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Summary: The onset of stomatal closure reduces transpiration during drought. In seed plants, drought causes declines in plant water status which increases leaf endogenous abscisic acid (ABA) levels required for stomatal closure. There are multiple possible points of increased belowground resistance in the soil–plant atmospheric continuum that could decrease leaf water potential enough to trigger ABA production and the subsequent decreases in transpiration.We investigate the dynamic patterns of leaf ABA levels, plant hydraulic conductance and the point of failure in the soil–plant conductance in the highly embolism‐resistant species Callitris tuberculata using continuous dendrometer measurements of leaf water potential during drought.We show that decreases in transpiration and ABA biosynthesis begin before any permanent decreases in predawn water potential, collapse in soil–plant hydraulic pathway and xylem embolism spread.We find that a dynamic but recoverable increases in hydraulic resistance in the soil in close proximity to the roots is the most likely driver of declines in midday leaf water potential needed for ABA biosynthesis and the onset of decreases in transpiration. [ABSTRACT FROM AUTHOR]

Periderm is a well‐known structural feature with vital roles in protection of inner plant tissues and wound healing. Despite its importance to plant survival, knowledge of periderm occurrences outside the seed plants is limited and the evolutionary origins of periderm remain poorly explored. Here, we review the current knowledge of the taxonomic distribution of periderm in its two main forms – canonical periderm (periderm formed as a typical ontogenetic stage) and wound periderm (periderm produced as a self‐repair mechanism) – with a focus on major plant lineages, living and extinct. We supplement the published occurrences with data based on our own observations and experiments. This updated body of data reveals that the distribution of wound periderm is more widespread taxonomically than previously recognized and some living and extinct groups are capable of producing wound periderm, despite canonical periderm being absent from their normal developmental program. A critical review of canonical and wound periderms in extant and fossil lineages indicates that not all periderms are created equal. Their organisation is widely variable and the differences can be characterised in terms of variations in three structural features: (i) the consistency in orientation of periclinal walls within individual files of periderm cells; (ii) the lateral coordination of periclinal walls between adjacent cell files; and (iii) whether a cambial layer and conspicuous layering of inward and outward derivatives can be distinguished. Using a new system of scoring periderm structure based on these criteria, we characterise the level of organisation of canonical and wound periderms in different lineages. Looking at periderms through the lens provided by their level of organisation reveals that the traditional image of periderm as a single generalised feature, is best viewed as a continuum of structural configurations that are all predicated by the same basic process (periclinal divisions), but can fall anywhere between very loosely organized (diffuse periclinal growth) to very tightly coordinated (organized periclinal growth). Overall, wound periderms in both seed plants and seed‐free plants have lower degrees of organisation than canonical periderms, which may be due to their initiation in response to inherently disruptive traumatic events. Wound and canonical periderms of seed plants have higher degrees of organisation than those of seed‐free plants, possibly due to co‐option of the programs responsible for organizing their vascular cambial growth. Given the importance of wound periderm to plant survival, its widespread taxonomic distribution, and its early occurrence in the fossil record, we hypothesise that wound periderm may have had a single origin in euphyllophytes and canonical periderm may have originated separately in different lineages by co‐option of the basic regulatory toolkit of wound periderm formation. In one evolutionary scenario, wound periderm regulators activated initially by tissue tearing due to tensional stresses elicited by woody growth underwent heterochronic change that switched their activation trigger from tissue tearing to the tensional stresses that precede it, with corresponding changes in the signalling that triggered the regulatory cascade of periderm development from tearing‐induced signals to signalling induced by tension in cells. [ABSTRACT FROM AUTHOR]

SUMMARY: The evolutionary and ecological success of spermatophytes is intrinsically linked to the seed habit, which provides a protective environment for the initial development of the new generation. This environment includes an ephemeral nourishing tissue that supports embryo growth. In gymnosperms this tissue originates from the asexual proliferation of the maternal megagametophyte, while in angiosperms it is a product of fertilization, and is called the endosperm. The emergence of these nourishing tissues is of profound evolutionary value, and they are also food staples for most of the world's population. Here, using Orthofinder to infer orthologue genes among newly generated and previously published datasets, we provide a comparative transcriptomic analysis of seed nourishing tissues from species of several angiosperm clades, including those of early diverging lineages, as well as of one gymnosperm. Our results show that, although the structure and composition of seed nourishing tissues has seen significant divergence along evolution, there are signatures that are conserved throughout the phylogeny. Conversely, we identified processes that are specific to species within the clades studied, and thus illustrate their functional divergence. With this, we aimed to provide a foundation for future studies on the evolutionary history of seed nourishing structures, as well as a resource for gene discovery in future functional studies. Significance Statement: Within seeds a specialized structure is responsible for nourishing the embryo during its development. These nourishing tissues are also important sources of staple foods and feed. Here, we provide gene expression datasets of nourishing tissues of early diverging angiosperms, and use this information for a meta‐analysis to identify pathways conserved, or divergent, throughout evolution. Thus, we aim to provide a resource for gene discovery for seed biology studies. [ABSTRACT FROM AUTHOR]

Resource allocation theory posits that organisms distribute limited resources across functions to maximize their overall fitness. In plants, the allocation of resources among maintenance, reproduction, and growth influences short‐term economics and long‐term evolutionary processes, especially during resource scarcity. The evolution of specialized structures to divide labor between reproduction and growth can create a feedback loop where selection can act on individual organs, further increasing specializaton and resource allocation. Ferns exhibit diverse reproductive strategies, including dimorphism, where leaves can either be sterile (only for photosynthesis) or fertile (for spore dispersal). This dimorphism is similar to processes in seed plants (e.g., the production of fertile flowers and sterile leaves), and presents an opportunity to investigate divergent resource allocation between reproductive and vegetative functions in specialized organs. Here, we conducted anatomical and hydraulic analyses on Onoclea sensibilis L., a widespread dimorphic fern species, to reveal significant structural and hydraulic divergences between fertile and sterile leaves. Fertile fronds invest less in hydraulic architecture, with nearly 1.5 times fewer water‐conducting cells and a nearly 0.5 times less drought‐resistant xylem compared to sterile fronds. This comes at the increased relative investment in structural support, which may help facilitate spore dispersal. These findings suggest that specialization in ferns—in the form of reproductive dimorphism—can enable independent selection pressures on each leaf type, potentially optimizing spore dispersal in fertile fronds and photosynthetic efficiency in sterile fronds. Overall, our study sheds light on the evolutionary implications of functional specialization and highlights the importance of reproductive strategies in shaping plant fitness and evolution. [ABSTRACT FROM AUTHOR]

SUMMARY: L‐Arabinose (L‐Ara) is a plant‐specific sugar found in cell wall polysaccharides, proteoglycans, glycoproteins, and small glycoconjugates, which play physiologically important roles in cell proliferation and other essential cellular processes. L‐Ara is synthesized as UDP‐L‐arabinose (UDP‐L‐Ara) from UDP‐xylose (UDP‐Xyl) by UDP‐Xyl 4‐epimerases (UXEs), a type of de novo synthesis of L‐Ara unique to plants. In Arabidopsis, the Golgi‐localized UXE AtMUR4 is the main contributor to UDP‐L‐Ara synthesis. However, cytosolic bifunctional UDP‐glucose 4‐epimerases (UGEs) with UXE activity, AtUGE1, and AtUGE3 also catalyze this reaction. For the present study, we first examined the physiological importance of bifunctional UGEs in Arabidopsis. The uge1 and uge3 mutants enhanced the dwarf phenotype of mur4 and further reduced the L‐Ara content in cell walls, suggesting that bifunctional UGEs contribute to UDP‐L‐Ara synthesis. Through the introduction of point mutations exchanging corresponding amino acid residues between AtUGE1 with high UXE activity and AtUGE2 with low UXE activity, two mutations that increase relative UXE activity of AtUGE2 were identified. The crystal structures of AtUGE2 in complex forms with NAD+ and NAD+/UDP revealed that the UDP‐binding domain of AtUGE2 has a more closed conformation and smaller sugar‐binding site than bacterial and mammalian UGEs, suggesting that plant UGEs have the appropriate size and shape for binding UDP‐Xyl and UDP‐L‐Ara to exhibit UXE activity. The presented results suggest that the capacity for cytosolic synthesis of UDP‐L‐Ara was acquired by the small sugar‐binding site and several mutations of UGEs, enabling diversified utilization of L‐Ara in seed plants. [ABSTRACT FROM AUTHOR]

Seagrasses provide key ecological services in coastal marine and estuarine environments. Human activities and environmental changes affect seagrasses compromising their structure and functioning. In this context, seagrass restoration has become a worldwide priority to halt and reverse degradation and to recover ecosystem functionality and associated services. Here, we investigate the sexual reproduction of Posidonia oceanica by describing the flowering and fruiting process. Furthermore, we compare the structural (survival and shoot density) and functional (daily leaf production, DLP) descriptors of seedlings with those derived from a P. oceanica transplantation performed through cuttings to assess their feasibility as an integrative source of vegetal material for restoration purposes. Despite many initial flowers and fruits, a small number of mature fruits are produced, confirming the low reproductive success of the phanerogam. A comparison of structural and functional features showed that seedlings and cuttings showed similar survival and shoot density rates after more than 2 years. In addition, DLP showed that seedlings increased in leaf length over the study period, reaching a similar value registered by cuttings. The study demonstrates the effectiveness of using seedlings in restoration efforts. It also emphasizes the importance of exploring P. oceanica reproductive ecology to better understand temporal and spatial variations in flowering, as well as fruiting success, at local and basin scales. [ABSTRACT FROM AUTHOR]

