Life history biology of early land plants: deciphering the gametophyte phase

The sexual lability hypothesis for the origin of the land plant generation cycle

The evolution of the land plant alternation of generations has been an open question for the past 150 years. Two hypotheses have dominated the discussion: the antithetic hypothesis, which posits that the diploid sporophyte generation arose de novo and gradually increased in complexity, and the homologous hypothesis, which holds that land plant ancestors had independently living sporophytes and haploid gametophytes of similar complexity. Changes in ploidy levels were unknown to early researchers. The antithetic hypothesis is contradicted by generation cycles in Lower Devonian Rhynie chert plants, whose sporophytes and gametophytes have similar morphologies and by some Silurian sporophytes whose complexity exceeds that of Rhynie chert sporophytes. The oldest unambiguous bryophyte gametophytes (thalli) are from the upper Middle Devonian, with an unconnected sporophyte nearby. Based on the 2024 discovery that conjugate algae are paraphyletic to land plants, we present a new hypothesis for the evolution of the land plant generation cycle, focusing on labile ploidy levels and types of reproduction found in conjugate algae. Our 'sexual lability' hypothesis assumes a period of unstable generation cycles (as regards ploidy), likely with predominant clonal growth, as is common in conjugate algae, resulting in sporophytes and gametophytes of similar morphology. When sexual reproduction became stabilized, the timing of gamete fusion, meiosis, and resistant wall formation, which are heterochronic in some conjugate algae, became standardized, with wall formation permanently delayed. In our scenario, independently living adult sporophytes are the land plant ancestral condition, and life-long sporophyte retention on the gametophyte is a bryophyte apomorphy.

Hidden functional complexity in the flora of an early land ecosystem

The first land ecosystems were composed of organisms considered simple in nature, yet the morphological diversity of their flora was extraordinary. The biological significance of this diversity remains a mystery largely due to the absence of feasible study approaches. To study the functional biology of Early Devonian flora, we have reconstructed extinct plants from fossilised remains in silico. We explored the morphological diversity of sporangia in relation to their mechanical properties using finite element method. Our approach highlights the impact of sporangia morphology on spore dispersal and adaptation. We discovered previously unidentified innovations among early land plants, discussing how different species might have opted for different spore dispersal strategies. We present examples of convergent evolution for turgor pressure resistance, achieved by homogenisation of stress in spherical sporangia and by torquing force in Tortilicaulis-like specimens. In addition, we show a potential mechanism for stress-assisted sporangium rupture. Our study reveals the deceptive complexity of this seemingly simple group of organisms. We leveraged the quantitative nature of our approach and constructed a fitness landscape to understand the different ecological niches present in the Early Devonian Welsh Borderland flora. By connecting morphology to functional biology, these findings facilitate a deeper understanding of the diversity of early land plants and their place within their ecosystem.

Terrestrial surface stabilisation by modern analogues of the earliest land plants: A multi-dimensional imaging study

The evolution of the first plant-based terrestrial ecosystems in the early Palaeozoic had a profound effect on the development of soils, the architecture of sedimentary systems, and shifts in global biogeochemical cycles. In part, this was due to the evolution of complex below-ground (root-like) anchorage systems in plants, which expanded and promoted plant-mineral interactions, weathering, and resulting surface sediment stabilisation. However, little is understood about how these micro-scale processes occurred, because of a lack of in situ plant fossils in sedimentary rocks/palaeosols that exhibit these interactions. Some modern plants (e.g., liverworts, mosses, lycophytes) share key features with the earliest land plants; these include uni- or multicellular rhizoid-like anchorage systems or simple roots, and the ability to develop below-ground networks through prostrate axes, and intimate associations with fungi, making them suitable analogues. Here, we investigated cryptogamic ground covers in Iceland and New Zealand to better understand these interactions, and how they initiate the sediment stabilisation process. We employed multi-dimensional and multi-scale imaging, including scanning electron microscopy (SEM) and X-ray Computed Tomography (μCT) of non-vascular liverworts (Haplomitriopsida and complex thalloids) and mosses, with additional imaging of vascular lycopods. We find that plants interact with their substrate in multiple ways, including: (1) through the development of extensive surface coverings as mats; (2) entrapment of sediment grains within and between networks of rhizoids; (3) grain entwining and adherence by rhizoids, through mucilage secretions, biofilm-like envelopment of thalli on surface grains; and (4) through grain entrapment within upright 'leafy' structures. Significantly, μCT imaging allows us to ascertain that rhizoids are the main method for entrapment and stabilisation of soil grains in the thalloid liverworts. This information provides us with details of how the earliest land plants may have significantly influenced early Palaeozoic sedimentary system architectures, promoted in situ weathering and proto-soil development, and how these interactions diversified over time with the evolution of new plant organ systems. Further, this study highlights the importance of cryptogamic organisms in the early stages of sediment stabilisation and soil formation today.

Green land: Multiple perspectives on green algal evolution and the earliest land plants

Green plants, broadly defined as green algae and the land plants (together, Viridiplantae), constitute the primary eukaryotic lineage that successfully colonized Earth's emergent landscape. Members of various clades of green plants have independently made the transition from fully aquatic to subaerial habitats many times throughout Earth's history. The transition, from unicells or simple filaments to complex multicellular plant bodies with functionally differentiated tissues and organs, was accompanied by innovations built upon a genetic and phenotypic toolkit that have served aquatic green phototrophs successfully for at least a billion years. These innovations opened an enormous array of new, drier places to live on the planet and resulted in a huge diversity of land plants that have dominated terrestrial ecosystems over the past 500 million years. This review examines the greening of the land from several perspectives, from paleontology to phylogenomics, to water stress responses and the genetic toolkit shared by green algae and plants, to the genomic evolution of the sporophyte generation. We summarize advances on disparate fronts in elucidating this important event in the evolution of the biosphere and the lacunae in our understanding of it. We present the process not as a step-by-step advancement from primitive green cells to an inevitable success of embryophytes, but rather as a process of adaptations and exaptations that allowed multiple clades of green plants, with various combinations of morphological and physiological terrestrialized traits, to become diverse and successful inhabitants of the land habitats of Earth.

The origin of a land flora

The origin of a land flora fundamentally shifted the course of evolution of life on earth, facilitating terrestrialization of other eukaryotic lineages and altering the planet's geology, from changing atmospheric and hydrological cycles to transforming continental erosion processes. Despite algal lineages inhabiting the terrestrial environment for a considerable preceding period, they failed to evolve complex multicellularity necessary to conquer the land. About 470 million years ago, one lineage of charophycean alga evolved complex multicellularity via developmental innovations in both haploid and diploid generations and became land plants (embryophytes), which rapidly diversified to dominate most terrestrial habitats. Genome sequences have provided unprecedented insights into the genetic and genomic bases for embryophyte origins, with some embryophyte-specific genes being associated with the evolution of key developmental or physiological attributes, such as meristems, rhizoids and the ability to form mycorrhizal associations. However, based on the fossil record, the evolution of the defining feature of embryophytes, the embryo, and consequently the sporangium that provided a reproductive advantage, may have been most critical in their rise to dominance. The long timeframe and singularity of a land flora were perhaps due to the stepwise assembly of a large constellation of genetic innovations required to conquer the terrestrial environment.

