Piecing together the eophytes - a new group of ancient plants containing cryptospores

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.

Evolution of the sporophyte shoot axis and functions of TALE HD transcription factors in stem development

The stem is one of the major organs in seed plants and is important for plant survival as well as in agriculture. However, due to the lack of clear external landmarks in many species, its developmental and evolutionary processes are understudied compared to other organs. Recent approaches tackling these problems, especially those focused on KNOX1 and BLH transcription factors belonging to the TALE homeodomain superfamily have started unveiling the patterning process of nodes and internodes by connecting previously accumulated knowledge on lateral organ regulators. Fossil records played crucial roles in understanding the evolutionary process of the stem. The aim of this review is to introduce how the stem evolved from ancestorial sporophyte axes and to provide frameworks for future efforts in understanding the developmental process of this elusive but pivotal organ.

Characterization of the fiber-like cortical cells in moss gametophytes

MAIN CONCLUSION

Fiber-like cells with thickened cell walls of specific structure and polymer composition that includes (1 → 4)-β-galactans develop in the outer stem cortex of several moss species gametophytes. The early land plants evolved several specialized cell types and tissues that did not exist in their aquatic ancestors. Of these, water-conducting elements and reproductive organs have received most of the research attention. The evolution of tissues specialized to fulfill a mechanical function is by far less studied despite their wide distribution in land plants. For vascular plants following a homoiohydric trajectory, the evolutionary emergence of mechanical tissues is mainly discussed starting with the fern-like plants with their hypodermal sterome or sclerified fibers that have xylan and lignin-based cell walls. However, mechanical challenges were also faced by bryophytes, which lack lignified cell-walls. To characterize mechanical tissues in the bryophyte lineage, following a poikilohydric trajectory, we used six wild moss species (Polytrichum juniperinum, Dicranum sp., Rhodobryum roseum, Eurhynchiadelphus sp., Climacium dendroides, and Hylocomium splendens) and analyzed the structure and composition of their cell walls. In all of them, the outer stem cortex of the leafy gametophytic generation had fiber-like cells with a thickened but non-lignified cell wall. Such cells have a spindle-like shape with pointed tips. The additional thick cell wall layer in those fiber-like cells is composed of sublayers with structural evidence for different cellulose microfibril orientation, and with specific polymer composition that includes (1 → 4)-β-galactans. Thus, the basic cellular characters of the cells that provide mechanical support in vascular plant taxa (elongated cell shape, location at the periphery of a primary organ, the thickened cell wall and its peculiar composition and structure) also exist in mosses.

Silurian Climatic Zonation of Cryptospore, Trilete Spore and Plant Megafossils, with Emphasis on the Přídolí Epoch

This paper describes dispersed cryptospores and trilete spores from tropical, temperate and cool climate belts within Přídolí and compares them with the land plant megafossil record. The palynology of earlier intervals in the Silurian are also reviewed. A common feature of the cryptospore and trilete spore records is that their number is surprisingly lowest in the tropical climatic belt and much higher in the temperate and especially in the cool latitude, and the highest number of cryptospore taxa occurring only in one belt is found in the cool belt while the highest number of trilete spore taxa that occurred only in one belt is recorded in the temperate belt. In general, based on the dispersed spore record, we can estimate that the plant assemblages of the tropical belt were dominated by rhyniophytes; trimerophytes probably prevailed over rhyniophytes in the temperate belt, and rhyniophytes again dominated within the cool belt.

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.

Quantifying the complexity of plant reproductive structures reveals a history of morphological and functional integration

Vascular plant reproductive structures have undoubtedly become more complex through time, evolving highly differentiated parts that interact in specialized ways. But quantifying these patterns at broad scales is challenging because lineages produce disparate reproductive structures that are often difficult to compare and homologize. We develop a novel approach for analysing interactions within reproductive structures using networks, treating component parts as nodes and a suite of physical and functional interactions among parts as edges. We apply this approach to the plant fossil record, showing that interactions have generally increased through time and that the concentration of these interactions has shifted towards differentiated surrounding organs, resulting in more compact, functionally integrated structures. These processes are widespread across plant lineages, but their extent and timing vary with reproductive biology; in particular, seed-producing structures show them more strongly than spore or pollen-producing structures. Our results demonstrate that major reproductive innovations like the origin of seeds and angiospermy were associated with increased integration through greater interactions among parts. But they also reveal that for certain groups, particularly Mesozoic gymnosperms, millions of years elapsed between the origin of reproductive innovations and increased interactions among parts within their reproductive structures.