Summary: Leaf venation is a pivotal trait in the success of vascular plants. Whereas gymnosperms have single or sparsely branched parallel veins, angiosperms developed a hierarchical structure of veins that form a complex reticulum. Its physiological consequences are considered to have enabled angiosperms to dominate terrestrial ecosystems in the Late Cretaceous and Cenozoic.Although a hierarchical‐reticulate venation also occurs in some groups of extinct seed plants, it is unclear whether these are stem relatives of angiosperms or have evolved these traits in parallel. Here, we re‐examine the morphology of the enigmatic foliage taxon Furcula, a potential early Mesozoic angiosperm relative, and argue that its hierarchical vein network represents convergent evolution (in the Late Triassic) with flowering plants (which developed in the Early Cretaceous) based on details of vein architecture and the absence of angiosperm‐like stomata and guard cells.We suggest that its nearest relatives are Peltaspermales similar to Scytophyllum and Vittaephyllum, the latter being a genus that originated during the Late Triassic (Carnian) and shares a hierarchical vein system with Furcula.We further suggest that the evolution of hierarchical venation systems in the early Permian, the Late Triassic, and the Early Cretaceous represent 'natural experiments' that might help resolve the selective pressures enabling this trait to evolve. [ABSTRACT FROM AUTHOR]

Summary: Ontogenetic shape change has long been recognized to be important in generating patterns of morphological diversity and may be especially important in plant reproductive structures. We explore how seed cone disparity in Cupressaceae changes over ontogeny by comparing pollination‐stage and mature cones.We sampled cones at pollen and seed release and measured cone scales using basic morphometric shape variables. We used multivariate statistical methods, particularly hypervolume overlap calculations, to measure morphospace occupation and disparity.Cone scales at both pollination and maturity exhibit substantial variability, although the disparity is greater at maturity. Mature cone scales are also more clustered in trait space, showing less overlap with other taxa than at pollination. These patterns reflect two growth strategies that generate closed cones over maturation, either through thin laminar scales or relatively thick, peltate scales, resulting in two distinct regions of morphospace occupation.Disparity patterns in Cupressaceae seed cones change over ontogeny, reflecting shifting functional demands that require specific patterns of cone scale growth. The evolution of Cupressaceae reproductive disparity therefore represents selection for trajectories of ontogenetic shape change, a phenomenon that should be widespread across seed plants. See also the Commentary on this article by Olson, 242: 1856–1859. [ABSTRACT FROM AUTHOR]

The evolution of the latitudinal diversity gradient (LDG), characterized by a peak in diversity toward the tropics, has captured significant attention in evolutionary biology and ecology. However, the inverse LDG (i‐LDG) mechanism, wherein species richness increases toward the poles, remains inadequately explored. Cycads are among one of the oldest lineages of extant seed plants and have undergone extensive diversification in the tropics. Intriguingly, the extant cycad abundance exhibits an i‐LDG pattern, and the underlying causes for this phenomenon remain largely elusive. Here, using 1,843 nuclear genes from a nearly complete sampling, we conducted comprehensive phylogenomic analyses to establish a robust species‐level phylogeny for Cycas, the largest genus within cycads. We then reconstructed the spatial‐temporal dynamics and integrated global environmental data to evaluate the roles of species ages, diversification rates, contemporary environment, and conservatism to ancestral niches in shaping the i‐LDG pattern. We found Cycas experienced decreased diversification rates, coupled with the cooling temperature since its origin in the Eocene from continental Asia. Different regions have distinctively contributed to the formation of i‐LDG for Cycas, with the northern hemisphere acting as evolutionary museums and the southern hemisphere serving as cradles. Moreover, water‐related climate variables, specifically precipitation seasonality and potential evapotranspiration, were identified as paramount factors constraining Cycas species richness in the rainforest biome near the equator. Notably, the adherence to ancestral monsoonal climates emerges as a critical factor in sustaining the diversity pattern. This study underscores the imperative of integrating both evolutionary and ecological approaches to comprehensively unravel the mechanisms underpinning global biodiversity patterns. [ABSTRACT FROM AUTHOR]

Beta diversity patterns are essential for understanding how biological communities are structured. Geographical and environmental factors, as well as species dispersal ability, are important drivers of beta diversity, but their relative importance may vary across spatial scales. In this study, we evaluate whether beta diversity changes across geographical scales and analyse how different drivers affect turnover patterns of native seed plants in an oceanic archipelago, the Azores (Portugal). Using a 500 × 500 m resolution grid, we selected cells that are covered by one of the following habitats: native forest, naturalized vegetation and seminatural pastures. We calculated species turnover at three spatial scales: 1) between islands, 2) between cells within each island, and finally 3) between cells of each of the habitats of interest in each island. We then calculated the contribution of dispersal syndromes (endozoochory, epizoochory, hydrochory and anemochory) to turnover at each of the scales. Lastly, we assessed the relationship between geographical and climatic distances and habitat type with turnover. Turnover was higher at the smallest spatial scale, particularly in seminatural pastures, and decreased with increasing spatial scales, a pattern potentially associated with the historical fragmentation and current patchy distribution of native forest and seminatural habitats in the Azores. Dispersal syndromes and habitat type had a negligible effect on turnover at all scales. Geographical distance had a positive effect on turnover at all scales, increasing its importance with scale. The relationship between turnover and climatic distance was only significant at the intermediate and small scales in specific islands and habitats. Therefore, scale plays an important role at determining the effect of the drivers of turnover, in particular geographical and climatic distance. These results highlight the need to carefully select the scale of analysis when studying turnover patterns, as well as identifying the potential drivers associated with each spatial scale. [ABSTRACT FROM AUTHOR]

Vertebrate‐mediated seed dispersal is a common attribute of many living plants, and variation in the size and abundance of fleshy diaspores is influenced by regional climate and by the nature of vertebrate seed dispersers among present‐day floras. However, potential drivers of large‐scale variation in the abundance and size distributions of fleshy diaspores through geological time, and the importance of geographic variation, are incompletely known. This knowledge gap is important because fleshy diaspores are a key mechanism of energy transfer from photosynthesis to animals and may in part explain the diversification of major groups within birds and mammals. Various hypotheses have been proposed to explain variation in the abundance and size distribution of fleshy diaspores through time, including plant–frugivore co‐evolution, angiosperm diversification, and changes in vegetational structure and climate. We present a new data set of more than 800 georeferenced fossil diaspore occurrences spanning the Triassic–Oligocene, across low to mid‐ to high palaeolatitudes. We use this to quantify patterns of long‐term change in fleshy diaspores, examining the timing and geographical context of important shifts as a test of the potential evolutionary and climatic explanations. We find that the fleshy fruit sizes of angiosperms increased for much of the Cretaceous, during the early diversification of angiosperms from herbaceous ancestors with small fruits. Nevertheless, this did not cause a substantial net change in the fleshy diaspore size distributions across seed plants, because gymnosperms had achieved a similar size distribution by at least the Late Triassic. Furthermore, gymnosperm‐dominated Mesozoic ecosystems were mostly open, and harboured low proportions of specialised frugivores until the latest Cretaceous, suggesting that changes in vegetation structure and plant–frugivore co‐evolution were probably not important drivers of fleshy diaspore size distributions over long timescales. Instead, fleshy diaspore size distributions may be largely constrained by physical or life‐history limits that are shared among groups and diversify as a plant group expands into different growth forms/sizes, habitats, and climate regimes. Mesozoic gymnosperm floras had a low abundance of fleshy diaspores (<50% fleshy diaspore taxa), that was surpassed by some low‐latitude angiosperm floras in the Cretaceous. Eocene angiosperm floras show a mid‐ to high latitude peak in fleshy fruit abundance, with very high proportions of fleshy fruits that even exceed those seen at low latitudes both in the Eocene and today. Mid‐ to high latitude proportions of fleshy fruits declined substantially over the Eocene–Oligocene transition, resulting in a shift to more modern‐like geographic distributions with the highest proportion of fleshy fruits occurring in low‐latitude tropical assemblages. This shift was coincident with global cooling and the onset of Southern Hemisphere glaciation, suggesting that rapid cooling at mid‐ and high latitudes caused a decrease in availability of the climate conditions most favourable for fleshy fruits in angiosperms. Future research could be focused on examining the environmental niches of modern fleshy fruits, and the potential effects of climate change on fleshy fruit and frugivore diversity. [ABSTRACT FROM AUTHOR]