The origin and evolution of stomata

The acquisition of stomata is one of the key innovations that led to the colonisation of the terrestrial environment by the earliest land plants. However, our understanding of the origin, evolution and the ancestral function of stomata is incomplete. Phylogenomic analyses indicate that, firstly, stomata are ancient structures, present in the common ancestor of land plants, prior to the divergence of bryophytes and tracheophytes and, secondly, there has been reductive stomatal evolution, especially in the bryophytes (with complete loss in the liverworts). From a review of the evidence, we conclude that the capacity of stomata to open and close in response to signals such as ABA, CO₂ and light (hydroactive movement) is an ancestral state, is present in all lineages and likely predates the divergence of the bryophytes and tracheophytes. We reject the hypothesis that hydroactive movement was acquired with the emergence of the gymnosperms. We also conclude that the role of stomata in the earliest land plants was to optimise carbon gain per unit water loss. There remain many other unanswered questions concerning the evolution and especially the origin of stomata. To address these questions, it will be necessary to: find more fossils representing the earliest land plants, revisit the existing early land plant fossil record in the light of novel phylogenomic hypotheses and carry out more functional studies that include both tracheophytes and bryophytes.

Sex determination and sex chromosome evolution in land plants

Linnaeus's very first opus, written when he was 22 years old, dealt with the analogy that exists between plants and animals in how they 'propagate their species', and a revised version with a plate depicting the union of male and female Mercurialis annua plants became a foundational text on the sexuality of plants. The question how systems with separate males and females have evolved in sedentary organisms that appear ancestrally bisexual has fascinated biologists ever since. The phenomenon, termed dioecy, has important consequences for plant reproductive success and is of commercial interest since it affects seed quality and fruit production. This theme issue presents a series of articles that synthesize and challenge the current understanding of how plants achieve dioecy. The articles deal with a broad set of taxa, including Coccinia, Ginkgo, Mercurialis, Populus, Rumex and Silene, as well as overarching topics, such as the field's terminology, analogies with animal sex determination systems, evolutionary pathways to dioecy, dosage compensation, and the longevity of the two sexes. In this introduction, we focus on four topics, each addressed by several articles from different angles and with different conclusions. Our highlighting of unclear or controversial issues may help future studies to build on the current understanding and to ask new questions that will expand our knowledge of plant sexual systems. This article is part of the theme issue 'Sex determination and sex chromosome evolution in land plants'.

Fossils and plant evolution: structural fingerprints and modularity in the evo-devo paradigm

Fossils constitute the principal repository of data that allow for independent tests of hypotheses of biological evolution derived from observations of the extant biota. Traditionally, transformational series of structure, consisting of sequences of fossils of the same lineage through time, have been employed to reconstruct and interpret morphological evolution. More recently, a move toward an updated paradigm was fueled by the deliberate integration of developmental thinking in the inclusion of fossils in reconstruction of morphological evolution. The vehicle for this is provided by structural fingerprints-recognizable morphological and anatomical structures generated by (and reflective of) the deployment of specific genes and regulatory pathways during development. Furthermore, because the regulation of plant development is both modular and hierarchical in nature, combining structural fingerprints recognized in the fossil record with our understanding of the developmental regulation of those structures produces a powerful tool for understanding plant evolution. This is particularly true when the systematic distribution of specific developmental regulatory mechanisms and modules is viewed within an evolutionary (paleo-evo-devo) framework. Here, we discuss several advances in understanding the processes and patterns of evolution, achieved by tracking structural fingerprints with their underlying regulatory modules across lineages, living and fossil: the role of polar auxin regulation in the cellular patterning of secondary xylem and the parallel evolution of arborescence in lycophytes and seed plants; the morphology and life history of early polysporangiophytes and tracheophytes; the role of modularity in the parallel evolution of leaves in euphyllophytes; leaf meristematic activity and the parallel evolution of venation patterns among euphyllophytes; mosaic deployment of regulatory modules and the diverse modes of secondary growth of euphyllophytes; modularity and hierarchy in developmental regulation and the evolution of equisetalean reproductive morphology. More generally, inclusion of plant fossils in the evo-devo paradigm has informed discussions on the evolution of growth patterns and growth responses, sporophyte body plans and their homology, sequences of character evolution, and the evolution of reproductive systems.

Methodologies for soil extraction and conservation analysis of ferns and lycophytes with belowground gametophytes

PREMISE

Studies of fern and lycophyte gametophyte biology in natural settings can be challenging, but such analyses are critical to understanding the dispersal, ecology, and conservation of these species. It is especially challenging to study species whose gametophytes and early sporophyte stages develop belowground, as is the case for species of the Ophioglossaceae, Psilotaceae, some species of the Schizeaceae (Actinostachys), and some species of the Lycopodiaceae. To study these taxa, gametophytes and young sporophytes must be extracted from the soil.

METHODS

In 1989, Mason and Farrar described a methodology for accomplishing the collection of belowground gametophytes and sporophytes using soil centrifugation. Here, we refine this procedure based on subsequent years of experience.

RESULTS

We found that many more sporophytes exist belowground than are represented by aboveground leaves, and that belowground sporophytes can survive indefinitely without production of aboveground leaves. Belowground gametophytes are common in areas where spore-releasing sporophyte leaves are present. Gametophytes are bisexual with male and female gametangia intermixed. Some species of Botrychium also reproduce asexually belowground through production of gemmae.

DISCUSSION

We conclude that in Botrychium, assessments of population health and structure must include analyses of the belowground plants and their habitat. Conservation management strategies must also include potential changes in the belowground habitat.

Techniques for locating and analyzing subterranean Lycopodium and Diphasiastrum gametophytes in the field

Homosporous club mosses have an archaic life cycle, alternating two locationally, nutritionally, and physiologically independent generations. The sexual generation of club mosses-the gametophytes (or prothallia)-are among the least researched botanical subjects. The gametophytes are responsible for not only sexual reproduction, but also the determination of recruitment of the new sporophyte generation, species habitat selection, migration, and evolution. Researchers often fail to find juvenile club moss populations and thus do not discover subterranean long-lived achlorophyllous gametophytes. To date, the gametophytes of most club moss species remain undiscovered in nature and are not scientifically documented. Almost all researchers who have previously located subterranean club moss gametophytes declared that their first find was due to luck and that subsequently the researcher's intuition plays the most important role; however, intuition and good luck are not scientific methods. In our review, we combine our knowledge with data available in the literature and discuss the following questions using a methodical approach: (1) How can we locate a subterranean club moss gametophyte population? (2) How can we extract the gametophytes? and (3) What new knowledge about club moss population development can be gained by analyzing juvenile club moss populations?

Morpho-anatomical affinities and evolutionary relationships of three paleoendemic podocarp genera based on seed cone traits

BACKGROUND AND AIMS

The three relict genera Pherosphaera, Microcachrys and Saxegothaea in Podocarpaceae produce quite distinct seed cone types in comparison with other genera and do not form a clade along with Acmopyle. The detailed seed cone morpho-anatomy of these three relict genera and affinities with other podocarps are poorly known. This study aims to understand the seed cone morpho-anatomy and affinities among these three disjunct relict genera and with other podocarps.

METHODS

We comparatively analysed the seed cone morpho-anatomical traits of the three podocarps genera and used ancestral state reconstruction to understand the evolution of these traits.

KEY RESULTS

We described the seed cone morpho-anatomical structures of the three relict genera in detail. The three genera produce aggregated multiovulate cones. Both Microcachrys and Saxegothaea have an asymmetrical free cup-like epimatium. Both species of Pherosphaera lack an epimatium. The ancestral state reconstruction implies that the presence of an epimatium is an ancestral trait in podocarps and is independently lost in Pherosphaera and Phyllocladus. The seed cones are fleshy in Microcachrys and non-fleshy in Saxegothaea and Pherosphaera. The seed cone macrofossils of both extinct and living podocarps also show the presence of an epimatium and fleshiness in podocarps.