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.

Diverse branching forms regulated by a core auxin transport mechanism in plants

Diverse branching forms have evolved multiple times across the tree of life to facilitate resource acquisition and exchange with the environment. In the vascular plant group, the ancestral pattern of branching involves dichotomy of a parent shoot apex to form two new daughter apices. The molecular basis of axillary branching in Arabidopsis is well understood, but few regulators of dichotomous branching are known. Through analyses of dichotomous branching in the lycophyte, Selaginella kraussiana, we identify PIN-mediated auxin transport as an ancestral branch regulator of vascular plants. We show that short-range auxin transport out of the apices promotes dichotomy and that branch dominance is globally coordinated by long-range auxin transport. Uniquely in Selaginella, angle meristems initiate at each dichotomy, and these can develop into rhizophores or branching angle shoots. We show that long-range auxin transport and a transitory drop in PIN expression are involved in angle shoot development. We conclude that PIN-mediated auxin transport is an ancestral mechanism for vascular plant branching that was independently recruited into Selaginella angle shoot development and seed plant axillary branching during evolution.

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.

How was apical growth regulated in the ancestral land plant? Insights from the development of non-seed plants

Land plant life cycles are separated into distinct haploid gametophyte and diploid sporophyte stages. Indeterminate apical growth evolved independently in bryophyte (moss, liverwort, and hornwort) and fern gametophytes, and tracheophyte (vascular plant) sporophytes. The extent to which apical growth in tracheophytes co-opted conserved gametophytic gene networks, or exploited ancestral sporophytic networks, is a long-standing question in plant evolution. The recent phylogenetic confirmation of bryophytes and tracheophytes as sister groups has led to a reassessment of the nature of the ancestral land plant. Here, we review developmental genetic studies of apical regulators and speculate on their likely evolutionary history.

Deep origin and gradual evolution of transporting tissues: Perspectives from across the land plants

The evolution of transporting tissues was an important innovation in terrestrial plants that allowed them to adapt to almost all nonaquatic environments. These tissues consist of water-conducting cells and food-conducting cells and bridge plant-soil and plant-air interfaces over long distances. The largest group of land plants, representing about 95% of all known plant species, is associated with morphologically complex transporting tissue in plants with a range of additional traits. Therefore, this entire clade was named tracheophytes, or vascular plants. However, some nonvascular plants possess conductive tissues that closely resemble vascular tissue in their organization, structure, and function. Recent molecular studies also point to a highly conserved toolbox of molecular regulators for transporting tissues. Here, we reflect on the distinguishing features of conductive and vascular tissues and their evolutionary history. Rather than sudden emergence of complex, vascular tissues, plant transporting tissues likely evolved gradually, building on pre-existing developmental mechanisms and genetic components. Improved knowledge of the intimate structure and developmental regulation of transporting tissues across the entire taxonomic breadth of extant plant lineages, combined with more comprehensive documentation of the fossil record of transporting tissues, is required for a full understanding of the evolutionary trajectory of transporting tissues.

Bryophyte ultraviolet-omics: from genes to the environment

Ultraviolet (UV) radiation has contributed to the evolution of organisms since the origins of life. Bryophytes also have evolutionary importance as the first clearly identified lineage of land plants (embryophytes) colonizing the terrestrial environment, thus facing high UV and water scarcity, among other new challenges. Here we review bryophyte UV-omics, the discipline relating bryophytes and UV, with an integrative perspective from genes to the environment. We consider species and habitats investigated, methodology, response variables, protection mechanisms, environmental interactions, UV biomonitoring, molecular and evolutionary aspects, and applications. Bryophyte UV-omics shows convergences and divergences with the UV-omics of other photosynthetic organisms, from algae to tracheophytes. All these organisms converge in that UV damage may be limited under realistic UV levels, due to structural protection and/or physiological acclimation capacity. Nevertheless, bryophytes diverge because they have a unique combination of vegetative and reproductive characteristics to cope with high UV and other concomitant adverse processes, such as desiccation. This interaction has both evolutionary and ecological implications. In addition, UV effects on bryophytes depend on the species and the evolutionary lineage considered, with mosses more UV-tolerant than liverworts. Thus, bryophytes do not constitute a homogeneous functional type with respect to their UV tolerance.