The phytohormone abscisic acid (ABA) is synthesised by plants during drought to close stomata and regulate desiccation tolerance pathways. Conifers and some angiosperms with embolism‐resistant xylem show a peaking‐type (p‐type) response in ABA levels, in which ABA levels increase early in drought then decrease as drought progresses, declining to pre‐stressed levels. The mechanism behind this dynamic remains unknown. Here, we sought to characterise the mechanism driving p‐type ABA dynamics in the conifer Callitris rhomboidea and the highly drought‐resistant angiosperm Umbellularia californica. We measured leaf water potentials (Ψl), stomatal conductance, ABA, conjugates and phaseic acid (PA) levels in potted plants during a prolonged but non‐fatal drought. Both species displayed a p‐type ABA dynamic during prolonged drought. In branches collected before and after the peak in endogenous ABA levels in planta, that were rehydrated overnight and then bench dried, ABA biosynthesis was deactivated beyond leaf turgor loss point. Considerable conversion of ABA to conjugates was found to occur during drought, but not catabolism to PA. The mechanism driving the decline in ABA levels in p‐type species may be conserved across embolism‐resistant seed plants and is mediated by sustained conjugation of ABA and the deactivation of ABA accumulation as Ψl becomes more negative than turgor loss. Summary Statement: We find that abscisic acid biosynthesis is deactivated after leaf turgor loss point during extreme drought, but that the conjugation of ABA to inactive forms remains constant, leading to a decline in ABA levels in embolism‐resistant species. [ABSTRACT FROM AUTHOR]

SUMMARY: DELAY OF GERMINATION 1 is a key regulator of dormancy in flowering plants before seed germination. Bryophytes develop haploid spores with an analogous function to seeds. Here, we investigate whether DOG1 function during germination is conserved between bryophytes and flowering plants and analyse the underlying mechanism of DOG1 action in the moss Physcomitrium patens. Phylogenetic and in silico expression analyses were performed to identify and characterise DOG1 domain‐containing genes in P. patens. Germination assays were performed to characterise a Ppdog1‐like1 mutant, and replacement with AtDOG1 was carried out. Yeast two‐hybrid assays were used to test the interaction of the PpDOG1‐like protein with DELLA proteins from P. patens and A. thaliana. P. patens possesses nine DOG1 domain‐containing genes. The DOG1‐like protein PpDOG1‐L1 (Pp3c3_9650) interacts with PpDELLAa and PpDELLAb and the A. thaliana DELLA protein AtRGA in yeast. Protein truncations revealed the DOG1 domain as necessary and sufficient for interaction with PpDELLA proteins. Spores of Ppdog1‐l1 mutant germinate faster than wild type, but replacement with AtDOG1 reverses this effect. Our data demonstrate a role for the PpDOG1‐LIKE1 protein in moss spore germination, possibly alongside PpDELLAs. This suggests a conserved DOG1 domain function in germination, albeit with differential adaptation of regulatory networks in seed and spore germination. Significance Statement: Seed and spore germination are considered analogous because they occur in the sporophyte (seed plants) and gametophyte (bryophytes). Here we show that an ortholog of Arabidopsis DELAY OF GERMINATION 1 (DOG1) controls spore germination in the moss P. patens, suggesting deep evolutionary conservation of germination control of reproductive diaspores. [ABSTRACT FROM AUTHOR]

Aim: In Taiwan island, recent land‐bridge and oversea dispersal after the appearance of proto‐Taiwan (<6.5 Ma) is responsible for its biodiversity assembly. Radiations have also been widely reported in mountain systems. The tempo‐spatial route to the floral hotspot was determined through a meta‐analysis of the evolution of endemic plants. Location: Taiwan island and its adjacent regions. Taxon: Seed plants. Methods: Published dated phylogenies were compiled to infer the origin times represented by the stem ages. To determine the speciation mode, either in situ origin or dispersal origin, the ancestral range shift pattern and/or current distribution range of the sister taxa were used with 10 different biogeographical regions classified. Histograms quantifying the numbers of different origin modes within bins of 0.5 Ma were constructed. Probabilities of long‐distance dispersal (LDD) were evaluated. Results: The 125 sampled species originate between the late Eocene and late Pleistocene, of which 14 (11.2%) and 111 (88.8%) were derived before and after the emergence of proto‐Taiwan, respectively. Spatially, in situ speciation would have a bigger contribution to the formation of endemism than dispersal events (56.8% vs. 43.2%). The species with in situ origin (mean = 1.83 Ma) were significantly younger than those with dispersal origin (mean = 6.34 Ma). The main regions where dispersal occurred were South‐Central China (n = 29) and Southeast China (n = 28), followed by Japan (n = 14). High probabilities (60.8%) of LDD were found. Main Conclusions: Spatially, recent land‐bridge and oversea dispersal from the adjacent Asian flora is supported and the southern part of China was found to be the most important source. In situ speciation that may have correlated with mountain uplift, monsoon intensification and Pleistocene climatic fluctuations exerted greater contributions to the biodiversity there. Temporally, floral endemism predominantly occurred after the emergence of proto‐Taiwan. Additional investigations with more sophisticated sampling and genetic data are needed in the future. [ABSTRACT FROM AUTHOR]

Summary: Seed germination is a vital developmental transition for the production of progeny by sexual reproduction in spermatophytes. The seed‐to‐seedling transition is predominately driven by hypocotyl cell elongation. However, the mechanism that underlies hypocotyl growth remains largely unknown.In this study, we characterized the actin array reorganization in embryonic hypocotyl epidermal cells. Live‐cell imaging revealed a basally organized actin array formed during hypocotyl cell elongation. This polarized actin assembly is a barrel‐shaped network, which comprises a backbone of longitudinally aligned actin cables and a fine actin cap linking these cables.We provide genetic evidence that the basal actin array formation requires formin‐mediated actin polymerization and directional movement of actin filaments powered by myosin XIs. In fh1‐1 and xi3ko mutants, actin filaments failed to reorganize into the basal actin array, and the hypocotyl cell elongation was inhibited compared with wild‐type plants.Collectively, our work uncovers the molecular mechanisms for basal actin array assembly and demonstrates the connection between actin polarization and hypocotyl elongation during seed‐to‐seedling transition. [ABSTRACT FROM AUTHOR]

SUMMARY: The non‐seed plants (e.g., charophyte algae, bryophytes, and ferns) have multiple human uses, but their contributions to agriculture and research have lagged behind seed plants. While sharing broadly conserved biology with seed plants and the major crops, non‐seed plants sometimes possess alternative molecular and physiological adaptations. These adaptations may guide crop improvements. One such area is the presence of multiple classes of insecticidal proteins found in non‐seed plant genomes which are either absent or widely diverged in seed plants. There are documented uses of non‐seed plants, and ferns for example have been used in human diets. Among the occasional identifiable toxins or antinutritive components present in non‐seed plants, none include these insecticidal proteins. Apart from these discrete risk factors which can be addressed in the safety assessment, there should be no general safety concern about sourcing genes from non‐seed plant species. Significance Statement: Lower plants such as ferns and mosses are underexplored resources for agriculture. Recent investigations have revealed that lower plants contain genes for insecticidal proteins that are now being leveraged for transgenic crop improvement. [ABSTRACT FROM AUTHOR]

Summary: Heterogeneity in gene trees, morphological characters, and composition has been associated with several major plant clades. Here, we examine heterogeneity in composition across a large transcriptomic dataset of plants to better understand whether locations of shifts in composition are shared across gene regions and whether directions of shifts within clades are shared across gene regions.We estimate mixed models of composition for both nucleotide and amino acids across a recent large‐scale transcriptomic dataset for plants.We find shifts in composition across both nucleotide and amino acid datasets, with more shifts detected in nucleotides. We find that Chlorophytes and lineages within experience the most shifts. However, many shifts occur at the origins of land, vascular, and seed plants. While genes in these clades do not typically share the same composition, they tend to shift in the same direction. We discuss potential causes of these patterns.Compositional heterogeneity has been highlighted as a potential problem for phylogenetic analysis, but the variation presented here highlights the need to further investigate these patterns for the signal of biological processes. [ABSTRACT FROM AUTHOR]

Summary: Phytochromes are photoreceptors enabling plants to respond to various light conditions. Independent gene duplications resulted in small phytochrome families in mosses, ferns and seed plants. This phytochrome diversity is hypothesised to be critical for sensing and adapting to different light conditions, but experimental evidence for this idea is lacking for mosses and ferns.The moss model species Physcomitrium patens contains seven phytochromes grouped into three clades, PHY1/3, PHY2/4 and PHY5. Here, we used CRISPR/Cas9‐generated single and higher order mutants to investigate their role in light regulation of protonema and gametophore growth, protonema branching and induction of gametophores.We found both specific and partially overlapping roles for the three phytochrome clades in regulating these responses in different light conditions. PHY1/3 clade phytochromes act as primary far‐red light receptors, while PHY5 clade phytochromes are the primary red light receptors. PHY2/4 clade phytochromes have functions in both red and far‐red light. We also observed that PHY1/3 and PHY2/4 clade phytochromes promote gametophore growth in simulated canopy shade and also play a role in blue light.Similar to seed plants, gene duplications in the phytochrome lineage in mosses were followed by functional diversification into red and far‐red light‐sensing phytochromes. [ABSTRACT FROM AUTHOR]