CONCLUSIONS

Altogether, the morpho-anatomy suggests that Pherosphaera, Microcachrys and Saxegothaea present affinities with each other and other podocarps, but the reconstruction of the ancestral seed cone in Podcarpaceae is quite complex due to multiple convergent evolutions of several structures. These structures (e.g. epimatium, aril and receptaculum) are of low taxonomic value but of great evolutionary and ecological significance, and are responsive adaptations to ever-changing environmental conditions.

Dynamics of Silurian Plants as Response to Climate Changes

The most ancient macroscopic plants fossils are Early Silurian cooksonioid sporophytes from the volcanic islands of the peri-Gondwanan palaeoregion (the Barrandian area, Prague Basin, Czech Republic). However, available palynological, phylogenetic and geological evidence indicates that the history of plant terrestrialization is much longer and it is recently accepted that land floras, producing different types of spores, already were established in the Ordovician Period. Here we attempt to correlate Silurian floral development with environmental dynamics based on our data from the Prague Basin, but also to compile known data on a global scale. Spore-assemblage analysis clearly indicates a significant and almost exponential expansion of trilete-spore producing plants starting during the Wenlock Epoch, while cryptospore-producers, which dominated until the Telychian Age, were evolutionarily stagnate. Interestingly cryptospore vs. trilete-spore producers seem to react differentially to Silurian glaciations-trilete-spore producing plants react more sensitively to glacial cooling, showing a reduction in species numbers. Both our own and compiled data indicate highly terrestrialized, advanced Silurian land-plant assemblage/flora types with obviously great ability to resist different dry-land stress conditions. As previously suggested some authors, they seem to evolve on different palaeo continents into quite disjunct specific plant assemblages, certainly reflecting the different geological, geographical and climatic conditions to which they were subject.

An evidence-based 3D reconstruction of Asteroxylon mackiei, the most complex plant preserved from the Rhynie chert

The Early Devonian Rhynie chert preserves the earliest terrestrial ecosystem and informs our understanding of early life on land. However, our knowledge of the 3D structure, and development of these plants is still rudimentary. Here we used digital 3D reconstruction techniques to produce the first well-evidenced reconstruction of the structure and development of the rooting system of the lycopsid Asteroxylon mackiei, the most complex plant in the Rhynie chert. The reconstruction reveals the organisation of the three distinct axis types - leafy shoot axes, root-bearing axes, and rooting axes - in the body plan. Combining this reconstruction with developmental data from fossilised meristems, we demonstrate that the A. mackiei rooting axis - a transitional lycophyte organ between the rootless ancestral state and true roots - developed from root-bearing axes by anisotomous dichotomy. Our discovery demonstrates how this unique organ developed and highlights the value of evidence-based reconstructions for understanding the development and evolution of the first complex vascular plants on Earth.

Friends, neighbours and enemies: an overview of the communal and social biology of plants

Plants were traditionally seen as rather passive actors in their environment, interacting with each other only in so far as they competed for the same resources. In the last 30 years, this view has been spectacularly overturned, with a wealth of evidence showing that plants actively detect and respond to their neighbours. Moreover, there is evidence that these responses depend on the identity of the neighbour, and that plants may cooperate with their kin, displaying social behaviour as complex as that observed in animals. These plant-plant interactions play a vital role in shaping natural ecosystems, and are also very important in determining agricultural productivity. However, in terms of mechanistic understanding, we have only just begun to scratch the surface, and many aspects of plant-plant interactions remain poorly understood. In this review, we aim to provide an overview of the field of plant-plant interactions, covering the communal interactions of plants with their neighbours as well as the social behaviour of plants towards their kin, and the consequences of these interactions. We particularly focus on the mechanisms that underpin neighbour detection and response, highlighting both progress and gaps in our understanding of these fascinating but previously overlooked interactions.

Archaeosporites rhyniensis gen. et sp. nov. (Glomeromycota, Archaeosporaceae) from the Lower Devonian Rhynie chert: a fungal lineage morphologically unchanged for more than 400 million years

BACKGROUND AND AIMS

Structurally preserved arbuscular mycorrhizas from the Lower Devonian Rhynie chert represent core fossil evidence of the evolutionary history of mycorrhizal systems. Moreover, Rhynie chert fossils of glomeromycotan propagules suggest that this lineage of arbuscular fungi was morphologically diverse by the Early Devonian; however, only a small fraction of this diversity has been formally described and critically evaluated.

METHODS

Thin sections, previously prepared by grinding wafers of chert from the Rhynie beds, were studied by transmitted light microscopy. Fossils corresponding to the description of Archaeospora spp. occurred in 29 slides, and were measured, photographed and compared with modern-day species in that genus.

KEY RESULTS

Sessile propagules <85 µm in diameter, some still attached to a sporiferous saccule, were found in early land plant axes and the chert matrix; they developed, in a similar manner to extant Archaeospora, laterally or centrally within the saccule neck. Microscopic examination and comparison with extant fungi showed that, morphologically, the fossils share the characters used to circumscribe the genus Archaeospora (Glomeromycota; Archaeosporales; Archaeosporaceae).

CONCLUSIONS

The fossils can be assigned with confidence to the extant family Archaeosporaceae, but because molecular analysis is necessary to place organisms in these taxa to present-day genera and species, they are placed in a newly proposed fossil taxon, Archaeosporites rhyniensis.

What can lycophytes teach us about plant evolution and development? Modern perspectives on an ancient lineage

All Evo-Devo studies rely on representative sampling across the tree of interest to elucidate evolutionary trajectories through time. In land plants, genetic resources are well established in model species representing lineages including bryophytes (mosses, liverworts, and hornworts), monilophytes (ferns and allies), and seed plants (gymnosperms and flowering plants), but few resources are available for lycophytes (club mosses, spike mosses, and quillworts). Living lycophytes are a sister group to the euphyllophytes (the fern and seed plant clade), and have retained several ancestral morphological traits despite divergence from a common ancestor of vascular plants around 420 million years ago. This sister relationship offers a unique opportunity to study the conservation of traits such as sporophyte branching, vasculature, and indeterminacy, as well as the convergent evolution of traits such as leaves and roots which have evolved independently in each vascular plant lineage. To elucidate the evolution of vascular development and leaf formation, molecular studies using RNA Seq, quantitative reverse transcription polymerase chain reaction, in situ hybridisation and phylogenetics have revealed the diversification and expression patterns of KNOX, ARP, HD-ZIP, KANADI, and WOX gene families in lycophytes. However, the molecular basis of further trait evolution is not known. Here we describe morphological traits of living lycophytes and their extinct relatives, consider the molecular underpinnings of trait evolution and discuss future research required in lycophytes to understand the key evolutionary innovations enabling the growth and development of all vascular plants.

Pollen competition is the mechanism underlying a variety of evolutionary phenomena in dioecious plants

It has long been known that more pollen grains often arrive on stigmas than there are ovules to fertilize, resulting in pollen competition. Moreover, this competition among pollen grains (gametophytes) depends, in part, on their extensive haploid gene expression. Here I review how this leads to a variety of phenomena in dioecious plants of interest to evolutionary biologists. For example, pollen competition can lead to extreme female-biased sex ratios. In addition, gene expression by individual pollen grains can slow mutation accumulation and degeneration of the Y chromosome. Lastly, I review work on how the haploid selection resulting from pollen competition has been proposed to influence which alleles are linked to the Y chromosome, and some recent empirical evidence in support of this theory.

