossils with either circular incisions in the cortex or complete separation of thickened cortical cells, presumably comprising a developmental sequence. By their stratified organization the nematophytes differ from extant and extinct algae and bryophytes and the enigmatic Spongiophyton. A complex anatomy and septate tubes suggest affinity with lichenized fungi. Limited data support a fungal rather than embryophyte chemistry, but a photobiont is missing. Nematophytes, globally widespread in cryptogamic covers from mid-Ordovician times, added to the biodiversity in early terrestrial ecosystems and enhanced chemical weathering.

Six monophyletic groups of charophycean green algae are recognized within the Streptophyta. Although incongruent with earlier studies based on genes from three cellular compartments, chloroplast and nuclear phylogenomic analyses have resolved identical relationships among these groups, placing the Zygnematales or the Zygnematales + Coleochaetales as sister to land plants. The present investigation aimed at determining whether this consensus view is supported by the mitochondrial genome and at gaining insight into mitochondrial DNA (mtDNA) evolution within and across streptophyte algal lineages and during the transition toward the first land plants. We present here the newly sequenced mtDNAs of representatives of the Klebsormidiales (Entransia fimbriata and Klebsormidium spec.) and Zygnematales (Closterium baillyanum and Roya obtusa) and compare them with their homologs in other charophycean lineages as well as in selected embryophyte and chlorophyte lineages. Our results indicate that important changes occurred at the levels of genome size, gene order, and intron content within the Zygnematales. Although the representatives of the Klebsormidiales display more similarity in genome size and intron content, gene order seems more fluid and gene losses more frequent than in other charophycean lineages. In contrast, the two members of the Charales display an extremely conservative pattern of mtDNA evolution. Collectively, our analyses of gene order and gene content and the phylogenies we inferred from 40 mtDNA-encoded proteins failed to resolve the relationships among the Zygnematales, Coleochaetales, and Charales; however, they are consistent with previous phylogenomic studies in favoring that the morphologically complex Charales are not sister to land plants.

in Undetermined Sporangia, with their in situ cryptospores, spore masses, and a possible axis were identified in marginal marine Ludlovian deposits from Gotland. Sweden by means of light- and scanning electron microscopy. The sporangia identified are elongate, with fragments of the sporangia covering preserved, and contain well-preserved in situ embryophyte cryptospores identified as Laevolancis divellomedia (monad) and Dyadospora murusdensa (dyad). A single detached axis was identified possessing superficial longitudinal striations resembling epidermal cell patterning. The axis ends in a cup-shaped structure that possibly represents the basal part of a sporangium. masses of cryptospore monads shrouded in amorphous organic material, most probably representing coprolites of terrestrial arthropods, were found in the same beds. The spores in these masses are degraded in sharp contrast to the excellent preservation of the dispersed and sporangia-hosted spores. The monad, L divellomedia, a common local constituent of the dispersed microflora, was identified in the coprolites. This is the first report of undisputed Silurian land plant remains in Baltica and the study reveals one of the earliest examples of arthropod-plant interactions. (Less)

As part of a study to explore diversity and disparity in Early Devonian terrestrial vegetation, several hundreds of sporangia with in situ spores have been isolated from a Lochkovian locality in Shropshire. These include a small number (seven) of sporangia showing dehiscence into four valves and containing permanent sculptured dyads, belonging to the Cymbohilates horridus complex and C. cymosus, which are recorded in coeval dispersed spore assemblages. A further, previously described, mesofossil comprises an incomplete sporangium containing C. horridus that terminates a naked isotomously branching stem with stomata. The valvate sporangia are placed in a new genus, Partitatheca, containing four species, P. splendida (type), P. horrida, P. densa and P. cymosa, their names reflecting the names of the dispersed spore species and varieties. Complex ultrastructure in the walls of the dyads is similar to that in earlier dyads in the Dyadospora complex where it provides evidence for a hepatic affinity of the earliest embryophytes, but the new taxa present a combination of bryophyte and tracheophyte characters and are considered to represent a new embryophyte lineage. General discussion includes the development of dyads, more particularly their relevance to understanding the diversity in meiotic processes, and the disappearance of dyads from the dispersed spore record prior to the Middle Devonian.