Although plastid genome (plastome) structure is highly conserved across most seed plants, investigations during the past two decades have revealed several disparately related lineages that experienced substantial rearrangements. Most plastomes contain a large inverted repeat and two single‐copy regions, and a few dispersed repeats; however, the plastomes of some taxa harbour long repeat sequences (>300 bp). These long repeats make it challenging to assemble complete plastomes using short‐read data, leading to misassemblies and consensus sequences with spurious rearrangements. Single‐molecule, long‐read sequencing has the potential to overcome these challenges, yet there is no consensus on the most effective method for accurately assembling plastomes using long‐read data. We generated a pipeline, plastid Genome Assembly Using Long‐read data (ptGAUL), to address the problem of plastome assembly using long‐read data from Oxford Nanopore Technologies (ONT) or Pacific Biosciences platforms. We demonstrated the efficacy of the ptGAUL pipeline using 16 published long‐read data sets. We showed that ptGAUL quickly produces accurate and unbiased assemblies using only ~50× coverage of plastome data. Additionally, we deployed ptGAUL to assemble four new Juncus (Juncaceae) plastomes using ONT long reads. Our results revealed many long repeats and rearrangements in Juncus plastomes compared with basal lineages of Poales. The ptGAUL pipeline is available on GitHub: https://github.com/Bean061/ptgaul. [ABSTRACT FROM AUTHOR]

Aim: Significant changes in species elevational ranges in mountains have been repeatedly documented, yet the direction, magnitude and drivers of these shifts remain controversial. Presently, there is still lacking evidence about the general nature of species elevational range shifts in eastern Eurasia in response to anthropogenic climate change. By using historical specimen records and recent field observations for 735 seed plant species across 29 China's mountains, we assessed changes in species' elevational centroids and their drivers. Location: China. Time Period: 1950–2018. Major Taxa Studied: Seed plant species. Methods: The elevation records of all sampled occurrences in each mountain during the two time periods were estimated, and the null models were developed to test the sampling bias. Ecological niche models (ENMs) were used to evaluate the relative importance of climate factors in constraining each species distribution. Generalized linear models (GLMs) to test the relationships between the centroid elevational range shifts of species and different divers. Results: We found that 54% of the species shifting upward and 46% downhill. However, species' elevational shifts significantly differed among species and mountains. Herbaceous and lowland species moved upward faster than woody and high‐elevation species. Species in temperate mountains and in mountains with taller elevational gradients moved upward, while species in subtropical mountains and in mountains with shorter elevational gradients moved downward. Precipitation changes experienced by species, species' climatic adaptations, several species' functional traits and mountain size all contributed to explain the magnitude of species' centroid elevational range shifts. Main Conclusions: Our results highlight complex biodiversity redistribution of seed plants across Chinese mountains, not necessarily conforming to the trend of species upward shifts in elevation. Changes in precipitation regimes may blur the simplistic assumption of isotherm tracking. This study fills an important geographic shortfall for our understanding of biodiversity redistribution under anthropogenic climate change. [ABSTRACT FROM AUTHOR]

Premise: In recent years, Doyleales have played an important role in the discussion and exploration of seed plant relationships and the origin of angiosperms. This order comprises a diversity of recently described genera with cupule‐bearing compound ovulate cones recovered from Early Cretaceous deposits in North America and Asia. Their relatively late appearance in the fossil record, stratigraphically near the appearance of angiosperms in the Early Cretaceous, has been noteworthy. Here, we report a new genus of Doyleales, Zirabia gen. nov. from the Early Jurassic of Iran, that was originally described as the ginkgophyte Karkenia. Methods: We reinvestigated material previously assigned to Karkenia cylindrica from the Lower Jurassic of the Zirab locality, Alborz Mountains, northern Iran. Results: The studied specimen features a main axis bearing helically to irregularly arranged bract‐cupule complexes, each composed by a long laminar bract subtending and sheathing a cupule stalk that bears a single‐seeded cupule with a dorsal protrusion. The morphological features of this taxon do not conform with those of Karkenia, and suggest affinities with Doyleales rather than Ginkgoales. Within Doyleales, this fossil has a unique combination of characters indicating that it is a new genus within the order; thus, a new combination is erected, Zirabia cylindrica. Conclusions: Our results indicate that Doyleales is significantly older than previously thought, with their stratigraphic range now extending from the Lower Jurassic to the Cretaceous. The Early Jurassic occurrence of Doyleales provides important data on the emergence of seed‐enclosing structures seen in seed plants throughout the Mesozoic. [ABSTRACT FROM AUTHOR]

Summary: The root system architecture in plants is a result of multiple evolutionary innovations over time in response to changing environmental cues. Dichotomy and endogenous lateral branching in the roots evolved in lycophytes lineage but extant seed plants use lateral branching instead. This has led to the development of complex and adaptive root systems, with lateral roots playing a key role in this process exhibiting conserved and divergent features in different plant species. The study of lateral root branching in diverse plant species can shed light on the orderly yet distinct nature of postembryonic organogenesis in plants. This insight provides an overview of the diversity in lateral root (LR) development in various plant species during the evolution of root system in plants. [ABSTRACT FROM AUTHOR]

Summary: The Cycadales are an ancient and charismatic group of seed plants. However, their morphological evolution in deep time is poorly understood. While molecular divergence time analyses estimate a Cretaceous origin for most major living cycad clades, much of the extant diversity is inferred to be a result of Neogene diversifications. This leads to long branches throughout the cycadalean phylogeny that, with few exceptions, have yet to be rectified by unequivocal fossil cycads.We report a permineralized pollen cone from the Campanian Holz Shale located in Silverado Canyon, CA, USA (c. 80 million yr ago). This fossil was studied via serial sectioning, SEM, 3D reconstruction and phylogenetic analyses.Microsporophyll and pollen morphology indicate this cone is assignable to Skyttegaardia, a recently described genus based on disarticulated lignitized microsporophylls from the Early Cretaceous of Denmark. Data from this new species, including a simple cone architecture, anatomical details and vasculature organization, indicate cycadalean affinities for Skyttegaardia. Phylogenetic analyses support this assignment and recover Skyttegaardia as crown‐group Cycadales, nested within Zamiaceae.Our findings support a Cretaceous diversification for crown‐group Zamiaceae, which included the evolution of morphological divergent extinct taxa with unique traits that have yet to be widely identified in the fossil record. [ABSTRACT FROM AUTHOR]

SUMMARY: Significant changes have occurred in plant cell wall composition during evolution and diversification of tracheophytes. As the sister lineage to seed plants, knowledge on the cell wall of ferns is key to track evolutionary changes across tracheophytes and to understand seed plant‐specific evolutionary innovations. Fern cell wall composition is not fully understood, including limited knowledge of glycoproteins such as the fern arabinogalactan proteins (AGPs). Here, we characterize the AGPs from the leptosporangiate fern genera Azolla, Salvinia, and Ceratopteris. The carbohydrate moiety of seed plant AGPs consists of a galactan backbone including mainly 1,3‐ and 1,3,6‐linked pyranosidic galactose, which is conserved across the investigated fern AGPs. Yet, unlike AGPs of angiosperms, those of ferns contained the unusual sugar 3‐O‐methylrhamnose. Besides terminal furanosidic arabinose, Ara (Araf), the main linkage type of Araf in the ferns was 1,2‐linked Araf, whereas in seed plants 1,5‐linked Araf is often dominating. Antibodies directed against carbohydrate epitopes of AGPs supported the structural differences between AGPs of ferns and seed plants. Comparison of AGP linkage types across the streptophyte lineage showed that angiosperms have rather conserved monosaccharide linkage types; by contrast bryophytes, ferns, and gymnosperms showed more variability. Phylogenetic analyses of glycosyltransferases involved in AGP biosynthesis and bioinformatic search for AGP protein backbones revealed a versatile genetic toolkit for AGP complexity in ferns. Our data reveal important differences across AGP diversity of which the functional significance is unknown. This diversity sheds light on the evolution of the hallmark feature of tracheophytes: their elaborate cell walls. [ABSTRACT FROM AUTHOR]

Aim: How spatial, historical and ecological processes drive diversity patterns remains one of the main foci of island biogeography. We determined how beta diversity varies across spatial scales and among organisms, disentangled the drivers of this variation, and examined how, consequently, biogeographic affinities within and among archipelagos vary among land plants. Location: Macaronesia. Taxon: Bryophytes, pteridophytes, spermatophytes. Methods: Species turnover and nestedness were compared within and among archipelagos across taxonomic groups. The relationship between species turnover and nestedness, climatic, geological and geographic factors was analysed using generalized dissimilarity models. Results: Species turnover, but not nestedness, increased with the geographic scale. This increment decreased from spermatophytes, pteridophytes and bryophytes, wherein the median turnover was less than half that in spermatophytes. Bryophytes exhibited a significantly higher nestedness and lower turnover than spermatophytes. Extant climatic conditions and island age contributed the most to all models but the importance of island age for bryophyte and pteridophyte turnover was marginal. Spermatophyte floras clustered by archipelago, whereas the clustering patterns in pteridophyte and bryophyte floras reflected macroclimatic conditions. Main Conclusions: The lower increment of species turnover with spatial scale and the higher nestedness in bryophytes and pteridophytes than in spermatophytes reflect the variation in dispersal capacities and distribution ranges among land plants. Accordingly, extant climatic conditions contributed more to explain turnover in bryophytes and pteridophytes than in spermatophytes, whereas factors associated with dispersal limitations, including island age, geographic distance and archipelago structure, exhibited the reverse trend. The differences in beta diversity patterns, caused by different responses of Macaronesian land plant lineages to the main factors shaping their community composition, explain their different biogeographic affinities. These differences reflect a distinct origin and different mechanisms of speciation among Macaronesian land plant lineages and archipelagos. [ABSTRACT FROM AUTHOR]

