HETEROSPORY: THE MOST ITERATIVE KEY INNOVATION IN THE EVOLUTIONARY HISTORY OF THE PLANT KINGDOM

The evolution and development of sporangia-The fundamental reproductive organ of land plant sporophytes

A key innovation of land plants is the origin and evolution of the sporangium, the fundamental reproductive structure of the diploid sporophyte. In vascular plants, whether the structure is a cone, fertile leaf, or flower-all are clusters of sporangia. The evolution of morphologically distinct sporangia (heterospory) and retention of the gametophyte evolved three times independently as a prerequisite for the evolution of seeds. This review summarizes the development of vascular plant sporangia, molecular genetics of angiosperm sporangia, and provides a framework to investigate evolution and development in vascular plant sporangia.

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.

No phylogenomic support for a Cenozoic origin of the "living fossil" Isoetes

PREMISE

The isoetalean lineage has a rich fossil record that extends to the Devonian, but the age of the living clade is unclear. Recent results indicate that it is young, from the Cenozoic, whereas earlier work based on less data from a denser taxon sampling yielded Mesozoic median ages.

METHODS

We analyzed node ages in Isoetes using two genomic data sets (plastome and nuclear ribosomal cistron), three clock models implemented in MrBayes (ILN, WN, and TK02 models), and a conservative approach to calibration.

RESULTS

While topological results were consistently resolved in Isoetes estimated crown group ages range from the latest Paleozoic (mid-Permian) to the Mesozoic depending on data type and clock model. The oldest estimates were retrieved using the autocorrelated TK02 clock model. An (early) Cenozoic age was only obtained under one specific condition (plastome data analyzed with the uncorrelated ILN clock model). That same plastome data set also yielded the oldest (mid-Permian) age estimate when analyzed with the autocorrelated TK02 clock model. Adding the highly divergent, recently established sister species Isoetes wormaldii to the data set approximately doubled the average median node depth to the Isoetes crown group.

CONCLUSIONS

There is no consistent support for a Cenozoic origin of the living clade Isoetes. We obtained seemingly well-founded, yet strongly deviating results depending on data type and clock model. The single most important future improvement is probably to add calibration points, which requires an improved understanding of the isoetalean fossil record or alternative bases for calibration.

The origin of a land flora

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

The biology of C. richardii as a tool to understand plant evolution

The fern Ceratopteris richardii has been studied as a model organism for over 50 years because it is easy to grow and has a short life cycle. In particular, as the first homosporous vascular plant for which genomic resources were developed, C. richardii has been an important system for studying plant evolution. However, we know relatively little about the natural history of C. richardii. In this article, we summarize what is known about this aspect of C. richardii, and discuss how learning more about its natural history could greatly increase our understanding of the evolution of land plants.

Phylogeny of Merlin's grass (Isoetaceae): revealing an "Amborella syndrome" and the importance of geographic distribution for understanding current and historical diversity

Background

Merlin’s grass (Isoetes, Isoetaceae, Lycopsida), is the extant remnant of the isoetalean wood-producing lycopsids that originated during the Paleozoic, possibly in aquatic or boggy habitats. Modern day species are aquatic, semi-aquatic or terrestrial and occur almost worldwide. They display little morphological variation; the lobed corm has helically arranged leaves with internal air channels and basal sporangia. Genetic variation has also proven limited, which has hampered phylogenetic inference. We investigate evolutionary relationships in Isoetes, using molecular data and an extended sample of species compared to previous work, adding species that have never before been included in a phylogenetic study.

Results

Our results reveal an unexpected discovery of an “Amborella syndrome” in Isoetaceae: a single poorly known species is sister to the remaining family. The species, Isoetes wormaldii, is a rare endemic to the Eastern Cape of South Africa. Its leaves are flattened with a rounded point, which sharply contrasts with the awl-shaped leaves of most other species of Isoetes. The remaining species of Isoetes are resolved in five major clades, also indicated in previous work. While the phylogeny shows geographic structure, the patterns are complex. For example, tropical-southern African species occur in at least five clades, and Indian, Australian and Mediterranean species in at least three clades each.