Liverworts occupy a pivotal position in land plant (embryophyte) phylogeny as the presumed earliest-branching major clade, sister to all other land plants, including the mosses, hornworts, lycophytes, monilophytes and seed plants. Molecular support for this earliest dichotomy in land plant phylogeny comes from strikingly different occurrences of introns in mitochondrial genes distinguishing liverworts from all other embryophytes. Exceptionally, however, the nad5 gene--the mitochondrial locus hitherto used most widely to elucidate early land plant phylogeny--carries a group I type intron that is shared between liverworts and mosses. We here explored whether a group II intron, the other major type of organellar intron, would similarly be conserved in position across the entire diversity of extant liverworts and could be of use for phylogenetic analyses in this supposedly most ancient embryophyte clade. To this end, we investigated the nad4 gene as a candidate locus possibly featuring different introns in liverworts as opposed to the non-liverwort embryophyte (NLE) lineage. We indeed found group II intron nad4i548 universally conserved in a wide phylogenetic sampling of 55 liverwort taxa, confirming clade specificity and surprising evolutionary stability of plant mitochondrial introns. As expected, intron nad4i548g2 carries phylogenetic information in its variable sequences, which confirms and extends previous cladistic insights on liverwort evolution. We integrate the new nad4 data with those of the previously established mitochondrial nad5 and the chloroplast rbcL and rps4 genes and present a phylogeny based on the fused datasets. Notably, the phylogenetic analyses suggest a reconsideration of previous phylogenetic and taxonomic assignments for the genera Calycularia and Mylia and resolve a sister group relationship of Ptilidiales and Porellales.

 Premise of the study : Investigating the early diversifi cation of major clades requires well-corroborated and accurate phylogenetic inferences. We examined the performance of a large set of plastid genes for inferring the broad phylogenetic backbone of mosses — the second largest major clade of land plants — and their nearest relatives.  Methods : We surveyed 14 – 17 plastid genes from a broadly representative taxonomic sampling of the major bryophyte lineages, including all major lines of non-peristomate mosses. We examined how well these new data corroborated or contradicted the fi ndings of other studies, and investigated the effect of removing rapidly evolving characters.  Key results : We inferred major clades with at least as strong support as other studies that used more taxa. We corroborated current views of overall embryophyte relationships, i.e., (liverworts, (mosses, (hornworts, tracheophytes))), with strong maximum likelihood (ML) bootstrap support, and also placed Zygnematales as the sister group of embryophytes with moderate ML bootstrap support. Within mosses, we confi rmed Oedipodiaceae as the sister group of the large clade of peristomate taxa. Likelihood analysis also fi rmly placed Takakiaceae as the sister group of all other mosses, a strong confl ict with parsimony results. Parsimony converged on the Takakia -sister result when rapidly evolving characters were removed, depending on the tree used to classify the site rates.  Conclusions : Our fi ndings broadly support the utility of a 14-gene set from the plastome for future, more densely sampled phylogenetic studies of mosses and relatives, potentially complementing anticipated whole-plastome studies. Likelihood and parsimony confl icts fl ag possible instances of long-branch attraction, including one involving the earliest split in moss phylogeny.

International audience; To better understand the biological affinities of cryptospores, micro-FTIR (Fourier transform infrared) spectroscopy analysis has been carried out on isolated specimens from the Upper Silurian of Gotland. The geobiochemical results have been compared to spectra of trilete spores, chitinozoans and leiospheres from the same sample. The palynomorphs are all very well preserved as attested by their pale yellow to orange colour indicative of a low thermal maturity. Micro-FTIR spectroscopy indicates that cryptospores display very similar spectra to those of the trilete spores, which are composed of sporopollenin characterised by absorption bands from aliphatic C–H in methylene (CH2) and methyl (CH3) groups, aromatic (C=C and C–H) groups and C=O groups of carboxylic acids. The sporopollenin composition of the cryptospore wall observed here is additional evidence demonstrating the embryophytic affinity of the cryptospores. In addition, several variations in other bands in the spectra of the different miospore morphospecies are evidenced and may be linked to their biological affinity or palaeoecological history.

Liverworts are well supported as the sister group to all other land plants (embryophytes) by molecular data. Observations strongly supporting this earliest dichotomy in embryophyte evolution are the strikingly different introns occurring in the mitochondrial DNAs of liverworts versus non-liverwort embryophytes (NLE), including the mosses. A final conclusion on the most basal lineages of mosses, for which genera such as Sphagnum and Takakia are the most likely candidates, is lacking. We have now investigated cox1i624, a mitochondrial group I intron conserved between the moss Physcomitrella patens and the liverwort Marchantia polymorpha. Focusing on a sampling of liverwort and moss genera, which had previously been identified as early branching taxa in their respective clades, we find that group I intron cox1i624 is universally conserved in all 33 mosses and 11 liverworts investigated. The group I intron core secondary structure is well conserved between the two ancient land plant clades. However, whereas dramatic size reductions are seen in the moss phylogeny, exactly the opposite is observed for liverworts. The cox1i624g1 locus was used for phylogenetic tree reconstruction also in combination with data sets of nad5i753g1 as well as chloroplast loci rbcL and rps4. The phylogenetic analyses revealed (i) very good support for the Treubiopsida as sister clade to all other liverworts, (ii) a sister group relationship of the nematodontous Tetraphidopsida and Polytrichopsida and (iii) two rivalling hypotheses about the basal-most moss genus with mitochondrial loci suggesting an isolated Takakia as sister to all other mosses and chloroplast loci indicating a Takakia-Sphagnum clade.