DNA barcode databases are increasingly available for a range of organisms, facilitating the wide application of DNA barcode‐based studies. Here we announce the development of a comprehensive DNA barcode reference library of Japanese native woody seed plants representing 43 orders, 99 families, 303 genera and 834 species, and comprising 77.3% of the genera and 72.2% of the species of native woody seed plants in Japan. A total of 6216 plant specimens were collected from 223 sites across the subtropical, temperate, boreal and alpine biomes in Japan with most species represented by multiple accessions. This reference library utilized three chloroplast DNA regions (rbcL, trnH‐psbA and matK) and consists of 14,403 barcode sequences. Individual regions varied in their identification rates, with species‐level and genus‐level rates for rbcL, trnH‐psbA and matK based on blast being 57.4%/96.2%, 78.5%/99.1% and 67.8%/98.1%, respectively. Identification rates were higher using region combinations, with total species‐level rates for two region combinations (rbcL & trnH‐psbA, rbcL & matK and trnH‐psbA & matK) ranging between 90.6% and 95.8%, and for all three regions being equal to 98.6%. Genus‐level identification rates were even higher, ranging between 99.7% and 100% for two region combinations and being 100% for the three regions. These results indicate that this DNA barcode reference library is an effective resource for investigations of native woody seed plants in Japan using DNA barcodes and provides a useful template for the development of libraries for other components of the Japanese flora. [ABSTRACT FROM AUTHOR]

Eumaeus butterflies are obligate herbivores of Zamia, the most diverse neotropical genus of cycads. Eumaeus–Zamia interactions have been characterized mainly for species distributed in North and Central America. However, larval host plant use by the southern Eumaeus clade remains largely unknown, precluding a comprehensive study of co‐evolution between the genera. Here, we combine fieldwork with museum and literature surveys to expand herbivory records for Eumaeus from 21 to 38 Zamia species. We inferred a time‐calibrated phylogeny of Eumaeus to test for distinct macroevolutionary scenarios of larval host plant conservatism and co‐evolution. We found a remarkable coincidence between Eumaeus and Zamia diversification, with the butterfly stem group diverging at the same time as the most recent radiation of Zamia in the Miocene. Cophylogenetic reconciliation analyses show a strong cophylogenetic signal between cycads and their butterfly herbivores. Bipartite model‐based approaches indicate that this is because closely related Zamia species are used by the same Eumaeus species, suggesting larval host plant resource tracking by the butterfly herbivores. Our results highlight a case of tight evolution between Eumaeus butterflies and cycads, pointing to the generality of correlated evolution and phylogenetic tracking in plant–herbivore interactions across seed plants. [ABSTRACT FROM AUTHOR]

Increased access to genome‐wide data provides new opportunities for plant conservation. However, information on neutral genetic diversity in a small number of marker loci can still be valuable because genomic data are not available to most rare plant species. In the hope of bridging the gap between conservation science and practice, we outline how conservation practitioners can more efficiently employ population genetic information in plant conservation. We first review the current knowledge about neutral genetic variation (NGV) and adaptive genetic variation (AGV) in seed plants, regarding both within‐population and among‐population components. We then introduce the estimates of among‐population genetic differentiation in quantitative traits (QST) and neutral markers (FST) to plant biology and summarize conservation applications derived from QST–FST comparisons, particularly on how to capture most AGV and NGV on both in‐situ and ex‐situ programs. Based on a review of published studies, we found that, on average, two and four populations would be needed for woody perennials (n = 18) to capture 99% of NGV and AGV, respectively, whereas four populations would be needed in case of herbaceous perennials (n = 14). On average, QST is about 3.6, 1.5, and 1.1 times greater than FST in woody plants, annuals, and herbaceous perennials, respectively. Hence, conservation and management policies or suggestions based solely on inference on FST could be misleading, particularly in woody species. To maximize the preservation of the maximum levels of both AGV and NGV, we suggest using maximum QST rather than average QST. We recommend conservation managers and practitioners consider this when formulating further conservation and restoration plans for plant species, particularly woody species. [ABSTRACT FROM AUTHOR]

Most seed plants produce both pollen and ovules. In principle, pollen export could interfere with pollen import through self‐pollination, resulting in ovule usurpation and reduced fruit set. Evidence for such interference exists under experimental settings but its importance under natural conditions is unknown. To test for sexual interference in nature, it is necessary to study together mating system, through paternity analyses, and fruit set, the proportion of flowers giving seeds or fruits. We developed a new model combining both processes, using chestnut (Castanea) as case study. We carried out a paternity analysis in an intensively studied plot of 273 trees belonging to three interfertile chestnut species and including a range of individuals with more or less functional stamens, resulting in a large data set of 1924 mating events. We then measured fruit set on 216 of these trees. Fruit set of male‐fertile trees was much lower than that of male‐sterile trees. Our process‐based model shows that pollen is not limiting in the study site and hence cannot account for reduced fruit set. It also indicates that self‐pollination is high (74%) but selfing rate is low (4%). Self‐pollen is less competitive than cross‐pollen, reducing sexual interference, but not sufficiently, as many ovules end up being self‐fertilized, 95% of which abort before fruit formation, resulting in the loss of 46% of the fruit crop. These results suggest that the main cause of reduced reproductive potential in chestnut is sexual interference by self‐pollen, raising questions on its evolutionary origins. [ABSTRACT FROM AUTHOR]

N‐terminal cysteine oxidases (NCOs) use molecular oxygen to oxidise the amino‐terminal cysteine of specific proteins, thereby initiating the proteolytic N‐degron pathway. To expand the characterisation of the plant family of NCOs (plant cysteine oxidases [PCOs]), we performed a phylogenetic analysis across different taxa in terms of sequence similarity and transcriptional regulation. Based on this survey, we propose a distinction of PCOs into two main groups. A‐type PCOs are conserved across all plant species and are generally unaffected at the messenger RNA level by oxygen availability. Instead, B‐type PCOs appeared in spermatophytes to acquire transcriptional regulation in response to hypoxia. The inactivation of two A‐type PCOs in Arabidopsis thaliana, PCO4 and PCO5, is sufficient to activate the anaerobic response in young seedlings, whereas the additional removal of B‐type PCOs leads to a stronger induction of anaerobic genes and impairs plant growth and development. Our results show that both PCO types are required to regulate the anaerobic response in angiosperms. Therefore, while it is possible to distinguish two clades within the PCO family, we conclude that they all contribute to restrain the anaerobic transcriptional programme in normoxic conditions and together generate a molecular switch to toggle the hypoxic response. Summary statement: Hypoxic induction of plant cysteine oxidases has been acquired and fixed in seed plants from ancestral proteins able to initiate the proteolysis of Cys‐initiating protein substrates by the Arg/N‐degron pathway. [ABSTRACT FROM AUTHOR]

Premise: Rhizomatous growth characterizes numerous taxa among vascular plants. While abundant information exists on nutrient sharing and demography, the question of how these metameric organisms move water through their bodies remains largely unstudied. Moreover, we lack an understanding of the evolutionary implications of rhizomatous growth across vascular plants. Here, we examined these questions by investigating how rhizomatous growth and vascular construction affect whole‐plant hydraulic function. Methods: In five terrestrial fern species with diverse vascular construction, we used microcomputed tomography and bright‐field microscopy to examine vascular construction across nodes along the rhizome. These data were integrated with measurements of leaf stomatal conductance under rooted and uprooted conditions to relate vascular patterning and hydraulic architecture to leaf water status. Results: Similar to phytomers of woody seed plants, nodal regions in rhizomatous ferns are areas of hydraulic resistance. While water is shared along the rhizomes of these investigated species, hydraulic conductivity drops at nodes and stomatal conductance declines when nodes were locally uprooted. Together, our data suggest that nodes are chokepoints in axial water movement along the rhizome. Conclusions: Nodal chokepoints decrease hydraulic integration between phytomers. At the same time, chokepoints may act as "safety valves", hydraulically localizing each phytomer—potentially decreasing embolism and pathogen spread. This suggests a potential trade‐off in the principal construction of the fern rhizome. Moreover, we propose that shoot‐borne roots (homorhizy) and the prostrate habit of rhizomatous ferns decrease the hydraulic and structural burdens that upright plants typically incur. The absence of these hydraulic and structural demands may be one reason ferns (and many rhizomatous plants) lack, or have minimally developed, secondary xylem. [ABSTRACT FROM AUTHOR]