The origin and evolution of mycorrhizal symbioses: from palaeomycology to phylogenomics

Contents Summary 1012 I. Introduction 1013 II. The mycorrhizal symbiosis at the dawn and rise of the land flora 1014 III. From early land plants to early trees: the origin of roots and true mycorrhizas 1016 IV. The diversification of the AM symbiosis 1019 V. The ECM symbiosis 1021 VI. The recently evolved ericoid and orchid mycorrhizas 1023 VII. Limits of paleontological vs genetic approaches and perspectives 1023 Acknowledgements 1025 References 1025 SUMMARY: The ability of fungi to form mycorrhizas with plants is one of the most remarkable and enduring adaptations to life on land. The occurrence of mycorrhizas is now well established in c. 85% of extant plants, yet the geological record of these associations is sparse. Fossils preserved under exceptional conditions provide tantalizing glimpses into the evolutionary history of mycorrhizas, showing the extent of their occurrence and aspects of their evolution in extinct plants. The fossil record has important roles to play in establishing a chronology of when key fungal associations evolved and in understanding their importance in ecosystems through time. Together with calibrated phylogenetic trees, these approaches extend our understanding of when and how groups evolved in the context of major environmental change on a global scale. Phylogenomics furthers this understanding into the evolution of different types of mycorrhizal associations, and genomic studies of both plants and fungi are shedding light on how the complex set of symbiotic traits evolved. Here we present a review of the main phases of the evolution of mycorrhizal interactions from palaeontological, phylogenetic and genomic perspectives, with the aim of highlighting the potential of fossil material and a geological perspective in a cross-disciplinary approach.

Evolution of root apical meristem structures in vascular plants: plasmodesmatal networks

PREMISE OF THE STUDY

The apical meristem generates indeterminate apical growth of the stem and root of vascular plants. Our previous examination showed that shoot apical meristems (SAMs) can be classified into two types based on plasmodesmatal networks (PNs), which are important elements in symplasmic signaling pathways within the apical meristem. Here, we examined the PNs of root apical meristems (RAMs) in comparison with those of SAMs.

METHODS

Root apical meristems of 18 families and 22 species of lycophytes and euphyllophytes were analyzed. Plasmodesmata (PD) in cell walls in median longitudinal sections of RAMs were enumerated using transmission electron micrographs, and the PD density per 1 μm² of each cell wall was calculated.

KEY RESULTS

Root apical meristems with prominent apical cells of monilophytes (euphyllophytes) and Selaginellaceae (lycophytes) had high PD densities, while RAMs with plural initial cells of gymnosperms and angiosperms (euphyllophytes), and of Lycopodiaceae and Isoetaceae (lycophytes) had low PD densities. This correlation between structures of apical meristems and PD densities is identical to that in SAMs already described.

CONCLUSIONS

Irrespective of their diversified structures, the RAMs of vascular plants can be classified into two types with respect to PNs: the fern (monilophyte) type, which has a lineage-specific PN with only primary PD, and the seed-plant type, which has an interspecific PN with secondary PD in addition to primary PD. PNs may have played a key role in the evolution of apical meristems in vascular plants.

Negative regulation of conserved RSL class I bHLH transcription factors evolved independently among land plants

Basic helix-loop-helix transcription factors encoded by RSL class I genes control a gene regulatory network that positively regulates the development of filamentous rooting cells – root hairs and rhizoids – in land plants. The GLABRA2 transcription factor negatively regulates these genes in the angiosperm Arabidopsis thaliana. To find negative regulators of RSL class I genes in early diverging land plants we conducted a mutant screen in the liverwort Marchantia polymorpha. This identified FEW RHIZOIDS1 (MpFRH1) microRNA (miRNA) that negatively regulates the RSL class I gene MpRSL1. The miRNA and its mRNA target constitute a feedback mechanism that controls epidermal cell differentiation. MpFRH1 miRNA target sites are conserved among liverwort RSL class I mRNAs but are not present in RSL class I mRNAs of other land plants. These findings indicate that while RSL class I genes are ancient and conserved, independent negative regulatory mechanisms evolved in different lineages during land plant evolution.

Plants colonised the land sometime more than 500 million years ago. The ancestors of the first land plants were algae that were most likely simple with a few different types of cell. Yet, when faced with the challenges of life on land, plants evolved new cell types and specialised structures with roles such as anchorage, nutrient uptake and gas exchange.

Many of these specialised structures, including the root hairs and rhizoids that allow plants to collect water and minerals from the soil, first develop as outgrowths from cells in the outer layer of the plant. An ancient and conserved mechanism activates the development of these outgrowths via genes belonging to a group known as RSL class I.

In the flowering plant Arabidopsis thaliana, a protein switches off RSL class I genes in a subset of these outer cells, to stop too many root hairs forming. To see whether this kind of negative regulation is also conserved among land plants, Honkanen et al. looked for regulators of RSL class I genes in liverworts. Small and without flowers, liverworts are a group of plants that first appeared during the earliest stages of land plant evolution.

Honkanen et al. discovered that RSL class I genes in liverworts are negatively regulated by a molecule named FEW RHIZOIDS1 (or FRH1). However, rather than being a protein, FRH1 is a microRNA – a short strand of genetic code that reduces how much protein is produced from a given gene. The FRH1 microRNA is conserved among liverworts and most likely evolved very early in the history of these plants. The findings indicate that different groups of land plants have evolved different negative regulators to control the conserved genes behind some of the specialised structures crucial to life on land.

Bilaterally symmetric axes with rhizoids composed the rooting structure of the common ancestor of vascular plants

There are two general types of rooting systems in extant land plants: gametophyte rhizoids and sporophyte root axes. These structures carry out the rooting function in the free-living stage of almost all land plant gametophytes and sporophytes, respectively. Extant vascular plants develop a dominant, free-living sporophyte on which roots form, with the exception of a small number of taxa that have secondarily lost roots. However, fossil evidence indicates that early vascular plants did not develop sporophyte roots. We propose that the common ancestor of vascular plants developed a unique rooting system—rhizoidal sporophyte axes. Here we present a synthesis and reinterpretation of the rootless sporophytes of Horneophyton lignieri, Aglaophyton majus, Rhynia gwynne-vaughanii and Nothia aphylla preserved in the Rhynie chert. We show that the sporophyte rooting structures of all four plants comprised regions of plagiotropic (horizontal) axes that developed unicellular rhizoids on their underside. These regions of axes with rhizoids developed bilateral symmetry making them distinct from the other regions which were radially symmetrical. We hypothesize that rhizoidal sporophyte axes constituted the rooting structures in the common ancestor of vascular plants because the phylogenetic positions of these plants span the origin of the vascular lineage.

This article is part of a discussion meeting issue ‘The Rhynie cherts: our earliest terrestrial ecosystem revisited’.

Fungi and fungal interactions in the Rhynie chert: a review of the evidence, with the description of Perexiflasca tayloriana gen. et sp. nov.†

The Lower Devonian Rhynie chert is one of the most important rock deposits yielding comprehensive information on early continental plant, animal and microbial life. Fungi are especially abundant among the microbial remains, and include representatives of all major fungal lineages except Basidiomycota. This paper surveys the evidence assembled to date of fungal hyphae, mycelial cords and reproductive units (e.g. spores, sporangia, sporocarps), and presents examples of fungal associations and interactions with land plants, other fungi, algae, cyanobacteria and animals from the Rhynie chert. Moreover, a small, chytrid-like organism that occurs singly, in chain-like, linear arrangements, planar assemblages and three-dimensional aggregates of less than 10 to [Formula: see text] individuals in degrading land plant tissue in the Rhynie chert is formally described, and the name Perexiflasca tayloriana proposed for the organism. Perexiflasca tayloriana probably colonized senescent or atrophied plant parts and participated in the process of biological degradation. The fungal fossils described to date from the Rhynie chert constitute the largest body of structurally preserved evidence of fungi and fungal interactions from any rock deposit, and strongly suggest that fungi played important roles in the functioning of the Early Devonian Rhynie ecosystem.This article is part of a discussion meeting issue 'The Rhynie cherts: our earliest terrestrial ecosystem revisited'.