The origin of land plants from aquatic ancestors and their subsequent evolutionary radiation was due to major modifications in an ancestral developmental program allowing for plants of increasing complexity and stature. By comparing the developmental programs in different kinds of plants, we can understand how developmental differences lead to morphological differences. The ability to dissect the developmental genetic pathways of model angiosperm taxa such as Arabidopsis and maize has revealed many important developmental gene families that comprise the tool kit for flowering plant growth, patterning, and differentiation. This knowledge has been used to a limited extent as the basis for candidate gene approaches to explore the distribution and expression/function of a few developmental gene families in other flowering plants, gymnosperms, and to some extent, more distantly related plants. With the addition of nearly complete sequenced genomes for the moss Physcomitrella and the lycophyte Selaginella, comp...

Mosses present several advantages for the analysis of phytohormone physiology. Their enormous regeneration capacity, the possibility of controlling their whole life cycle under in vitro culture conditions, as well as the small number of cell types facilitate studies of hormone homeostasis. This review focuses on the metabolism and biosynthesis of cytokinins, mostly summarising data obtained using the moss Physcomitrella patens (Hedw.) B.S.G. which has served as a model system for cytokinin research for many years. A comparison of metabolic differences with respect to seed plants is presented, pointing out an important role of adenosine kinase for the formation of nucleotides during cytokinin interconversion in Physcomitrella. Results on cytokinin biosynthesis in Physcomitrella are summarised with respect to the OVE mutants, which can be considered unique in the plant kingdom due to their strong overproduction of cytokinins. The OVE phenotype is correlated with both increased activity in early stages of cytokinin biosynthesis as well as increased conversion of cytokinin riboside to the base. Cytokinin interconverting reactions can contribute to the increased levels of cytokinins in OVE mutants. Further studies on hormone physiology in moss will help to complete our understanding of hormonal homeostasis by elucidating the situation in an evolutionary early embryophyte.

The phylum Streptophyta comprises all land plants and six monophyletic groups of charophycean green algae (Mesostigmatales, Chlorokybales, Klebsormidiales, Zygnematales, Coleochaetales, and Charales). Phylogenetic analyses of four genes encoded in three cellular compartments suggest that the Charales are sister to land plants and that charophycean green algae evolved progressively toward an increasing cellular complexity. To validate this phylogenetic hypothesis and to understand how and when the highly conservative pattern displayed by land plant chloroplast DNAs (cpDNAs) originated in the Streptophyta, we have determined the complete chloroplast genome sequence (184,933 bp) of a representative of the Charales, Chara vulgaris, and compared this genome to those of Mesostigma (Mesostigmatales), Chlorokybus (Chlorokybales), Staurastrum and Zygnema (Zygnematales), Chaetosphaeridium (Coleochaetales), and selected land plants. The phylogenies we inferred from 76 cpDNA-encoded proteins and genes using various methods favor the hypothesis that the Charales diverged before the Coleochaetales and Zygnematales. The Zygnematales were identified as sister to land plants in the best tree topology (T1), whereas Chaetosphaeridium (T2) or a clade uniting the Zygnematales and Chaetosphaeridium (T3) occupied this position in alternative topologies. Chara remained at the same basal position in trees including more land plant taxa and inferred from 56 proteins/genes. Phylogenetic inference from gene order data yielded two most parsimonious trees displaying the T1 and T3 topologies. Analyses of additional structural cpDNA features (gene order, gene content, intron content, and indels in coding regions) provided better support for T1 than for the topology of the above-mentioned four-gene tree. Our structural analyses also revealed that many of the features conserved in land plant cpDNAs were inherited from their green algal ancestors. The intron content data predicted that at least 15 of the 21 land plant group II introns were gained early during the evolution of streptophytes and that a single intron was acquired during the transition from charophycean green algae to land plants. Analyses of genome rearrangements based on inversions predicted no alteration in gene order during the transition from charophycean green algae to land plants.

Deserts are not usually considered biodiversity hotspots, but desert microbiotic crust communities exhibit a rich diversity of both eukaryotic and prokaryotic life forms. Like many communities dominated by microscopic organisms, they defy characterization by traditional species-counting approaches to assessing biodiversity. Here we use exclusive molecular phylodiversity (E) to quantify the amount of evolutionary divergence unique to desert-dwelling green algae (Chlorophyta) in microbiotic crust communities. Given a phylogenetic tree with branch lengths expressed in units of expected substitutions per site, E is the total length of all tree segments representing exclusively desert lineages. Using MCMC to integrate over tree topologies and branch lengths provides 95% Bayesian credible intervals for phylodiversity measures. We found substantial exclusive molecular phylodiversity based on 18S rDNA data, showing that desert lineages are distantly related to their nearest aquatic relatives. Our results challenge conventional wisdom, which holds that there was a single origin of terrestrial green plants and that green algae are merely incidental visitors rather than indigenous components of desert communities. We identify examples of lineage diversification within deserts and at least 12 separate transitions from aquatic to terrestrial life apart from the most celebrated transition leading to the embryophyte land plants. [Bayesian phylogenetics; biodiversity; exclusive molecular phylodiversity; microbiotic crusts.].