Premise: Trimerophytes are a plexus of early tracheophytes that form the base of the euphyllophyte clade and, thus, represent the link between the earliest land plants and modern‐day ferns, sphenophytes, and seed plants. As the best‐characterized trimerophyte, the genus Psilophyton occupies a key position in the euphyllophyte fossil record. We describe a new Psilophyton species that has implications for the evolution of plant–animal interactions. Methods: The fossil material is preserved by permineralization in the Lower Devonian (Emsian) Battery Point Formation (Québec, Canada) and was studied in serial sections using the cellulose acetate peel technique. Results: Psilophyton diakanthon sp. nov. differs from other Psilophyton species in possessing fibers that form a discontinuous layer in the inner cortex and two distinct types of spinescent emergences whose anatomy and morphology are consistent with roles in anti‐herbivore defense. Conclusions: Psilophyton diakanthon adds another species to an already diverse genus. Its two morphologically distinct types of spinescence suggest that herbivory was rampant in plant–animal interactions and demonstrate that anti‐herbivory defenses had reached a previously unrecognized level of sophistication by 400 million years ago, in the Early Devonian. [ABSTRACT FROM AUTHOR]

Current and previous studies have extensively studied the physiological and ecological consequences of genome size (GS) on plants because of the limiting effect of GS on cell size. However, it is still obscure whether such limiting effect could be shifted by environmental pressures, or not. Here, we compiled a global dataset comprised of GS, xylem vessel diameter (Vdia), xylem hydraulic conductivity (KS), P50 (xylem water potential at the loss of 50% maximum KS), and climate factors of 251 phylogeny and habitat divergent species from 59 families. The results showed that GS could limit the Vdia of the species from the same family sampled in the similar climate conditions. But the expected positive relationship between GS and Vdia became uncertain and even negative across different environmental conditions. Vdia was strongly positively coordinated with mean annual temperature (MAT), mean annual precipitation (MAP), and potential evapotranspiration (PET). Furthermore, Vdia as the anatomic foundation of plant hydraulic performance was strongly positively coordinated with KS and negatively coordinated with −P50. The strong environmental selection on KS and P50 explained the concerted regulation of Vdia by environmental factors. The findings revealed the combined regulation of GS and environmental pressures on xylem cell size and thus affected plant eco‐physiological performance. The shifted cell size limiting effect of GS by environmental factors manifests plants great plasticity under changed environmental conditions. [ABSTRACT FROM AUTHOR]

The plant economics spectrum describes the trade‐off between plant resource acquisition and storage, and sheds light on plant responses to environmental changes. However, the data used to construct the plant economics spectrum comes mainly from seed plants, thereby neglecting vascular non‐seed plant lineages such as the ferns. To address this omission, we evaluated whether a fern economics spectrum exists using leaf and root traits of 23 fern species living under three subtropical forest conditions differing in light intensity and nutrient gradients. The fern leaf and root traits were found to be highly correlated and formed a plant economics spectrum. Specific leaf mass and root tissue density were found to be on one side of the spectrum (conservative strategy), whereas photosynthesis rate, specific root area, and specific root length were on the other side of the spectrum (acquisitive strategy). Ferns had higher photosynthesis and respiration rates, and photosynthetic nitrogen‐use efficiency under high light conditions and higher specific root area and lower root tissue density in high nutrient environments. However, environmental changes did not significantly affect their resource acquisition strategies. Thus, the plant economics spectrum can be broadened to include ferns, which expands its phylogenetic and ecological implications and utility. [ABSTRACT FROM AUTHOR]

The delivery of sperm cells via tip‐growing pollen tubes is an innovation of seed plants and shows the importance of pollen tubes for reproduction and their specific growth kinetics. Fast‐growing pollen tubes demand an extensive and dynamic vesicular trafficking network to build new cell membrane and wall, to deliver proteins among endomembrane compartments, and also to respond to external stimuli for growth adjustment. In this review, we summarize current findings on endomembrane compartments and vesicular trafficking routes of pollen tubes, comparing and contrasting their features with those of most somatic cells. We discuss the importance of membrane homeostasis, either at the plasma membrane (PM) or between PM‐targeted trafficking and vacuolar trafficking, for pollen tube growth. We also provide perspectives to facilitate future studies of vesicular trafficking in pollen tubes. [ABSTRACT FROM AUTHOR]

Summary: MicroRNA (miRNA)‐directed posttranscriptional gene silencing (miR‐PTGS) is an integral component of gene regulatory networks governing plant development and responses to the environment. The sequence homology between Sly‐miR4376, a miRNA common to Solanaceae and reported to target autoinhibited Ca2+‐ATPase 10 (ACA10) messenger RNA (mRNA) in tomato, and Arabidopsis miR391 (Ath‐miR391), previously annotated as a nonconserved member of the deeply conserved miR390 family, has prompted us to revisit the function of Ath‐miR391, as well as its regulatory conservation.A combination of genetic, molecular, and bioinformatic analyses revealed a hidden conservation for miR‐PTGS of ACA10 homologs in spermatophytes.We found that the Arabidopsis ACA10 mRNA undergoes miR391‐directed cleavage in vivo. Furthermore, transgenic overexpression of miR391 recapitulated the compact inflorescence (cif) phenotypes characteristic of ACA10 loss‐of‐function mutants, due to miR391‐directed PTGS of ACA10. Significantly, comprehensive data mining revealed robust evidence for widespread PTGS of ACA10 homologs directed by a superfamily of related miRNAs sharing a conserved sequence core. Intriguingly, the ACA‐targeting miRNAs in Poaceae also direct PTGS for calmodulin‐like proteins which are putative Ca2+ sensors.The PTGS of ACA10 homologs is therefore directed by a miRNA superfamily that is of ancient origin and has undergone rapid sequence diversification associated with functional innovation. [ABSTRACT FROM AUTHOR]

The Darwinian shortfall, i.e. the lack of knowledge of phylogenetic relationships, significantly impedes our understanding of evolutionary drivers of global patterns of biodiversity. Spatial bias in the Darwinian shortfall, where phylogenetic knowledge in some regions is more complete than others, could undermine eco‐ and biogeographic inferences. Yet, spatial biases in phylogenetic knowledge for major groups – such as plants – remain poorly understood. Using data for 337 023 species (99.7%) of seed plants (Spermatophyta), we produced a global map of phylogenetic knowledge based on regional data and tested several potential drivers of the observed spatial variation. Regional phylogenetic knowledge was defined as the proportion of the regional seed plant flora represented in GenBank's nucleotide database with phylogenetically relevant data. We used simultaneous autoregressive models to explain variation in phylogenetic knowledge based on three biodiversity variables (species richness, range size and endemism) and six socioeconomic variables representing funding and accessibility. We compared observed patterns and relationships to established patterns of the Wallacean shortfall (the lack of knowledge of species distributions). We found that the Darwinian shortfall is strongly and significantly related to the macroecological distribution of species' range sizes. Small‐ranged species were significantly less likely to have phylogenetic data, leading to a concentration of the Darwinian shortfall in species‐rich, tropical countries where range sizes are small on average. Socioeconomic factors were less important, with significant but quantitatively small effects of accessibility and funding. In conclusion, reducing the Darwinian shortfall and smoothen its spatial bias will require increased efforts to sequence the world's small‐ranged (endemic) species. [ABSTRACT FROM AUTHOR]

Seed dormancy varies greatly between species, clades, communities, and regions. We propose that fireprone ecosystems create ideal conditions for the selection of seed dormancy as fire provides a mechanism for dormancy release and postfire conditions are optimal for germination. Thus, fire‐released seed dormancy should vary in type and abundance under different fire regimes. To test these predictions, we compiled data from a wide range of fire‐related germination experiments for species in different ecosystems across the globe. We identified four dormancy syndromes: heat‐released (physical) dormancy, smoke‐released (physiological) dormancy, non‐fire‐released dormancy, and non‐dormancy. In fireprone ecosystems, fire, in the form of heat and/or chemical by‐products (collectively termed 'smoke'), are the predominant stimuli for dormancy release and subsequent germination, with climate (cold or warm stratification) and light sometimes playing important secondary roles. Fire (heat or smoke)‐released dormancy is best expressed where woody vegetation is dense and fires are intense, i.e. in crown‐fire ecosystems. In such environments, seed dormancy allows shade‐intolerant species to take advantage of vegetation gaps created by fire and synchronize germination with optimal recruitment conditions. In grassy fireprone ecosystems (e.g. savannas), where fires are less intense but more frequent, seed dormancy is less common and dormancy release is often not directly related to fire (non‐fire‐released dormancy). Rates of germination, whether controls or postfire, are twice as fast in savannas than in mediterranean ecosystems. Fire‐released dormancy is rare to absent in arid ecosystems and rainforests. The seeds of many species with fire‐released dormancy also possess elaiosomes that promote ant dispersal. Burial by ants increases insulation of seeds from fires and places them in a suitable location for fire‐released dormancy. The distribution of these dormancy syndromes across seed plants is not random – certain dormancy types are associated with particular lineages (phylogenetic conservatism). Heat‐released dormancy can be traced back to fireprone floras in the 'fiery' mid‐Cretaceous, followed by smoke‐released dormancy, with loss of fire‐related dormancy among recent events associated with the advent of open savannas and non‐fireprone habitats. Anthropogenic influences are now modifying dormancy‐release mechanisms, usually decreasing the role of fire as exaptive effects. We conclude that contrasting fire regimes are a key driver of the evolution and maintenance of diverse seed dormancy types in many of the world's natural ecosystems. [ABSTRACT FROM AUTHOR]