Conclusion

The evolutionary and biogeographical history of Isoetes is not easily explained, and may conceivably include ample extinction and a mixture of ancient and more recent processes. Previously shown difficulties with node age estimation increase the problem. The here demonstrated sister-relationship between the phylogenetically, morphologically and genetically distinct Isoetes wormaldii and the remaining family appears to bridge the morphological gap between Isoetes and its extinct relatives, although further studies are needed. Moreover, it shortens the branch length to its living sister genus Selaginella, and may enhance node age estimation in future studies. Isoetes wormaldii is critically endangered, known only from one (to a few) minor populations. Immediate actions need to be taken if we want to prevent this unique species from going extinct.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12862-022-01988-w.

Why Do Heterosporous Plants Have So Few Chromosomes?

The mechanisms controlling chromosome number, size, and shape, and the relationship of these traits to genome size, remain some of the least understood aspects of genome evolution. Across vascular plants, there is a striking disparity in chromosome number between homosporous and heterosporous lineages. Homosporous plants (comprising most ferns and some lycophytes) have high chromosome numbers compared to heterosporous lineages (some ferns and lycophytes and all seed plants). Many studies have investigated why homosporous plants have so many chromosomes. However, homospory is the ancestral condition from which heterospory has been derived several times. Following this phylogenetic perspective, a more appropriate question to ask is why heterosporous plants have so few chromosomes. Here, we review life history differences between heterosporous and homosporous plants, previous work on chromosome number and genome size in each lineage, known mechanisms of genome downsizing and chromosomal rearrangements, and conclude with future prospects for comparative research.

A novel reproductive strategy in an Early Devonian plant

Bonacorsi et al. describe a new fossil from the Early Devonian that provides the earliest clear evidence for more advanced reproductive biology in land plants. The plant produced multiple spore size classes, which is an essential innovation necessary for all advanced plant reproductive strategies, including seeds and flowers.

Reproduction Multitasking: The Male Gametophyte

The gametophyte represents the sexual phase in the alternation of generations in plants; the other, nonsexual phase is the sporophyte. Here, we review the evolutionary origins of the male gametophyte among land plants and, in particular, its ontogenesis in flowering plants. The highly reduced male gametophyte of angiosperm plants is a two- or three-celled pollen grain. Its task is the production of two male gametes and their transport to the female gametophyte, the embryo sac, where double fertilization takes place. We describe two phases of pollen ontogenesis-a developmental phase leading to the differentiation of the male germline and the formation of a mature pollen grain and a functional phase representing the pollen tube growth, beginning with the landing of the pollen grain on the stigma and ending with double fertilization. We highlight recent advances in the complex regulatory mechanisms involved, including posttranscriptional regulation and transcript storage, intracellular metabolic signaling, pollen cell wall structure and synthesis, protein secretion, and phased cell-cell communication within the reproductive tissues.

Plastome-based phylogenomics elucidate relationships in rare Isoëtes species groups from the Neotropics