Organs and tissues of Rhynie chert plants

The Early Devonian Rhynie chert and the nearby Windyfield chert contain the oldest in situ preserved terrestrial ecosystem. Two of the seven species of anatomically preserved land plants had naked axes, one an axis with a more or less regular pattern of short-longitudinal ribs, two species had spiny axes and one species had small leaf-like appendages. All plants mainly consist of parenchymatous tissues. In some species, conducting elements comprise uniformly thickened thick-walled cells resembling hydroids of larger bryophytes, whereas others have real tracheids with annular and/or spiral secondary wall thickenings. True phloem has never been demonstrated but in all species the thick-walled water-conducting cells are encircled by a zone of thin-walled cells without intercellular spaces. The cortex is differentiated into two or three zones and forms the major part of the axes; in one species the cells of the middle cortex are sclerified. Some species have a hypodermis. In all species the epidermis is covered by a well-developed cuticle. Sporangia are known from all species. Sporangia are spindle-shaped, lobed or kidney-shaped and attached terminally or laterally with a short stalk. Gametophytes of four species have been described. Gametophytes are unisexual, isomorphic but much smaller than the sporophytes.This article is part of a discussion meeting issue 'The Rhynie cherts: our earliest terrestrial ecosystem revisited'.

Changing expressions: a hypothesis for the origin of the vascular plant life cycle

Plant life cycles underwent fundamental changes during the initial colonization of the land in the Early Palaeozoic, shaping the direction of evolution. Fossils reveal unanticipated diversity, including new variants of meiotic cell division and leafless gametophytes with mycorrhizal-like symbioses, rhizoids, vascular tissues and stomata. Exceptional fossils from the 407-Ma Rhynie chert (Scotland) play a key role in unlocking this diversity. These fossils are reviewed against progress in our understanding of the plant tree of life and recent advances in developmental genetics. Combining data from different sources sheds light on a switch in life cycle that gave rise to the vascular plants. One crucial step was the establishment of a free-living sporophyte from one that was an obligate matrotroph borne on the gametophyte. It is proposed that this difficult evolutionary transition was achieved through expansion of gene expression primarily from the gametophyte to the sporophyte, establishing a now extinct life cycle variant that was more isomorphic than heteromorphic. These changes also linked for the first time in one developmental system rhizoids, vascular tissues and stomata, putting in place the critical components that regulate transpiration and forming a physiological platform of primary importance to the diversification of vascular plants.This article is part of a discussion meeting issue 'The Rhynie cherts: our earliest terrestrial ecosystem revisited'.

New insights into the evolutionary history of Fungi from a 407 Ma Blastocladiomycota fossil showing a complex hyphal thallus

Zoosporic fungi are key saprotrophs and parasites of plants, animals and other fungi, playing important roles in ecosystems. They comprise at least three phyla, of which two, Chytridiomycota and Blastocladiomycota, developed a range of thallus morphologies including branching hyphae. Here we describe Retesporangicus lyonii gen. et sp. nov., an exceptionally well preserved fossil, which is the earliest known to produce multiple sporangia on an expanded hyphal network. To better characterize the fungus we develop a new method to render surfaces from image stacks generated by confocal laser scanning microscopy. Here, the method helps to reveal thallus structure. Comparisons with cultures of living species and character state reconstructions analysed against recent molecular phylogenies of 24 modern zoosporic fungi indicate an affinity with Blastocladiomycota. We argue that in zoosporic fungi, kinds of filaments such as hyphae, rhizoids and rhizomycelium are developmentally similar structures adapted for varied functions including nutrient absorption and anchorage. The fossil is the earliest known type to develop hyphae which likely served as a saprotrophic adaptation to patchy resource availability. Evidence from the Rhynie chert provides our earliest insights into the biology of fungi and their roles in the environment. It demonstrates that zoosporic fungi were already diverse in 407 million-year-old terrestrial ecosystems.This article is part of a discussion meeting issue 'The Rhynie cherts: our earliest terrestrial ecosystem revisited'.

Evolution and ecology of plant architecture: integrating insights from the fossil record, extant morphology, developmental genetics and phylogenies

BACKGROUND

In contrast to most animals, plants have an indeterminate body plan, which allows them to add new body parts during their lifetime. A plant's realized modular construction is the result of exogenous constraints and endogenous processes. This review focuses on endogenous processes that shape plant architectures and their evolution.

SCOPE

The phylogenetic distribution of plant growth forms across the phylogeny implies that body architectures have originated and been lost repeatedly, being shaped by a limited set of genetic pathways. We (1) synthesize concepts of plant architecture, so far captured in 23 models; (2) extend them to the fossil record; (3) summarize what is known about their developmental genetics; (4) use a phylogenetic approach in several groups to infer how plant architecture has changed and by which intermediate steps; and (5) discuss which macroecological factors may constrain the geographic and ecological distribution of plant architectures.

CONCLUSIONS

Dichotomously branching Paleozoic plants already encompassed a considerable diversity of growth forms, here captured in 12 new architectural models. Plotting the frequency of branching types through time based on an analysis of 58 927 land plant fossils revealed a decrease in dichotomous branching throughout the Devonian and Carboniferous, mirrored by an increase in other branching types including axillary branching. We suggest that the evolution of seed plant megaphyllous leaves enabling axillary branching contributed to the demise of dichotomous architectures. The developmental-genetic bases for key architectural traits underlying sympodial vs. monopodial branching, rhythmic vs. continuous growth, and axillary branching and its localization are becoming well understood, while the molecular basis of dichotomous branching and plagiotropy remains elusive. Three phylogenetic case studies of architecture evolution in conifers, Aloe and monocaulous arborescent vascular plants reveal relationships between architectural models and show that some are labile in given groups, whereas others are widely conserved, apparently shaped by ecological factors, such as intercepted sunlight, temperature, humidity and seasonality.

Root apical meristem diversity in extant lycophytes and implications for root origins

Root apical meristem (RAM) organization in lycophytes could be a key to understanding the early evolution of roots, but this topic has been insufficiently explored. We examined the RAM organization of lycophytes in terms of cell division activities and anatomies, and compared RAMs among vascular plants. RAMs of 13 species of lycophytes were semi-thin-sectioned and observed under a light microscope. Furthermore, the frequency of cell division in the RAM of species was analyzed using thymidine analogs. RAMs of lycophytes exhibited four organization types: type I (Lycopodium and Diphasiastrum), II (Huperzia and Lycopodiella), III (Isoetes) and RAM with apical cell (Selaginella). The type I RAM found in Lycopodium had a region with a very low cell division frequency, reminiscent of the quiescent center (QC) in angiosperm roots. This is the first clear indication that a QC-like region is present in nonseed plants. At least four types of RAM are present in extant lycophytes, suggesting that RAM organization is more diverse than expected. Our results support the paleobotanical hypothesis that roots evolved several times in lycophytes, as well as in euphyllophytes.

