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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.

Diatoms are responsible for up to 40% of primary productivity in the ocean, and complete genome sequences are available for two species. However, there are very significant gaps in our understanding of how diatoms take up and assimilate inorganic C. Diatom plastids originate from secondary endosymbiosis with a red alga and their Form ID Rubisco (ribulose-1,5-bisphosphate carboxylase-oxygenase) from horizontal gene transfer, which means that embryophyte paradigms can only give general guidance as to their C acquisition mechanisms. Although diatom Rubiscos have relatively high CO(2) affinity and CO(2)/O(2) selectivity, the low diffusion coefficient for CO(2) in water has the potential to restrict the rate of photosynthesis. Diatoms growing in their natural aquatic habitats operate inorganic C concentrating mechanisms (CCMs), which provide a steady-state CO(2) concentration around Rubisco higher than that in the medium. How these CCMs work is still a matter of debate. However, it is known that both CO(2) and HCO (3) (-) are taken up, and an obvious but as yet unproven possibility is that active transport of these species across the plasmalemma and/or the four-membrane plastid envelope is the basis of the CCM. In one marine diatom there is evidence of C(4)-like biochemistry which could act as, or be part of, a CCM. Alternative mechanisms which have not been eliminated include the production of CO(2) from HCO (3) (-) at low pH maintained by a H(+) pump, in a compartment close to that containing Rubisco.

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.

The first evidence for the emergence of land plants (embryophytes) consists of mid-Ordovician spore tetrads (∼476 Myr old)1,2. The identity of the early plants that produced these spores is unclear; they are sometimes claimed to be liverworts3,4, but there are no associated megafossils, and similar spores can be produced by a diversity of plants2. Indeed, the earliest unequivocal megafossils of land plants consist of early vascular plants and various plants of uncertain affinity1. Different phylogenetic analyses have identified liverworts, hornworts and bryophytes as each being the first lineage of land plants1,2,5,6,7,8,9,10,11,12,13; the consensus of these conflicting topologies yields an unresolved polychotomy at the base of land plants. Here we survey 352 diverse land plants and find that three mitochondrial group II introns are present, with occasional losses, in mosses, hornworts and all major lineages of vascular plants, but are entirely absent from liverworts, green algae and all other eukaryotes. These results indicate that liverworts are the earliest land plants, with the three introns having been acquired in a common ancestor of all other land plants, and have important implications concerning the early stages of plant evolution.

The origin and early evolution of land plants in the mid-Palaeozoic era, between about 480 and 360 million years ago, was an important event in the history of life, with far-reaching consequences for the evolution of terrestrial organisms and global environments. A recent surge of interest, catalysed by palaeobotanical discoveries and advances in the systematics of living plants, provides a revised perspective on the evolution of early land plants and suggests new directions for future research.

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.

Previously, a database characterizing examples of Embryophyte gene family lineages showing evidence of positive selection was reported. Of the gene family trees, 138 Embryophyte branches showed Ka/Ks>>1 and are candidates for functional adaptation. The database and these examples have now been studied in further detail to better understand the molecular basis for plant genome evolution. Neutral modeling showed an excess of positive and/or negative selection in the database over a neutral expectation centered on the mean Ka/Ks ratio. Out of 673 families with assigned structures, 490 have at least one branch with Ka/Ks >>1 in a region of the protein, enabling a picture of selective pressures delineated by protein structure. Most gene families allowed reconstruction back to the last common ancestor of flowering plants (Magnoliophytes) without saturation of 4- fold degenerate codon position. Positive selection occurred in a wide variety of gene families with different functions, including in the self incompatibility locus, in defense against pathogens, in embryogenesis, in cold acclimation, and in electrontransport. Structurally, selective pressures were similar between alpha-helices and beta- sheets, but were less negative and more variant on the surface and away from the hydrophobic core. Positive selection was detected statistically significantly in a small and nonrandom minority of gene families in a systematic analysis of embryophyte gene families. More sensitive methods increased the level of positive selection that was detected and presented a structural basis for the role of positive selection in plant genomes.

EVIDENCE for terrestrial vegetation in Ordovician and Silurian times, before the advent of vascular plants, comes from palyno-morphs (cryptospores1), that is, non-dissociating tetrads and dyads2,3 and cuticles4. The lack of a megafossil record for the spore producers is usually attributed to low fossilization potential of vegetative tissues, and this, plus spore type5, contributes to the hypothesis that the plants were embryophytes/archegoniates at a bryophyte level of organization3,5,6 and perhaps most similar in organization to modern hepatics5. Here we describe a minute coal-ified fossil from the Lower Devonian (Lochkovian: micrornatus-newportensis Spore Biozone) of the Welsh Borderland7, which contains obligate, smooth-walled tetrahedral tetrads, similar (by scanning electron microscopy) to those first recorded in the Ordovician. To our knowledge, these are the first data on the gross morphology and tissues of the plants that comprised the earliest embryophyte land flora (Gray's Eoembryophytic epoch3), albeit obtained from a relict Devonian example fossilized at a time when the composition of dispersed spore and megafossil assemblages suggests that tracheophytes and tracheophyte-like plants (rhyniophytoids) had generally begun to dominate land vegetation (Gray's Eotracheophyta3). Its anatomy in toto finds no exact parallels in embryophytes, but many of the individual cellular features match those in extant hepatics (liverworts).

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.