The genus Isoëtes is globally distributed. Within the Neotropics, Isoëtes occurs in various habitats and ecosystems, making it an interesting case study to address phylogenetic and biogeographic questions. We sequenced and assembled plastomes and ribosomal DNA (rDNA) sequences to reconstruct phylogenetic relationships in Isoëtes from tropical regions in the Neotropics. The ploidy level of nine taxa was established to address the potential source of phylogenetic incongruence in the genus. Node ages were estimated using MCMCTree. The ancestral range estimates were conducted in BioGeoBEARS. Plastome-based phylogenies were congruent throughout distinct matrices and partition schemes, exhibiting high support for almost all nodes. Whereas, we found incongruences between the rDNA and plastome datasets. Chromosome counts identified three diploids, five tetraploids and one likely hexaploid among Neotropical species. Plastome-based node age estimates showed that the radiation of the crown Isoëtes group occurred at 20 Ma, with the diversification of the tropical American (TAA) clade taking place in the Pleistocene at 1.7 Ma. Ancestral range estimates showed that the ancestor of the TAA clade may have evolved first in the dry diagonal area in South America before reaching more humid regions. In addition, the colonization of the Brazilian semiarid region occurred three times, while the occupation of the Cerrado and Amazon regions occurred twice and once, respectively. Our study showed a large unobserved diversity within the genus in warm-dry regions in the Neotropics. Plastomes provided sufficient genomic information to establish a robust phylogenetic framework to answer evolutionary questions in Isoëtes from the Neotropics.

Plant sex chromosomes defy evolutionary models of expanding recombination suppression and genetic degeneration

Hundreds of land plant lineages have independently evolved separate sexes in either gametophytes (dioicy) or sporophytes (dioecy), but 43% of all dioecious angiosperms are found in just 34 entirely dioecious clades, suggesting that their mode of sex determination evolved a long time ago. Here, we review recent insights on the molecular mechanisms that underlie the evolutionary change from individuals that each produce male and female gametes to individuals specializing in the production of just one type of gamete. The canonical model of sex chromosome evolution in plants predicts that two sex-determining genes will become linked in a sex-determining region (SDR), followed by expanding recombination suppression, chromosome differentiation and, ultimately, degeneration. Experimental work, however, is showing that single genes function as master regulators in model systems, such as the liverwort Marchantia and the angiosperms Diospyros and Populus. In Populus, this type of regulatory function has been demonstrated by genome editing. In other systems, including Actinidia, Asparagus and Vitis, two coinherited factors appear to independently regulate female and male function, yet sex chromosome differentiation has remained low. We discuss the best-understood systems and evolutionary pathways to dioecy, and present a meta-analysis of the sizes and ages of SDRs. We propose that limited sexual conflict explains why most SDRs are small and sex chromosomes remain homomorphic. It appears that models of increasing recombination suppression with age do not apply because selection favours mechanisms in which sex determination depends on minimal differences, keeping it surgically precise.

A dynamical model for the origin of anisogamy

The vast majority of multi-cellular organisms are anisogamous, meaning that male and female sex cells differ in size. It remains an open question how this asymmetric state evolved, presumably from the symmetric isogamous state where all gametes are roughly the same size (drawn from the same distribution). Here, we use tools from the study of nonlinear dynamical systems to develop a simple mathematical model for this phenomenon. Unlike some prior work, we do not assume the existence of mating types. We also model frequency dependent selection via "mean-field coupling," whereby the likelihood that a gamete survives is an increasing function of its size relative to the population's mean gamete size. Using theoretical analysis and numerical simulation, we demonstrate that this mean-referenced competition will almost inevitably result in a stable anisogamous equilibrium, and thus isogamy may naturally lead to anisogamy.

Ancient noeggerathialean reveals the seed plant sister group diversified alongside the primary seed plant radiation

There were two heterosporous lignophyte lineages of which only one, the seed plants, survived the Permian–Triassic mass extinction. Based on exceptionally complete fossil trees from a 300-My-old volcanic ash, the enigmatic Noeggerathiales are now recognized as belonging to the other lineage. They diversified alongside the primary seed plant radiation and constitute seed plants’ closest relatives. Noeggerathiales are reconstructed as members of a plexus of free-sporing woody plants called progymnosperms, extending their age range by 60 My. Following the origin of seed plants, progymnosperms were previously thought to have become gradually less abundant before dying out in Carboniferous. We show they diversified and evolved complex morphologies including cone-like structures from modified leaves before going extinct at the Permian–Triassic extinction.