An organismal concept for Sengelia radicans gen. et sp. nov. - morphology and natural history of an Early Devonian lycophyte

BACKGROUND AND AIMS

Fossil plants are found as fragmentary remains and understanding them as natural species requires assembly of whole-organism concepts that integrate different plant parts. Such concepts are essential for incorporating fossils in hypotheses of plant evolution and phylogeny. Plants of the Early Devonian are crucial to reconstructing the initial radiation of tracheophytes, yet few are understood as whole organisms.

METHODS

This study assembles a whole-plant concept for the Early Devonian lycophyte Sengelia radicans gen. et sp. nov., based on morphometric data and taphonomic observations from >1000 specimens collected in the Beartooth Butte Formation (Wyoming, USA).

KEY RESULTS

Sengelia radicans occupies a key position between stem-group and derived lycophyte lineages. Sengelia had a rooting system of downward-growing root-bearing stems, formed dense monotypic mats of prostrate shoots in areas that experienced periodic flooding, and was characterized by a life-history strategy adapted for survival after floods, dominated by clonality, and featuring infrequent sexual reproduction.

CONCLUSIONS

Sengelia radicans is the oldest among the very few early tracheophytes for which a detailed, rigorous whole-plant concept integrates morphology, growth habit, life history and growth environment. This plant adds to the diversity of body plans documented among lycophytes and may help elucidate patterns of morphological evolution in the clade.

A Transcriptome Atlas of Physcomitrella patens Provides Insights into the Evolution and Development of Land Plants

Identifying the genetic mechanisms that underpin the evolution of new organ and tissue systems is an aim of evolutionary developmental biology. Comparative functional genetic studies between angiosperms and bryophytes can define those genetic changes that were responsible for developmental innovations. Here, we report the generation of a transcriptome atlas covering most phases in the life cycle of the model bryophyte Physcomitrella patens, including detailed sporophyte developmental progression. We identified a comprehensive set of sporophyte-specific transcription factors, and found that many of these genes have homologs in angiosperms that function in developmental processes such as flowering and shoot branching. Deletion of the PpTCP5 transcription factor results in development of supernumerary sporangia attached to a single seta, suggesting that it negatively regulates branching in the moss sporophyte. Given that TCP genes repress branching in angiosperms, we suggest that this activity is ancient. Finally, comparison of P. patens and Arabidopsis thaliana transcriptomes led us to the identification of a conserved core of transcription factors expressed in tip-growing cells. We identified modifications in the expression patterns of these genes that could account for developmental differences between P. patens tip-growing cells and A. thaliana pollen tubes and root hairs.

An enigmatic fossil fungus from the 410 Ma Rhynie chert that resembles Macrochytrium (Chytridiomycota) and Blastocladiella (Blastocladiomycota)

Litter layers in the Lower Devonian (~ 410 Ma) Rhynie chert were inhabited by a wide variety of saprotrophic fungi, however, only a few of these organisms have been described formally. A new microfungus, Trewinomyces annulifer gen. et sp. nov., occurs as tufts on decaying land plant axes from the Rhynie chert. The fungus consists of an intramatrical rhizoidal system and an erect extramatrical hypha (stalk) that bears a single, terminal sporangium. One or two successive rings often are present in the stalk immediately below the sporangium base. Overall morphology of T. annulifer resembles the extant genera Macrochytrium (Chytridiomycota) and Blastocladiella (Blastocladiomycota). However, the rhizoids are septate or pseudoseptate, a feature not known in extant zoosporic fungi, and thus render the systematic affinities of T. annulifer unresolved. Trewinomyces annulifer offers a rare view of the morphology of a distinctive Early Devonian saprotrophic microfungus.

The early evolution of land plants, from fossils to genomics: a commentary on Lang (1937) 'On the plant-remains from the Downtonian of England and Wales'

During the 1920s, the botanist W. H. Lang set out to collect and investigate some very unpromising fossils of uncertain affinity, which predated the known geological record of life on land. His discoveries led to a landmark publication in 1937, 'On the plant-remains from the Downtonian of England and Wales', in which he revealed a diversity of small fossil organisms of great simplicity that shed light on the nature of the earliest known land plants. These and subsequent discoveries have taken on new relevance as botanists seek to understand the plant genome and the early evolution of fundamental organ systems. Also, our developing knowledge of the composition of early land-based ecosystems and the interactions among their various components is contributing to our understanding of how life on land affects key Earth Systems (e.g. carbon cycle). The emerging paradigm is one of early life on land dominated by microbes, small bryophyte-like organisms and lichens. Collectively called cryptogamic covers, these are comparable with those that dominate certain ecosystems today. This commentary was written to celebrate the 350th anniversary of the journal Philosophical Transactions of the Royal Society.

Three ancient hormonal cues co-ordinate shoot branching in a moss

Shoot branching is a primary contributor to plant architecture, evolving independently in flowering plant sporophytes and moss gametophytes. Mechanistic understanding of branching is largely limited to flowering plants such as Arabidopsis, which have a recent evolutionary origin. We show that in gametophytic shoots of Physcomitrella, lateral branches arise by re-specification of epidermal cells into branch initials. A simple model co-ordinating the activity of leafy shoot tips can account for branching patterns, and three known and ancient hormonal regulators of sporophytic branching interact to generate the branching pattern- auxin, cytokinin and strigolactone. The mode of auxin transport required in branch patterning is a key divergence point from known sporophytic pathways. Although PIN-mediated basipetal auxin transport regulates branching patterns in flowering plants, this is not so in Physcomitrella, where bi-directional transport is required to generate realistic branching patterns. Experiments with callose synthesis inhibitors suggest plasmodesmal connectivity as a potential mechanism for transport.

DOI:http://dx.doi.org/10.7554/eLife.06808.001

Most land plants have shoots that form branches and plants can regulate when and where they grow these branches to best exploit their environment. Plants with flowers and the more ancient mosses both have branching shoots, but these two groups of plants evolved to grow in this way independently of each other. Most studies on shoot branching have focused on flowering plants and so it is less clear how branching works in mosses.

Three plant hormones—called auxin, cytokinin and strigolactone—control shoot branching in flowering plants. Auxin moves down the main shoot of the plant to prevent new branches from forming. This movement is controlled by the PIN proteins and several other families of proteins. On the other hand, cytokinin promotes the growth of new branches; and strigolactone can either promote or inhibit shoot branching depending on how the auxin is travelling around the plant.

Coudert, Palubicki et al. studied shoot branching in a species of moss called Physcomitrella patens. The experiments show that cells on the outer surface of the main shoot are essentially reprogrammed to become so-called ‘branch initials’, which will then develop into new branches. Next, Coudert, Palubicki et al. made a computational model that was able to simulate the pattern of shoot branching in the moss.

Further experiments supported the predictions made by the model. Coudert, Palubicki et al. found that, as in flowering plants, auxin from the tip of the main shoot suppresses branching in the moss, and cytokinin promotes branching. The experiments also showed that strigolactone inhibits shoot branching, but its role is restricted to the base of the shoots. The model predicts that, unlike in flowering plants, auxin must flow in both directions in moss shoots to produce the observed patterns of shoot branching. Also, the experiments suggest that the PIN proteins and another group of proteins that control the movement of auxin do not regulate shoot branching in moss. Instead, it appears that auxin may move through microscopic channels that link one moss cell to the next.