Summary: The origin of land plants and their descendants was marked by the evolution of key adaptations to life in terrestrial environments such as roots, vascular tissue and stomata. Though these innovations are well characterized, the evolution of the genetic toolkit underlying their development and function is poorly understood.We analysed molecular data from 532 species to investigate the evolutionary origin and diversification of genes involved in the development and regulation of these adaptations.We show that novel genes in the first land plants led to the single origin of stomata, but the stomatal closure of seed plants resulted from later gene expansions. By contrast, the major mechanism leading to the origin of vascular tissue was cooption of genes that emerged in the first land plants, enabling continuous water transport throughout the ancestral vascular plant. In turn, new key genes in the ancestors of plants with true leaves and seed plants led to the emergence of roots and lateral roots.The analysis highlights the different modes of evolution that enabled plants to conquer land, suggesting that gene expansion and cooption are the most common mechanisms of biological innovation in plant evolutionary history. See also the Commentary on this article by Fürst‐Jansen et al., 235: 380–383. [ABSTRACT FROM AUTHOR]

Summary: Seed dormancy is an important life history state that increases survival and fitness of seed plants, and thus it has attracted much attention. However, global biogeography, effects of paleoenvironment, evolutionary roles of dormancy transitions, and differences in adaptations of seed dormancy between life‐forms are poorly understood.We compiled global distribution records for seed dormancy of 12 743 species and their phylogeny to explore the biogeographic patterns, environmental drivers, and evolutionary transitions between seed dormancy and nondormancy.Biogeographic patterns reveal a low proportion of dormancy in tropical rainforest regions and arctic regions and a high proportion of dormancy in remaining tropical, subtropical, and temperate regions for all species and woody species. Herbaceous plants show a greater proportion of dormancy in most global regions except arctic regions. Seasonal environments have a consistent positive influence on the dormancy pattern for both life‐forms, but precipitation and temperature were important driving factors for woody and herbaceous plants, respectively. Seed dormancy was the dominating state during the evolutionary history of seed plants, and dormancy transitions had a significant relationship with paleotemperatures. Dormancy and nondormancy transitions in response to fluctuating environments during long‐term evolutionary history may have played important roles in the diversification of seed plants.Our results add to the current knowledge about seed dormancy from macro‐adaptive perspectives and the potential adaptive mechanisms of seed plants. [ABSTRACT FROM AUTHOR]

SUMMARY: The exocyst complex is an octameric evolutionarily conserved tethering complex engaged in the regulation of polarized secretion in eukaryotic cells. Here, we focus on the systematic comparison of two isoforms of the SEC15 exocyst subunit, SEC15a and SEC15b. We infer that SEC15 gene duplication and diversification occurred in the common ancestor of seed plants (Spermatophytes). In Arabidopsis, SEC15a represents the main SEC15 isoform in the male gametophyte, and localizes to the pollen tube tip at the plasma membrane. Although pollen tubes of sec15a mutants are impaired, sporophytes show no phenotypic deviations. Conversely, SEC15b is the dominant isoform in the sporophyte and localizes to the plasma membrane in root and leaf cells. Loss‐of‐function sec15b mutants exhibit retarded elongation of hypocotyls and root hairs, a loss of apical dominance, dwarfed plant stature and reduced seed coat mucilage formation. Surprisingly, the sec15b mutants also exhibit compromised pollen tube elongation in vitro, despite its very low expression in pollen, suggesting a non‐redundant role for the SEC15b isoform there. In pollen tubes, SEC15b localizes to distinct cytoplasmic structures. Reciprocally to this, SEC15a also functions in the sporophyte, where it accumulates at plasmodesmata. Importantly, although overexpressed SEC15a could fully complement the sec15b phenotypic deviations in the sporophyte, the pollen‐specific overexpression of SEC15b was unable to fully compensate for the loss of SEC15a function in pollen. We conclude that the SEC15a and SEC15b isoforms evolved in seed plants, with SEC15a functioning mostly in pollen and SEC15b functioning mostly in the sporophyte. Significance Statement: The functional differentiation of two isoforms of the anciently duplicated and diverged (in seed plants) SEC15 exocyst subunit is manifest by their differential expression between the sporophyte and male gametophyte, distinct subcellular localization and phenotypic devations in Arabidopsis. Although SEC15a is crucial for pollen tube elongation, it also acquired specific functions in the sporophyte. Conversely, SEC15b is essential for sporophyte morphogenesis but also contributes to pollen tube elongation. Gene expression data indicate that this split of functions is conserved within Angiosperms. [ABSTRACT FROM AUTHOR]

Premise: In Arabidopsis thaliana, the role of the most important key genes that regulate ovule development is widely known. In nonmodel species, and especially in gymnosperms, the ovule developmental processes are still quite obscure. In this study, we describe the putative roles of Ginkgo biloba orthologs of regulatory genes during ovule development. Specifically, we studied AGAMOUS (AG), AGAMOUS‐like 6 (AGL6), AINTEGUMENTA (ANT), BELL1 (BEL1), Class III HD‐Zip, and YABBY Ginkgo genes. Methods: We analyzed their expression domains through in situ hybridizations on two stages of ovule development: the very early stage that corresponds to the ovule primordium, still within wintering buds, and the late stage at pollination time. Results: GBM5 (Ginkgo ortholog of AG), GbMADS8 (ortholog of AGL6) and GbC3HDZ1‐2‐3 were expressed in both the stages of ovule development, while GbMADS1, GbAGL6‐like genes (orthologs of AGL6), GbBEL1‐2 and YABBY Ginkgo orthologs (GbiYAB1B and GbiYABC) seem mostly involved at pollination time. GbANTL1 was not expressed in the studied stages and was different from GbANTL2 and GbBEL1, which seem to be involved at both stages of ovule development. In Ginkgo, the investigated genes display patterns of expression only partially comparable to those of other studied seed plants. Conclusions: The expression of most of these regulatory genes in the female gametophyte region at pollination time leads to suggest a communication between the sporophytic maternal tissue and the developing female gametophyte, as demonstrated for well‐studied model angiosperms. [ABSTRACT FROM AUTHOR]

Premise: Anatomically preserved evidence for a novel clade of gymnosperms emphasizes diversity of seed plants immediately prior to the appearance of angiosperm fossils in the paleontological record. Methods: Cupulate seeds from the Early Cretaceous Apple Bay locality (Vancouver Island) are described from serial cellulose acetate peels and three‐dimensional reconstruction. Phylogenetic context is assessed through the comparative analysis of gymnosperm seed producing fructifications and maximum parsimony analysis of a revised morphological data set for seed plant phylogeny. Results: Xadzigacalix quatsinoensis gen. et sp. nov. is characterized by an orthotropous ovule with an elongated micropyle and complex integument, enclosed within a radial cupule. The micropylar canal is elongated; and the nucellus extends into the micropyle to seal the post pollination ovule. Except at the apex of the micropyle, the seed is completely enclosed by a parenchymatous cupule with ca. 20 axially elongated secretory ducts. The cupulate seed is produced upon a triangular woody stele, consisting of a parenchymatous pith surrounded by radially aligned tracheids. The stele produces three short terete traces that terminate within the base of the cupule as transfusion tissue at the seed chalaza. Conclusions: Organography, vascularization, nature of the integument and nucellus, and configuration of the micropylar canal distinguish Xadzigacalix quatsinoensis from all other gymnosperm clades. Cladistic analyses suggest the new plant may have affinities with gnetophytes or angiosperms. These results are complemented with a critical re‐evaluation of ovulate structures for Mesozoic gymnosperms, providing new insight into plant diversity immediately antecedent to the explosive diversification of flowering plants. [ABSTRACT FROM AUTHOR]

SUMMARY: In seed plants, phospho‐base N‐methyltransferase (PMT) catalyzes a key step in the biosynthesis pathway of phosphatidylcholine (PC), the most abundant phospholipid class. Arabidopsis thaliana possesses three copies of PMT, with PMT1 and PMT3 play a primary role because the pmt1 pmt3 double mutant shows considerably reduced PC content with a pale seedling phenotype. Although the function of PMT1 and PMT3 may be redundant because neither of the parental single mutants showed a similar mutant phenotype, major developmental defects and possible functional divergence of these PMTs underlying the pale pmt1 pmt3 seedling phenotype are unknown. Here, we show the major developmental defect of the pale seedlings in xylem of the hypocotyl with partial impairments in chloroplast development and photosynthetic activity in leaves. Although PMT1 and PMT3 are localized at the endoplasmic reticulum, their tissue‐specific expression pattern was distinct in hypocotyls and roots. Intriguingly, the function of PMT3 but not PMT1 requires its characteristic N‐terminal sequence in addition to the promoter because truncation of the N‐terminal sequence of PMT3 or substitution with PMT1 driven by the PMT3 promoter failed to rescue the pale pmt1 pmt3 seedling phenotype. Thus, PMT3 function requires the N‐terminal sequence in addition to its promoter, whereas the PMT1 function is defined by the promoter. Significance Statement: Although Arabidopsis PMT1 and PMT3 are redundant in seedling growth, their functional divergence is conferred by the N‐terminal sequence in addition to their respective promoter activity. [ABSTRACT FROM AUTHOR]