Noeggerathiales are enigmatic plants that existed during Carboniferous and Permian times, ∼323 to 252 Mya. Although their morphology, diversity, and distribution are well known, their systematic affinity remained enigmatic because their anatomy was unknown. Here, we report from a 298-My-old volcanic ash deposit, an in situ, complete, anatomically preserved noeggerathialean. The plant resolves the group’s affinity and places it in a key evolutionary position within the seed plant sister group. Paratingia wuhaia sp. nov. is a small tree producing gymnospermous wood with a crown of pinnate, compound megaphyllous leaves and fertile shoots each with Ω-shaped vascular bundles. The heterosporous (containing both microspores and megaspores), bisporangiate fertile shoots appear cylindrical and cone-like, but their bilateral vasculature demonstrates that they are complex, three-dimensional sporophylls, representing leaf homologs that are unique to Noeggerathiales. The combination of heterospory and gymnospermous wood confirms that Paratingia, and thus the Noeggerathiales, are progymnosperms. Progymnosperms constitute the seed plant stem group, and Paratingia extends their range 60 My, to the end of the Permian. Cladistic analysis resolves the position of the Noeggerathiales as the most derived members of a heterosporous progymnosperm clade that are the seed plant sister group, altering our understanding of the relationships within the seed plant stem lineage and the transition from pteridophytic spore-based reproduction to the seed. Permian Noeggerathiales show that the heterosporous progymnosperm sister group to seed plants diversified alongside the primary radiation of seed plants for ∼110 My, independently evolving sophisticated cone-like fertile organs from modified leaves.

A De Novo Transcriptome Assembly of Ceratopteris richardii Provides Insights into the Evolutionary Dynamics of Complex Gene Families in Land Plants

As the closest extant sister group to seed plants, ferns are an important reference point to study the origin and evolution of plant genes and traits. One bottleneck to the use of ferns in phylogenetic and genetic studies is the fact that genome-level sequence information of this group is limited, due to the extreme genome sizes of most ferns. Ceratopteris richardii (hereafter Ceratopteris) has been widely used as a model system for ferns. In this study, we generated a transcriptome of Ceratopteris, through the de novo assembly of the RNA-seq data from 17 sequencing libraries that are derived from two sexual types of gametophytes and five different sporophyte tissues. The Ceratopteris transcriptome, together with 38 genomes and transcriptomes from other species across the Viridiplantae, were used to uncover the evolutionary dynamics of orthogroups (predicted gene families using OrthoFinder) within the euphyllophytes and identify proteins associated with the major shifts in plant morphology and physiology that occurred in the last common ancestors of euphyllophytes, ferns, and seed plants. Furthermore, this resource was used to identify and classify the GRAS domain transcriptional regulators of many developmental processes in plants. Through the phylogenetic analysis within each of the 15 GRAS orthogroups, we uncovered which GRAS family members are conserved or have diversified in ferns and seed plants. Taken together, the transcriptome database and analyses reported here provide an important platform for exploring the evolution of gene families in land plants and for studying gene function in seed-free vascular plants.

Reconstructing development of the earliest seed integuments raises a new hypothesis for the evolution of ancestral seed-bearing structures

How plant seeds originated remains unresolved, in part due to disconnects between fossil intermediates and developmental genetics in extant species. The Carboniferous fossil Genomosperma is considered among the most primitive known seeds, with highly lobed integument and exposed nucellus. We have used this key fossil taxon to investigate the evolutionary origins of seed development. We examined sectioned Genomosperma specimens using modern digital 3D reconstruction techniques and established population-level measurements of Genomosperma ovules for quantitative analysis. Genomosperma ovules show significant variation in integumentary lobe fusion and curvature. Our analysis suggests that this variation represents a single species with significant variations in lobe number and fusion, reminiscent of floral development in extant species. We conclude that changes in lobe flexure occurred late in development, consistent with a previously hypothesized function in pollen guidance/retention. We also identify seeds of Genomosperma within cupules for the first time. The presence of a cupule adds evidence towards the plesiomorphy of cupules within seed plants. Together with the similarities identified between the Genomosperma lobed integument and floral organs, we propose that the cupule, integument and nucellus together developed in a shoot-like fashion, potentially ancestral to extant seed plant reproductive shoots.