The problem of relationships among the major basal living groups of land plants is long standing, yet the uncertainty as to the phylogenetic affinity of these lines persists in the literature. Molecular and modern cladistic studies of the phylogenetic relationships of the above groups resulted in a large number of conflicting topologies. However, with the exception of the cladistic analyses of spermatogenesis, suggesting monophyly of extant bryophytes, these studies agree the paraphyletic bryophyte grade is basal within the embryophyte tree. Here we would like to present analyses on the basis of the concatenated datasets of nucleotide and amino-acid sequences of 57 protein-coding genes common to 17 chloroplast genomes of land plants and a charophyte alga Chaetosphaeridium globosum. Character-wise, these are the largest datasets currently available to address the problem of basal relationships within embryophytes. Main lineages of bryophytes, i.e liverworts, hornworts and mosses are represented in our alignments with a single taxon, whereas 14 taxa represent the tracheophytes. With our data, phylogeny with liverwort basal appears to be and artifact related to high and unequal A+T contents among the sequences analysed. Reducing this compositional bias and applying methods developed to counter it, we recovered an alternative, strongly supported topology wherein both bryophytes and tracheophytes are monophyletic. Within bryophytes, hornworts are basal and liverworts are sister to mosses.

Seven trilete spores from lower Wenlock to lower Ludlow sediments, all assignable to the form genus Ambitisporites, display a range of ultrastructural features. Various combinations of distal vs. proximal wall thickness, prominence of crassitude and structure/presence of trilete mark and suture distinguish the various types. Comparisons with coeval in situ spores support affinities for some of the specimens, but not others. A review of modern plant spores suggests possible production by lycophytes and hornworts, but these associations are speculative. The controversial Ordovician spore Virgatasporites possesses a robust wall and equatorial crassitude, but its relationship to the embryophyte lineage remains equivocal.

Green algae are present in desert soils as components of microbiotic communities that also include cyanobacteria and other prokaryotes, lichens, non-lichenized fungi, invertebrates, and other photosynthetic eukaryotes such as diatoms, eustigmatophytes, and xanthophytes. The green algae that occur in crusts are morphologically simple unicells, packets of cells, or weak filaments, yet represent a diverse assemblage of taxa spanning the classes Chlorophyceae, Trebouxiophyceae, and Charophyceae. As part of an ongoing study of the biodiversity of microbiotic crust communities in the western United States and Northern Mexico, a large number of green algae were isolated and characterized morphologically and genetically. Phylogenetic analyses using ribosomal RNA gene sequence data have greatly aided our understanding of the diversity and evolution of desert green algae. Our results indicate that desert green algae evolved from aquatic green algae at least five independent times. In addition, the desert green algae are derived from freshwater, not marine, green ancestors. Some lineages of green algae have a high proportion of desert taxa, while other lineages thus far have no known desert representatives. Many of the isolates are likely to be new taxa. These taxa represent independent lineages of green plants that have evolved to inhabit desert environments. Because they are distinct from but phylogenetically related to embryophyte taxa, these other "land plants" can offer important biochemical and physiological comparisons to desert-dwelling embryophytes.

A phylogenetic affinity between charophytes and embryophytes (land plants) has been explained by a few chloroplast genomic characters including gene and intron (Manhart and Palmer 1990; Baldauf et al. 1990; Lew and Manhart 1993). Here we show that a charophyte, Spirogyra maxima, has the largest operon of angiosperm chloroplast genomes, rpl23 operon (trnⅠ-rpl23-rpl2-rps19-rpl22-rps3-rpl16-rpl14-rps8-infA-rpl36-rps11-rpoA) containing both embryophyte introns, rpl16.i and rpl2.i. The rpl23 gene cluster of Spirogyra contains a distinct eubacterial promoter sequence upstream of rpl23, which is the first gene of the green algal rpl23 gene cluster. This sequence is completely absent in angiosperms but is present in non-flowering plants. The results imply that, in the rpl23 gene cluster, early charophytes had at least two promoters, one upstream of trnⅠ and and another upstream of rpl23, which partially or completely lost its function in land plants. A comparison of gene clusters of prokaryotes, algal chloroplast DNAs and land plant cpDNAs indicated a loss of numerous genes in chlorophyll a+b eukaryotes. A phylogenetic analysis using presence/absence of genes and introns as characters produced trees with a strongly supported clade containing chlorophyll a+b eukaryotes. Spirogyra and embryophytes formed a clade characterized by the loss of rpl5 and rps9 and the gain of trnⅠ (CAU) and introns in rpl2 and rpl16. The analyses support the hypothesis that the rpl23 gene cluster and the rpl2 and rpl16 introns of land plants originated from a common ancestor of Spirogyra and land plants.