Aim: How tree taxonomic and phylogenetic diversity vary with elevation at multiple spatial scales may provide new insights into the ecological and evolutionary processes influencing biogeographical patterns. The effect of water‐ and energy‐related climatic variables on forests diversity across elevations, as well as how clades have evolved on and established across mountain regions lack consensus. Here, we tested whether changes in biodiversity with elevation are consistent with one of, or multiple, competing hypotheses: the water–energy dynamics (WED), species–energy relationship (SER), Tropical Niche Conservatism (TNC) and Out of The Tropics hypothesis (OTT). Location: Patia watershed, Colombia Taxon Seed plants (trees) Methods: We used a large dataset of 490 0.1 ha forest plots in nine elevational belts (545–3410 m a.s.l) that correspond to three different life zones, and quantified alpha and gamma scales using taxonomic and phylogenetic diversity indices. We fitted linear mixed‐effects models to evaluate how taxonomic and phylogenetic alpha diversity changed with elevation, precipitation and aboveground biomass. We assessed taxonomic and phylogenetic beta diversity using the Sørensen index and its spatial turnover and nestedness components. Results: Taxonomic and phylogenetic alpha diversity decrease with elevation. Yet, at the gamma scale, taxonomic and phylogenetic diversity predominantly increased with elevation. Taxonomic and phylogenetic beta diversity were strongly influenced by species turnover, and followed a hump‐shaped pattern with elevation. Main conclusions: Overall, diversity shows a decreasing trend at the local scale, while coarse‐scale gamma diversity followed a pattern of nonlinear increases for both taxonomic and phylogenetic diversity. Evidence supports the influence of SER and WED on diversity patterns across elevations, yet neither evolutionary hypotheses had sufficient empirical support to be conclusive. [ABSTRACT FROM AUTHOR]

Cell wall thickness (Tcw) has been proposed as an important anatomical trait that could determine photosynthesis through land plants' phylogeny, bryophytes being the plant group presenting the thickest walls and the lowest photosynthetic rates. Also, it has recently been suggested that cell wall composition may have the potential to influence both thickness and mesophyll conductance (gm), representing a novel trait that could ultimately affect photosynthesis. However, only a few studies in spermatophytes have demonstrated this issue. In order to explore the role of cell wall composition in determining both Tcw and gm in mosses, we tested six species grown under field conditions in Antarctica. We performed gas exchange and chlorophyll fluorescence measurements, an anatomical characterization, and a quantitative analysis of cell wall main composition (i.e., cellulose, hemicelluloses and pectins) in these six species. We found the photosynthetic rates to vary between the species, and they also presented differences in anatomical characteristics and in cell wall composition. Whilst gm correlated negatively with Tcw and pectins content, a positive relationship between Tcw and pectins emerged, suggesting that pectins could contribute to determine cell wall porosity. Although our results do not allow us to provide conclusive statements, we suggest for the first time that cell wall composition—with pectins playing a key role—could strongly influence Tcw and gm in Antarctic mosses, ultimately defining photosynthesis. [ABSTRACT FROM AUTHOR]

The suppressor of gamma response 1 (SOG1), a NAM, ATAF1, 2, and CUC2 (NAC)‐type transcription factor found in seed plants, is a master regulator of DNA damage responses (DDRs). Upon DNA damage, SOG1 regulates the expression of downstream DDR genes. To know the origin of the DDR network in land plants, we searched for a homolog(s) of SOG1 in a moss Physcomitrium (Physcomitrella) patens and identified PpSOG1a and PpSOG1b. To assess if either or both of them function(s) in DDR, we knocked out the PpSOG1s using CRISPR/Cas9‐mediated gene editing and analyzed the responses to DNA‐damaging treatments. The double‐knockout (KO) sog1a sog1b plants showed resistance to γ‐rays, bleomycin, and ultraviolet B (UVB) treatments similarly seen in Arabidopsis sog1 plants. Next, we irradiated wild‐type (WT) and KO plants with γ‐rays and analyzed the whole transcriptome to examine the effect on the expression of DDR genes. The results revealed that many P. patens genes involved in the checkpoint, DNA repair, replication, and cell cycle‐related genes were upregulated after γ‐irradiation, which was not seen in sog1a sog1b plant. These results suggest that PpSOG1a and PpSOG1b work redundantly on DDR response in P. patens; in addition, plant‐specific DDR systems had been established before the emergence of vascular plants. [ABSTRACT FROM AUTHOR]

Summary: Identifying the contours and correlates of species turnover is central to understanding the nature of biogeographical regions. The Hengduan Mountains region of south‐central China (HMR) is well known for its high diversity of plants, but its boundaries and internal floristic structure are poorly understood, especially in relation to geographical and environmental factors.With data on occurrences and elevational ranges of seed plants across the HMR and adjacent areas of the greater Qinghai‐Tibet Plateau, we identified motifs (distinct species assemblages) by Grade of Membership models, and characterized relative contributions of geography, elevation, and climate to their spatial patterns.Motifs segregate primarily by latitude, elevation, and correlated environmental variables, most sharply across the tropical‐temperate divide. Secondarily, they segregate by longitude and geographical features, and reveal a novel divide across the Jinsha River. A core set of motifs corresponds to previous delineations of the HMR.The HMR biodiversity hotspot is more a mosaic of floristic elements than a cohesive entity. Grade of Membership models effectively reveal the geographical contours of biotic structure, and are a valuable new tool for biogeographical analysis. See also the Commentary on this article by Muellner‐Riehl & Favre, 232: 964–966. [ABSTRACT FROM AUTHOR]

Summary: An abrupt transition in the fossil record separates Early Devonian euphyllophytes with a simple structure from a broad diversity of structurally complex Middle–Late Devonian plants. Morphological evolution and phylogeny across this transition are poorly understood due to incomplete sampling of the fossil record. We document a new Early Devonian radiatopsid and integrate it in analyses addressing euphyllophyte relationships.Anatomically preserved Emsian fossils (402–394 Ma) from the Battery Point Formation (Gaspé, Quebec, Canada) are studied in serial sections. The phylogenetic analysis is based on a matrix of 31 taxa and 50 characters emphasising vegetative morphology (41 discrete, nine continuous).The new plant, Kenrickia bivena gen. et sp. nov., is one of very few structurally complex euphyllophytes documented in the Early Devonian. Inclusion of Kenrickia overturns previously established phylogenetic relationships among Radiatopses, reiterating the need for increased density of Early Devonian taxon sampling. Kenrickia is recovered as the sister lineage to all other radiatopsids, a clade in which paraphyletic Stenokoleales led to a lignophyte clade where archaeopterids and seed plants fall into sister clades.Our results shed light on early euphyllophyte relationships and evolution, indicating early exploration of structural complexity by multiple lineages and reiterating the potential of a single origin of secondary growth in euphyllophytes. [ABSTRACT FROM AUTHOR]

Aim: Root traits play important roles in plant growth and ecosystem processes. Clarifying the primary drivers of variation in root traits is indispensable for understanding and predicting ecosystem responses to environmental changes. Location: China. Taxon: Seed plant species. Methods: We compiled six key first‐order root traits of 437 seed plant species from different biomes, phylogenetic affiliations, plant growth forms and mycorrhizal types in China. The six root traits included root diameter (RD), root tissue density (RTD), specific root length (SRL), root C content (RCC), root N content (RNC) and root C:N ratio (RCN), which are highly relevant for plant growth rate and resource acquisition. The phylogenetic linear mixed model was employed to examine the effects of climate and soil variables on root traits and to quantify the relative contributions of environment, phylogeny, plant growth form and mycorrhizal type to root trait variation. Results: Environment explained most of the variations in RTD and RCC (37.4% and 24.2%, respectively). Mean precipitation of the wettest quarter and mean diurnal temperature range were the main climate drivers of RTD and RCC, respectively. Phylogeny contributed the most to the variation in RD, RNC and RCN (27.0%–52.3%). SRL showed strong links to both environment and phylogeny (35.0% and 27.8%, respectively). However, plant growth form and mycorrhizal type had little effect on root trait variation (<6.0%). Main conclusions: Our study revealed the primary drivers of variations in different root traits of seed plants in China. Climate variability and seasonality variables were more important factors driving root trait variation than the annual averages of temperature and precipitation. Incorporating the different responses of root traits to changing environments and phylogenetic affiliations observed in the present study into terrestrial ecosystem models will improve our ability to predict future vegetation distribution and ecosystem functions under global change. [ABSTRACT FROM AUTHOR]