Evolution and patterning of the ovule in seed plants

The ovule and its developmental successor, the seed, together represent a highly characteristic feature of seed plants that has strongly enhanced the reproductive and dispersal potential of this diverse group of taxa. Ovules encompass multiple tissues that perform various roles within a highly constrained space, requiring a complex cascade of genes that generate localized cell proliferation and programmed cell death during different developmental stages. Many heritable morphological differences among lineages reflect relative displacement of these tissues, but others, such as the second (outer) integuments of angiosperms and Gnetales, represent novel and apparently profound and independent innovations. Recent studies, mostly on model taxa, have considerably enhanced our understanding of gene expression in the ovule. However, understanding its evolutionary history requires a comparative and phylogenetic approach that is problematic when comparing extant angiosperms not only with phylogenetically distant extant gymnosperms but also with taxa known only from fossils. This paper reviews ovule characters across a phylogenetically broad range of seed plants in a dynamic developmental context. It discusses both well-established and recent theories of ovule and seed evolution and highlights potential gaps in comparative data that will usefully enhance our understanding of evolutionary transitions and developmental mechanisms.

Insights into the evolutionary history and widespread occurrence of antheridiogen systems in ferns

Sex expression of homosporous ferns is controlled by multiple factors, one being the antheridiogen system. Antheridiogens are pheromones released by sexually mature female fern gametophytes, turning nearby asexual gametophytes precociously male. Nevertheless, not all species respond. It is still unknown how many fern species use antheridiogens, how the antheridiogen system evolved, and whether it is affected by polyploidy and/or apomixis. We tested the response of 68 fern species to antheridiogens in cultivation. These results were combined with a comprehensive review of literature to form the largest dataset of antheridiogen interactions to date. Analyzed species also were coded as apomictic or sexual and diploid or polyploid. Our final dataset contains a total of 498 interactions involving 208 species (c. 2% of all ferns). About 65% of studied species respond to antheridiogen. Multiple antheridiogen types were delimited and their evolution is discussed. Antheridiogen responsiveness was not significantly affected by apomixis or polyploidy. Antheridiogens are widely used by ferns to direct sex expression. The antheridiogen system likely evolved multiple times and provides homosporous ferns with the benefits often associated with heterospory, such as increased rates of outcrossing. Despite expectations, antheridiogens may be beneficial to polyploids and apomicts.

Reinterpretation of Paleoazolla: a heterosporous water fern from the Late Cretaceous of Patagonia, Argentina

PREMISE

Undoubtedly, fossils are critical for understanding evolutionary transformations in deep time. Here, we reinvestigate the microspores and megaspores of Paleoazolla patagonica, a water fern found in Late Cretaceous sediments of the Chubut Province, Patagonia, Argentina, which provides novel evidence on the past history of the water fern clade. The study was based on recently collected specimens and additional observations of the original material.

METHODS

Most specimens analyzed herein were obtained from new palynological samples collected at the Cerro Bosta and Cañadón del Irupé localities, La Colonia Formation. Samples were mechanically disaggregated and treated with hydrofluoric and hydrochloric acid. Spores were studied using standard light microscopy and scanning electron microscopy. We also reexamined the original materials.

RESULTS

The newly described characters of Paleoazolla include the presence of heterosporangiate sori composed of one ellipsoidal megasporangium surrounded by three to four oval microsporangia, megasporangium containing one hairy massula that encloses two trilete megaspores (rarely one or three), and microsporangia containing numerous microspore massulae with non-septate multibarbed glochidia and one trilete microspore per massula.