The transition of plant life from aquatic algae to land to land plants was one of the major events in the history of life. However, in hypothesizing the exact evolutionary path of the transition, limited shared phenotypic characters in aquatic algae and land plants (embryophytes) have been a major hinderance. Chloroplast genomes contain characters useful in tracing evolutionary histories. Embryophyte chloroplast genomes are distinguished from algal cpDNAs by having over 20 group Ⅱ introns, some of which were gained during the transition from algae to embryophytes (Manhart and Palmer 1990; Lew and Manhart 1993;Lee and Manhart 2002). Here we examine a gene cluster that, in land plants, contains psbB, psbT, psbH, petB and petD with introns found in petB and petD (petB.i and petD.i). In addition the presence/absence of introns in trnA and trnI (trnA.i and trnI.i) were determined in all five major lineages of charophytes. We found that the psbB gene cluster occurs in most surveyed charophytes and embryophytes except Spirogyra (Zygnematales) which lacks it due to intra-genomic rearrangement. All four introns are absent in Chlorokybus but present in some or all of the other four charophyte lineages (Klebsormidiales, Zygnematales, Coleochaetales, and Charales). In addition, Chlorokybus is distinguished from other charophytes and embryophytes by having an unusually long spacer (over 2 kb) between psbH-petB. The results indicate that Chlorokybus diverged before the intron gains but after psbB gene cluster formation, placing the other charophyte lineages closer to embryophytes.

A new taxon Sporathylacium salopense gen. et sp. nov. is based on small isolated coalified sporangia from the Lower Devonian (Lochkovian: micrornatus—newportensis spore zone) from the Welsh Borderland. The sporangia have two equal valves with multi-layered walls and thickened borders, and contain trilete crassitate, non-curvaturate isospores that are completely covered by a microgranular ornament with possible distal verrucate/murornate structures. They differ from zosterophyll sporangia in details of the presumed dehiscence zone extending around the entire free convex margin, particularly in the presence of a wedge of amorphous material between the valves, and in spore characters. Absence of any information relating to water-conducting cells prevents further assignment within the embryophytes. Spherical bodies associated with spores and a resilient sporangial lining are compared with similar structures in extant free-sporing plants and with Ubisch bodies. The mode of sporangial dehiscence involving anatomical modifications of the valve margins and the novel wedge of tissue which connects them remains speculative.

Phylogenetic relationships among embryophytes (tracheophytes, mosses, liverworts, and hornworts) were examined using 21 newly generated mitochondrial small-subunit (19S) rDNA sequences. The "core" 19S rDNA contained more phylogenetically informative sites and lower homoplasy than either nuclear 18S or plastid 16S rDNA. Results of phylogenetic analyses using parsimony (MP) and likelihood (ML) were generally congruent. Using MP, two trees were obtained that resolved either liverworts or hornworts as the basal land plant clade. The optimal ML tree showed hornworts as basal. That topology was not statistically different from the two MP trees, thus both appear to be equally viable evolutionary hypotheses. High bootstrap support was obtained for the majority of higher level embryophyte clades named in a recent morphologically based classification, e.g., Tracheophyta, Euphyllophytina, Lycophytina, and Spermatophytata. Strong support was also obtained for the following monophyletic groups: hornworts, liverworts, mosses, lycopsids, leptosporangiate and eusporangiate ferns, gymnosperms and angiosperms. This molecular analysis supported a sister relationship between Equisetum and leptosporangiate ferns and a monophyletic gymnosperms sister to angiosperms. The topologies of deeper clades were affected by taxon inclusion (particularly hornworts) as demonstrated by jackknife analyses. This study represents the first use of mitochondrial 19S rDNA for phylogenetic purposes and it appears well-suited for examining intermediate to deep evolutionary relationships among embryophytes.

Sequence data from the chloroplast-encoded gene rbcL were obtained for 24 liverworts, a basal group of embryophytes. Maximum likelihood and parsimony analyses of these data, along with data from other major green plant lineages, confirm hypotheses based on morphological data, such as the paraphyly of bryophytes, and the basal position of liverworts. Molecular data corroborate the deep separation between the complex thalloid and leafy/simple thalloid liverworts implied by morphological data, but the monophyly of liverworts could not be rejected. The effects of accounting for site-to-site rate heterogeneity in these data were examined using maximum likelihood methods. Comparison of trees obtained with and without rate heterogeneity showed that simply allowing for heterogeneity had a greater improvement on likelihood score than optimization of transition/transversion bias. Incorporation of site-to-site rate heterogeneity in the larger analysis, however, did not necessarily change which topology was favored. Properties of rbcL sequences from the two liverwort groups were compared. Significantly different substitution rates were found between leafy/simple thalloid and complex thalloid liverwort taxa, with rates of rbcL sequence evolution in leafy/simple thalloid taxa being higher and more indicative of those of vascular plants, and with those of complex thalloid taxa (such as Marchantia) being slower. Codon usage in rbcL in complex thalloid liverworts was biased toward NNU and NNA, compared to the leafy/simple thalloid liverworts. Although base composition and relative substitution rates differed between the two groups, no significant differences were detected within each of the two groups of liverworts. The signal present in first and second codon sites versus third codon sites was compared. While the third codon positions in rbcL across this taxon sampling are highly variable (with only 15 constant sites of 439), the trees obtained were in general agreement with trees from the entire data set and with trees obtained from independent sources of data. The presence of signal in third codon positions across greater than 400 MY of plant evolution means that definitions of saturation based on pair-wise comparisons of sequences inadequately assess phylogenetic signal.