Coudert, Palubicki et al.'s findings suggest that both flowering plants and mosses have evolved to use the same three hormones to control shoot branching, but that these hormones interact in different ways. One key next step will be to find out how auxin is transported during shoot branching in moss by manipulating the opening of the channels between the cells. A further challenge will be to find out the precise details of how the hormones control the activity of the branch initial cells.

DOI:http://dx.doi.org/10.7554/eLife.06808.002

Three ancient hormonal cues co-ordinate shoot branching in a moss

Shoot branching is a primary contributor to plant architecture, evolving independently in flowering plant sporophytes and moss gametophytes. Mechanistic understanding of branching is largely limited to flowering plants such as Arabidopsis, which have a recent evolutionary origin. We show that in gametophytic shoots of Physcomitrella, lateral branches arise by re-specification of epidermal cells into branch initials. A simple model co-ordinating the activity of leafy shoot tips can account for branching patterns, and three known and ancient hormonal regulators of sporophytic branching interact to generate the branching pattern- auxin, cytokinin and strigolactone. The mode of auxin transport required in branch patterning is a key divergence point from known sporophytic pathways. Although PIN-mediated basipetal auxin transport regulates branching patterns in flowering plants, this is not so in Physcomitrella, where bi-directional transport is required to generate realistic branching patterns. Experiments with callose synthesis inhibitors suggest plasmodesmal connectivity as a potential mechanism for transport.

The origin and early evolution of roots

Geological sites of exceptional fossil preservation are becoming a focus of research on root evolution because they retain edaphic and ecological context, and the remains of plant soft tissues are preserved in some. New information is emerging on the origins of rooting systems, their interactions with fungi, and their nature and diversity in the earliest forest ecosystems. Remarkably well-preserved fossils prove that mycorrhizal symbionts were diverse in simple rhizoid-based systems. Roots evolved in a piecemeal fashion and independently in several major clades through the Devonian Period (416 to 360 million years ago), rapidly extending functionality and complexity. Evidence from extinct arborescent clades indicates that polar auxin transport was recruited independently in several to regulate wood and root development. The broader impact of root evolution on the geochemical carbon cycle is a developing area and one in which the interests of the plant physiologist intersect with those of the geochemist.

Fungal associations in Horneophyton ligneri from the Rhynie Chert (c. 407 million year old) closely resemble those in extant lower land plants: novel insights into ancestral plant-fungus symbioses

Fungi (Eumycota) form close associations with plants, with which they have co-existed since the dawn of life on land, but their diversity in early terrestrial ecosystems is still poorly understood. We studied petrographic sections of exceptionally well-preserved petrified plants from the 407 million yr-old Rhynie Chert (Scotland, UK). For comparative purposes, we illustrate fungal associations in four extant lower land plants. We document two new endophytes in the plant Horneophyton lignieri: Palaeoglomus boullardii (sp. nov. Glomeromycota) colonizes parenchyma in a discontinuous zone of the outer cortex of the aerial axes, forming arbuscule-like structures, vesicles and spores; Palaeoendogone gwynne-vaughaniae (gen. nov., sp. nov. Mucoromycotina) colonizes parenchyma in the basal part of the plant, where it is present in intercellular spaces and as intracellular coils but absent from rhizoids. Critical comparisons between the newly discovered Horneophyton endophytes, fungi previously described from the Rhynie Chert and fungal colonization in extant lower land plants reveal several features characteristic of both Mucoromycotina and Glomeromycota. A reappraisal of fungal associations in early land plants indicates that they are more diverse than assumed hitherto, overturning the long-held paradigm that the early endophytes were exclusively Glomeromycota.

Mitochondrial phylogenomics of early land plants: mitigating the effects of saturation, compositional heterogeneity, and codon-usage bias

Phylogenetic analyses using concatenation of genomic-scale data have been seen as the panacea for resolving the incongruences among inferences from few or single genes. However, phylogenomics may also suffer from systematic errors, due to the, perhaps cumulative, effects of saturation, among-taxa compositional (GC content) heterogeneity, or codon-usage bias plaguing the individual nucleotide loci that are concatenated. Here, we provide an example of how these factors affect the inferences of the phylogeny of early land plants based on mitochondrial genomic data. Mitochondrial sequences evolve slowly in plants and hence are thought to be suitable for resolving deep relationships. We newly assembled mitochondrial genomes from 20 bryophytes, complemented these with 40 other streptophytes (land plants plus algal outgroups), compiling a data matrix of 60 taxa and 41 mitochondrial genes. Homogeneous analyses of the concatenated nucleotide data resolve mosses as sister-group to the remaining land plants. However, the corresponding translated amino acid data support the liverwort lineage in this position. Both results receive weak to moderate support in maximum-likelihood analyses, but strong support in Bayesian inferences. Tests of alternative hypotheses using either nucleotide or amino acid data provide implicit support for their respective optimal topologies, and clearly reject the hypotheses that bryophytes are monophyletic, liverworts and mosses share a unique common ancestor, or hornworts are sister to the remaining land plants. We determined that land plant lineages differ in their nucleotide composition, and in their usage of synonymous codon variants. Composition heterogeneous Bayesian analyses employing a nonstationary model that accounts for variation in among-lineage composition, and inferences from degenerated nucleotide data that avoid the effects of synonymous substitutions that underlie codon-usage bias, again recovered liverworts being sister to the remaining land plants but without support. These analyses indicate that the inference of an early-branching moss lineage based on the nucleotide data is caused by convergent compositional biases. Accommodating among-site amino acid compositional heterogeneity (CAT-model) yields no support for the optimal resolution of liverwort as sister to the rest of land plants, suggesting that the robust inference of the liverwort position in homogeneous analyses may be due in part to compositional biases among sites. All analyses support a paraphyletic bryophytes with hornworts composing the sister-group to tracheophytes. We conclude that while genomic data may generate highly supported phylogenetic trees, these inferences may be artifacts. We suggest that phylogenomic analyses should assess the possible impact of potential biases through comparisons of protein-coding gene data and their amino acid translations by evaluating the impact of substitutional saturation, synonymous substitutions, and compositional biases through data deletion strategies and by analyzing the data using heterogeneous composition models. We caution against relying on any one presentation of the data (nucleotide or amino acid) or any one type of analysis even when analyzing large-scale data sets, no matter how well-supported, without fully exploring the effects of substitution models.

Calcium-dependent protein kinases in plants: evolution, expression and function

Calcium-dependent protein kinases (CPKs) are plant proteins that directly bind calcium ions before phosphorylating substrates involved in metabolism, osmosis, hormone response and stress signaling pathways. CPKs are a large multigene family of proteins that are present in all plants studied to date, as well as in protists, oomycetes and green algae, but are not found in animals and fungi. Despite the increasing evidence of the importance of CPKs in developmental and stress responses from various plants, a comprehensive genome-wide analysis of CPKs from algae to higher plants has not been undertaken. This paper describes the evolution of CPKs from green algae to plants using a broadly sampled phylogenetic analysis and demonstrates the functional diversification of CPKs based on expression and functional studies in different plant species. Our findings reveal that CPK sequence diversification into four major groups occurred in parallel with the terrestrial transition of plants. Despite significant expansion of the CPK gene family during evolution from green algae to higher plants, there is a high level of sequence conservation among CPKs in all plant species. This sequence conservation results in very little correlation between CPK evolutionary groupings and functional diversity, making the search for CPK functional orthologs a challenge.