Apical dominance control by TAR-YUC-mediated auxin biosynthesis is a deep homology of land plants

A key aim in biology is to identify which genetic changes contributed to the evolution of form through time. Apical dominance, the inhibitory effect exerted by shoot apices on the initiation or outgrowth of distant lateral buds, is a major regulatory mechanism of plant form.¹ Nearly a century of studies in the sporophyte of flowering plants have established the phytohormone auxin as a front-runner in the search for key factors controlling apical dominance,^2,3 identifying critical roles for long-range polar auxin transport and local auxin biosynthesis in modulating shoot branching.^4-10 A capacity for lateral branching evolved by convergence in the gametophytic shoot of mosses and primed its diversification;¹¹ however, polar auxin transport is relatively unimportant in this developmental process,¹² the contribution of auxin biosynthesis genes has not been assessed, and more generally, the extent of conservation in apical dominance regulation within the land plants remains largely unknown. To fill this knowledge gap, we sought to identify genetic determinants of apical dominance in the moss Physcomitrium patens. Here, we show that leafy shoot apex decapitation releases apical dominance through massive and rapid transcriptional reprogramming of auxin-responsive genes and altering auxin biosynthesis gene activity. We pinpoint a subset of P. patens TRYPTOPHAN AMINO-TRANSFERASE (TAR) and YUCCA FLAVIN MONOOXYGENASE-LIKE (YUC) auxin biosynthesis genes expressed in the main and lateral shoot apices and show that they are essential for coordinating branch initiation and outgrowth. Our results demonstrate that local auxin biosynthesis acts as a pivotal regulator of apical dominance in moss and constitutes a shared mechanism underpinning shoot architecture control in land plants.

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.

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.

Earliest record of transfer cells in Lower Devonian plants

Key sources of information on the nature of early terrestrial ecosystems are the fossilized remains of plants and associated organic encrustations, which are interpreted as either biofilms, biological soil crusts or lichens. The hypothesis that some of these encrustations might be the remains of the thalloid gametophytes of embryophytes provided the stimulus for this investigation. Fossils preserved in charcoal were extracted from Devonian Period (Lochkovian Stage, c. 410-419 Myr old) sediments at a geological site in Shropshire (UK). Scanning electron micrographs (SEMs) of the fossils were compared with new and published SEMs of extant bryophytes and tracheophytes, respectively. One specimen was further prepared and imaged by transmission electron microscopy. Fossils of thalloid morphology were composed almost entirely of cells with labyrinthine ingrowths; these also were present in fossils of axial morphology where they were associated with putative food-conducting cells. Comparison with modern embryophytes demonstrates that these distinctive cells are transfer cells (TCs). Our fossils provide by far the earliest geological evidence of TCs. They also show that some organic encrustations are the remains of thalloid land plants and that these are possibly part of the life cycle of a newly recognized group of plants called the eophytes.

Low tropical diversity during the adaptive radiation of early land plants

The latitudinal biodiversity gradient, with tropical regions acting as 'evolutionary cradles', is a cornerstone of current biogeographical and ecological theory¹. In the modern world floral biodiversity and biomass are overwhelmingly concentrated in the tropics, and it is often assumed that the tropics were evolutionary cradles throughout land plant evolutionary history. For example, the origination and diversification of angiosperms is believed to have taken place in the Cretaceous tropics² and modern gymnosperms in the Permian tropics³. Here, we show that during the first major diversification of land plants, in the Late Silurian-Early Devonian, land plant biodiversity was much lower at the equator compared to medium-high southern latitudes. Throughout this crucial interval of plant evolution, tropical vegetation remained depauperate and of very low taxonomic biodiversity, although with similar morphological disparity to the more diverse higher latitude floras. Possible explanations for this low tropical floral biodiversity include palaeocontinental configuration or adverse palaeotropical environmental conditions. We discount the possibility that it was simply a fortuitous feature of the biogeographical spread of the earliest vascular land plants.