Although chloroplast transcriptional and translational mechanisms were derived originally from prokaryote endosymbionts, chloroplasts retain comparatively few genes as a consequence of the overall transfer to the nucleus of functions associated formerly with prokaryotic genomes. Various modifications reflect other evolutionary shifts toward eukaryotic regulation such as posttranscriptional transcript cleavage with individually processed cistrons in operons and gene expression regulated by nuclear-encoded sigma factors. We report a notable exception for the psaA-psaB-rps14 operon of land plant (embryophyte) chloroplasts, where the first two cistrons are separated by a spacer region to which no significant role had been attributed. We infer an important function of this region, as indicated by the conservation of identical, structurally significant sequences across embryophytes and their ancestral protist lineages, which diverged some 0.5 billion years ago. The psaA/psaB spacers of embryophytes and their progenitors exhibit few sequence and length variants, with most modeled transcripts resolving the same secondary structure: a loop with projecting Shine-Dalgarno site and well-defined stem that interacts with adjacent coding regions to sequester the psaB start codon. Although many functions of the original endosymbiont have been usurped by nuclear genes or interactions, conserved functional elements of embryophyte psaA/psaB spacers provide compelling evidence that translation of psaB is regulated here by a cis-acting mechanism comparable to those common in prokaryotes. Modeled transcripts also indicate that spacer variants in some plants (e.g., aquatic genus Najas) potentially reflect ecological adaptations to facilitate temperature-regulated translation of psaB.

A cladistic analysis was carried out to resolve phylogenetic pattern among bryophytes and other land plants. The analysis used 22 taxa of land plants and 90 characters relating to male gametogenesis.Coleochaete orChara/Nitella were the outgroups in various analyses using HENNIG86, PAUP, and MacClade, and the land plant phylogeny was unchanged regardless of outgroup utilized. The most parsimonious cladograms from HENNIG86 (7 trees) have treelengths of 243 (C.I. = 0.58, R.I. = 0.82). Bryophytes are monophyletic as are hornworts, liverworts, and mosses, with hornworts identified as the sister group of a liverwort/moss assemblage. In vascular plants, lycophytes are polyphyletic andSelaginella is close to the bryophytes.Lycopodium is the sister group of the remaining vascular plants (minusSelaginella). Longer treelengths (over 250) are required to produce tree topologies in which either lycophytes are monophyletic or to reconstruct the paraphyletic bryophyte phylogeny of recent authors. This analysis challenges existing concepts of bryophyte phylogeny based on more classical data and interpretations, and provides new insight into land plant evolution.

The 22 published chloroplast genomes of green algae, representing sparse taxonomic sampling of diverse lineages that span over one billion years of evolution, each possess a unique gene arrangement. In contrast, many of the >190 published embryophyte (land plant) chloroplast genomes have relatively conserved architectures. To determine the phylogenetic depth at which chloroplast gene rearrangements occur in green algae, a 1.5–4 kb segment of the chloroplast genome was compared across nine species in three closely related genera of Trebouxiophyceae (Chlorophyta). In total, four distinct gene arrangements were obtained for the three genera Elliptochloris, Hemichloris, and Coccomyxa. In Elliptochloris, three distinct chloroplast gene arrangements were detected, one of which is shared with members of its sister genus Hemichloris. Both species of Coccomyxa examined share the fourth arrangement of this genome region, one characterized by very long spacers. Next, the order of genes found in this segment of the chloroplast genome was compared across green algae and land plants. As taxonomic ranks are not equivalent among different groups of organisms, the maximum molecular divergence among taxa sharing a common gene arrangement in this genome segment was compared. Well-supported clades possessing a single gene order had similar phylogenetic depth in green algae and embryophytes. When the dominant gene order of this chloroplast segment in embryophytes was assumed to be ancestral for land plants, the maximum molecular divergence was found to be over two times greater in embryophytes than in trebouxiophyte green algae. This study greatly expands information about chloroplast genome variation in green algae, is the first to demonstrate such variation among congeneric green algae, and further illustrates the fluidity of green algal chloroplast genome architecture in comparison to that of many embryophytes.