Arbuscular mycorrhiza formation in cordate gametophytes of two ferns, Angiopteris lygodiifolia and Osmunda japonica

Mycorrhizal symbiosis is common among land plants including pteridophytes (monilophytes and lycophytes). In pteridophytes with diplohaplontic life cycle, mycorrhizal formations were mostly reported for sporophytes, but very few for gametophytes. To clarify the mycorrhizal association of photosynthetic gametophytes, field-collected gametophytes of Angiopteris lygodiifolia (Marattiaceae, n = 52) and Osmunda japonica (Osmundaceae, n = 45) were examined using microscopic and molecular techniques. Collected gametophytes were mostly cut into two pieces. One piece was used for light and scanning microscopic observations, and the other for molecular identification of plant species (chloroplast rbcL sequences) and mycorrhizal fungi (small subunit rDNA sequences). Microscopic observations showed that 96 % (50/52) of Angiopteris and 95 % (41/43) of Osmunda gametophytes contained intracellular hyphae with arbuscules and/or vesicles and fungal colonization was limited to the inner tissue of the thick midribs (cushion). Fungal DNA analyses showed that 92 % (48/52) of Angiopteris and 92 % (35/38) of Osmunda have sequences of arbuscular mycorrhizal fungi, which were highly divergent but all belonged to Glomus group A. These results suggest that A. lygodiifolia and O. japonica gametophytes consistently form arbuscular mycorrhizae. Mycorrhizal formation in wild fern gametophytes, based on large-scale sampling with molecular identification of host plant species, was demonstrated for the first time.

Origin and early evolution of land plants: Problems and considerations

The origin of the sporophyte in land plants represents a fundamental phase in plant evolution. Today this subject is controversial, and scarcely considered in textbooks and journals of botany, in spite of its importance. There are two conflicting theories concerning the origin of the alternating generations in land-plants: the "antithetic" theory and the "homologous" theory. These have never been fully resolved, although, on the ground of the evidences on the probable ancestors of land plants, the antithetic theory is considered more plausible than the homologous theory. However, additional phylogenetic dilemmas are the evolution of bryophytes from algae and the transition from these first land plants to the pteridophytes. All these very large evolutionary jumps are discussed on the basis of the phyletic gradualist neo-Darwinian theory and other genetic evolutionary mechanisms.

Contrasting arbuscular mycorrhizal responses of vascular and non-vascular plants to a simulated Palaeozoic CO₂ decline

The arbuscular mycorrhizal (AM) fungal symbiosis is widely hypothesized to have promoted the evolution of land plants from rootless gametophytes to rooted sporophytes during the mid-Palaeozoic (480-360 Myr, ago), at a time coincident with a 90% fall in the atmospheric CO(2) concentration ([CO(2)](a)). Here we show using standardized dual isotopic tracers ((14)C and (33)P) that AM symbiosis efficiency (defined as plant P gain per unit of C invested into fungi) of liverwort gametophytes declines, but increases in the sporophytes of vascular plants (ferns and angiosperms), at 440 p.p.m. compared with 1,500 p.p.m. [CO(2)](a). These contrasting responses are associated with larger AM hyphal networks, and structural advances in vascular plant water-conducting systems, promoting P transport that enhances AM efficiency at 440 p.p.m. [CO(2)](a). Our results suggest that non-vascular land plants not only faced intense competition for light, as vascular land floras grew taller in the Palaeozoic, but also markedly reduced efficiency and total capture of P as [CO(2)](a) fell.

Major transitions in the evolution of early land plants: a bryological perspective

Background Molecular phylogeny has resolved the liverworts as the earliest-divergent clade of land plants and mosses as the sister group to hornworts plus tracheophytes, with alternative topologies resolving the hornworts as sister to mosses plus tracheophytes less well supported. The tracheophytes plus fossil plants putatively lacking lignified vascular tissue form the polysporangiophyte clade. Scope This paper reviews phylogenetic, developmental, anatomical, genetic and paleontological data with the aim of reconstructing the succession of events that shaped major land plant lineages. Conclusions Fundamental land plant characters primarily evolved in the bryophyte grade, and hence the key to a better understanding of the early evolution of land plants is in bryophytes. The last common ancestor of land plants was probably a leafless axial gametophyte bearing simple unisporangiate sporophytes. Water-conducting tissue, if present, was restricted to the gametophyte and presumably consisted of perforate cells similar to those in the early-divergent bryophytes Haplomitrium and Takakia. Stomata were a sporophyte innovation with the possible ancestral functions of producing a transpiration-driven flow of water and solutes from the parental gametophyte and facilitating spore separation before release. Stomata in mosses, hornworts and polysporangiophytes are viewed as homologous, and hence these three lineages are collectively referred to as the 'stomatophytes'. An indeterminate sporophyte body (the sporophyte shoot) developing from an apical meristem was the key innovation in polysporangiophytes. Poikilohydry is the ancestral condition in land plants; homoiohydry evolved in the sporophyte of polysporangiophytes. Fungal symbiotic associations ancestral to modern arbuscular mycorrhizas evolved in the gametophytic generation before the separation of major present-living lineages. Hydroids are imperforate water-conducting cells specific to advanced mosses. Xylem vascular cells in polysporangiophytes arose either from perforate cells or de novo. Food-conducting cells were a very early innovation in land plant evolution. The inferences presented here await testing by molecular genetics.

Bryophyte diversity and evolution: windows into the early evolution of land plants

The "bryophytes" comprise three phyla of plants united by a similar haploid-dominant life cycle and unbranched sporophytes bearing one sporangium: the liverworts (Marchantiophyta), mosses (Bryophyta), and hornworts (Anthocerophyta). Combined, these groups include some 20000 species. As descendents of embryophytes that diverged before tracheophytes appeared, bryophytes offer unique windows into the early evolution of land plants. We review insights into the evolution of plant life cycles, in particular the elaboration of the sporophyte generation, the major lineages within bryophyte phyla, and reproductive processes that shape patterns of bryophyte evolution. Recent transcriptomic work suggests extensive overlap in gene expression in bryophyte sporophytes vs. gametophytes, but also novel patterns in the sporophyte, supporting Bower's antithetic hypothesis for origin of alternation of generations. Major lineages of liverworts, mosses, and hornworts have been resolved and general patterns of morphological evolution can now be inferred. The life cycles of bryophytes, arguably more similar to those of early embryophytes than are those in any other living plant group, provide unique insights into gametophyte mating patterns, sexual conflicts, and the efficacy and effects of spore dispersal during early land plant evolution.

Out of the mouths of plants: the molecular basis of the evolution and diversity of stomatal development

Stomata are microscopic valves on the plant epidermis that played a critical role in the evolution of land plants. Studies in the model dicot Arabidopsis thaliana have identified key transcription factors and signaling pathways controlling stomatal patterning and differentiation. Three paralogous Arabidopsis basic helix-loop-helix proteins, SPEECHLESS (SPCH), MUTE, and FAMA, mediate sequential steps of cell-state transitions together with their heterodimeric partners SCREAM (SCRM) and SCRM2. Cell-cell signaling components, including putative ligands, putative receptors, and mitogen-activated protein kinase cascades, orient asymmetric cell divisions and prevent overproduction and clustering of stomata. The recent availability of genome sequence and reverse genetics tools for model monocots and basal land plants allows for the examination of the conservation of genes important in stomatal patterning and differentiation. Studies in grasses have revealed that divergence of SPCH-MUTE-FAMA predates the evolutionary split of monocots and dicots and that these proteins show conserved and novel roles in stomatal differentiation. By contrast, specific asymmetric cell divisions in Arabidopsis and grasses require unique molecular components. Molecular phylogenetic analysis implies potential conservation of signaling pathways and prototypical functions of the transcription factors specifying stomatal differentiation.