The bryophytes comprise three phyla of embryophytes that are well established to occupy the first nodes among extant lineages in the land-plant tree of life. The three bryophyte groups (hornworts, liverworts, mosses) may not form a monophyletic clade, but they share life history features including dominant free-living gametophytes and matrotrophic monosporangiate sporophytes. Because of their unique vegetative and reproductive innovations and their critical position in embryophyte phylogeny, studies of bryophytes are crucial to understanding the evolution of land plant morphology and genomes. This review focuses on phylogenetic relationships within each of the three divisions of bryophytes and relates morphological diversity to new insights about those relationships. Most previous work has been on the mosses, but progress on understanding the phylogeny of hornworts and liverworts is advancing at a rapid pace. Multilocus multigenome studies have been successful at resolving deep relationships within the mosses and liverworts, whereas single-gene analyses have advanced understanding of hornwort evolution.

Over the past two decades, molecular phylogenetic data have allowed evaluations of hypotheses on the evolution of green algae based on vegetative morphological and ultrastructural characters. Higher taxa are now generally recognized on the basis of ultrastructural characters. Molecular analyses have mostly employed primarily nuclear small subunit rDNA (18S) and plastid rbcL data, as well as data on intron gain, complete genome sequencing, and mitochondrial sequences. Molecular-based revisions of classification at nearly all levels have occurred, from dismemberment of long-established genera and families into multiple classes, to the circumscription of two major lineages within the green algae. One lineage, the chlorophyte algae or Chlorophyta sensu stricto, comprises most of what are commonly called green algae and includes most members of the grade of putatively ancestral scaly flagellates in Prasinophyceae plus members of Ulvophyceae, Trebouxiophyceae, and Chlorophyceae. The other lineage (charophyte algae and embryophyte land plants), comprises at least five monophyletic groups of green algae, plus embryophytes. A recent multigene analysis corroborates a close relationship between Mesostigma (formerly in the Prasinophyceae) and the charophyte algae, although sequence data of the Mesostigma mitochondrial genome analysis places the genus as sister to charophyte and chlorophyte algae. These studies also support Charales as sister to land plants. The reorganization of taxa stimulated by molecular analyses is expected to continue as more data accumulate and new taxa and habitats are sampled. Twenty years ago, a relatively slim volume with chapters by leading chlorophycologists celebrated the systematics of green algae (Irvine and John, 1984), a field that was undergoing rapid and fascinating changes, both in content and theory. ‘‘The present period may be termed the ‘Age of Ultrastructure’ in green algal systematics,’’ wrote Frank Round (1984, p. 7) in the introductory chapter, which summarized the history and state of the art. Round (1984) argued that light microscopy had laid the foundation in the preceding two centuries, but that the foundation was largely descriptive—alpha taxonomy in the most restricted sense. Ultrastructure, he asserted, had enlarged and presumably would continue to expand our horizons to unify systematics of green algae and overcome the fragmented alpha taxonomy that had dominated the field. Little did Round know that this golden age of green algal systematics was about to go platinum. Molecular systematics, in concert with a rigorous theoretical approach to data analysis and hypothesis testing (Theriot, 1992; Swofford et al., 1996), would at first complement and then transform the age of ultrastructure and usher in the ‘‘Age of Molecules.’’ In this article, we review the major advances in green algal systematics in the past 20 years, with a focus on well-supported, monophyletic taxa and the larger picture of phylogeny and evolution of green algae. We will review the types of data that have fueled these advances. As will become obvious, this perspective entails discussion of some embryophytes as well as their closest green algal relatives. In addition, we will point

Across the streptophyte lineage, which includes charophycean algae and embryophytic plants, there have been at least four independent transitions to the terrestrial habitat. One of these involved the evolution of embryophytes (bryophytes and tracheophytes) from a charophycean ancestor, while others involved the earliest branching lineages, containing the monotypic genera Mesostigma and Chlorokybus, and within the Klebsormidiales and Zygnematales lineages. To overcome heat, water stress, and increased exposure to ultraviolet radiation, which must have accompanied these transitions, adaptive mechanisms would have been required. During periods of dehydration and/or desiccation, proteomes struggle to maintain adequate cytoplasmic solute concentrations. The increased usage of charged amino acids (DEHKR) may be one way of maintaining protein hydration, while increased use of aromatic residues (FHWY) protects proteins and nucleic acids by absorbing damaging UV, with both groups of residues thought to be important for the stabilization of protein structures. To test these hypotheses we examined amino acid sequences of orthologous proteins representing both mitochondrion- and plastid-encoded proteomes across streptophytic lineages. We compared relative differences within categories of amino acid residues and found consistent patterns of amino acid compositional fluxuation in extra-membranous regions that correspond with episodes of terrestrialization: positive change in usage frequency for residues with charged side-chains, and aromatic residues of the light-capturing chloroplast proteomes. We also found a general decrease in the usage frequency of hydrophobic, aliphatic, and small residues. These results suggest that amino acid compositional shifts in extra-membrane regions of plastid and mitochondrial proteins may represent biochemical adaptations that allowed green plants to colonize the land.

The pyrimidine exchange type of RNA editing in land plant (embryophyte) organelles has largely remained an enigma with respect to its biochemical mechanisms, the underlying specificities, and its raison d'etre. Apparently arising with the earliest embryophytes, RNA editing is conspicuously absent in one clade of liverworts, the complex thalloid Marchantiidae. Several lines of evidence suggest that the large gene family of organelle-targeted RNA-binding pentatricopeptide repeat (PPR) proteins plays a fundamental role in the sequence-specific editing of organelle transcripts. We here describe the identification of PPR protein genes with plant-specific carboxyterminal (C-terminal) sequence signatures (E, E+, and DYW domains) in ferns, lycopodiophytes, mosses, hornworts, and jungermanniid liverworts, one subclass of the basal most clade of embryophytes, on DNA and cDNA level. In contrast, we were unable to identify these genes in a wide sampling of marchantiid liverworts (including the phylogenetic basal genus Blasia)--taxa for which no RNA editing is observed in the organelle transcripts. On the other hand, we found significant diversity of this type of PPR proteins also in Haplomitrium, a genus with an extremely high rate of RNA editing and a phylogenetic placement basal to all other liverworts. Although the presence of modularly extended PPR proteins correlates well with organelle RNA editing, the now apparent complete loss of an entire gene family from one clade of embryophytes, the marchantiid liverworts, remains puzzling.

Considerable progress has been made recently, based on classical morphological characters and newly described ultrastructural features, in understanding the phylogenetic relationships of the tracheophytes to the green algae and bryophytes. Recent technological advances in molecular biology, particularly the advent of the polymerase chain reaction (PCR), have allowed nucleotide sequence data relevant to such large-scale phylogenetic questions to accumulate, especially ribosomal RNA gene sequences (both the large and small subunits) from the nucleus and the chloroplast. We present synthetic cladistic analyses of the green plants that combine and compare available morphological and molecular data sets

Background The terrestrial habitat was colonized by the ancestors of modern land plants about 500 to 470 million years ago. Today it is widely accepted that land plants (embryophytes) evolved from streptophyte algae, also referred to as charophycean algae. The streptophyte algae are a paraphyletic group of green algae, ranging from unicellular flagellates to morphologically complex forms such as the stoneworts (Charales). For a better understanding of the evolution of land plants, it is of prime importance to identify the streptophyte algae that are the sister-group to the embryophytes. The Charales, the Coleochaetales or more recently the Zygnematales have been considered to be the sister group of the embryophytes However, despite many years of phylogenetic studies, this question has not been resolved and remains controversial. Results Here, we use a large data set of nuclear-encoded genes (129 proteins) from 40 green plant taxa (Viridiplantae) including 21 embryophytes and six streptophyte algae, representing all major streptophyte algal lineages, to investigate the phylogenetic relationships of streptophyte algae and embryophytes. Our phylogenetic analyses indicate that either the Zygnematales or a clade consisting of the Zygnematales and the Coleochaetales are the sister group to embryophytes. Conclusions Our analyses support the notion that the Charales are not the closest living relatives of embryophytes. Instead, the Zygnematales or a clade consisting of Zygnematales and Coleochaetales are most likely the sister group of embryophytes. Although this result is in agreement with a previously published phylogenetic study of chloroplast genomes, additional data are needed to confirm this conclusion. A Zygnematales/embryophyte sister group relationship has important implications for early land plant evolution. If substantiated, it should allow us to address important questions regarding the primary adaptations of viridiplants during the conquest of land. Clearly, the biology of the Zygnematales will receive renewed interest in the future.

The importance of a cladistic approach in reconstructing the phylogeny of bryophytes is discussed and illustrated by an analysis of the major groups of bryophytes with respect to the tracheophytes and the green algae. The cladistic analysis, using 51 characters taken from the literature, gives the following tentative results: (1) the embryophytes as a whole are monophyletic; (2) the bryophytes (sensu lato) are paraphyletic; (3) the mosses share a more recent common ancestor with the tracheophytes than do the liverworts or hornworts; (4) the hornworts appear to share a more recent common ancestor with the moss-tracheophyte lineage than with the liverworts; however, the existence of several homoplasies makes this placement more problematical; (5) the origin of alternation of generations in the embryophytes, based on out-group comparison with their oogamous, haplontic, algal sister groups, was by progressive elaboration of the primitively epiphytic sporophyte generation; and (6) the presence of vascular tissue (xylem and phloem) can best be interpreted as a synapomorphy of the moss-tracheophyte clade, and tracheids (xylem with ornamented walls) as a synapomorphy of the tracheophytes; therefore, the prevailing designation of “vascular plants” for the tracheophytes alone is inaccurate.