CONCLUSIONS

The reinterpretation has revealed a novel set of characters for understanding the evolution of heterosporous water ferns. The presence of two megaspores in the megasporangium of Paleoazolla exposes serious gaps in the current knowledge on the evolution of monomegaspory in heterosporous water ferns, a fact that emphasizes the need of including fossils within phylogenies to elucidate patterns of character acquisition among water ferns.

Morphology of the megaspore Lagenoisporites magnus (Chi and Hills 1976) Candilier et al. (1982), from the Carboniferous (lower Mississippian: mid-upper Tournaisian) of Bolivia

The morphology and structure of megaspores assigned to Lagenoisporites magnus from the Toregua Formation, Retama Group, mid-upper Tournaisian of Bolivia were studied. The analysis was performed with light, fluorescence and scanning electron microscopy. Megaspores were laterally compressed and presented a spherical body with a proximal gula, of the hologula type. Gula had verrucae ornamentation and the spore body presented complex processes consisting of a bulbous base and an internally partitioned projection with sharp apex. In addition to this main ornamentation, perforations were present throughout the spore surface. Megaspores showed well marked curvaturae perfectae due to the abrupt transition existing between the gula ornamentation and the spore body processes. These megaspores were assigned to heterosporous arborescent lycopsids of the Lepidocarpaceae family, as in section view, exospore structure presented a three-dimensional network of fused elements. Likewise, due to a similarity found between sporoderm and Isoetes L. structure, it is evident that megaspores structure has remained intact inside the heterosporous lycopsids. Therefore; the L. magnus structure not only would confirm its affinity with the Lycophyta fossils but also with the living ones.

Pollen Developmental Arrest: Maintaining Pollen Fertility in a World With a Changing Climate

During evolution of land plants, the haploid gametophytic stage has been strongly reduced in size and the diploid sporophytic phase has become the dominant growth form. Both male and female gametophytes are parasitic to the sporophyte and reside in separate parts of the flower located either on the same plant or on different plants. For fertilization to occur, bi-cellular or tri-cellular male gametophytes (pollen grains) have to travel to the immobile female gametophyte in the ovary. To survive exposure to a hostile atmosphere, pollen grains are thought to enter a state of complete or partial developmental arrest (DA). DA in pollen is strongly associated with acquisition of desiccation tolerance (DT) to extend pollen viability during air travel, but occurrence of DA in pollen is both species-dependent and at the same time strongly dependent on the reigning environmental conditions at the time of dispersal. Several environmental stresses (heat, drought, cold, humidity) are known to affect pollen production and viability. Climate change is also posing a serious threat to plant reproductive behavior and crop productivity. It is therefore timely to gain a better understanding of how DA and pollen viability are controlled in plants and how pollen viability can be protected to secure crop yields in a changing environment. Here, we provide an overview of how DA and pollen viability are controlled and how the environment affects them. We make emphasis on what is known and areas where a deeper understanding is needed.

Key innovations in transition from homospory to heterospory

Heterospory (i.e. dimorphic spores) is a long-lasting topic discussed in plant biology. It is observed in many of ferns, fern allies, and seed plants. The rise of heterospory and the mechanisms underlying its success in plant evolution are not clearly elucidated. In this short communication, an attempt is made to shed some light on these two questions.

The evolution and patterning of male gametophyte development

The reproductive adaptations of land plants have played a key role in their terrestrial colonization and radiation. This encompasses mechanisms used for the production, dispersal and union of gametes to support sexual reproduction. The production of small motile male gametes and larger immotile female gametes (oogamy) in specialized multicellular gametangia evolved in the charophyte algae, the closest extant relatives of land plants. Reliance on water and motile male gametes for sexual reproduction was retained by bryophytes and basal vascular plants, but was overcome in seed plants by the dispersal of pollen and the guided delivery of non-motile sperm to the female gametes. Here we discuss the evolutionary history of male gametogenesis in streptophytes (green plants) and the underlying developmental biology, including recent advances in bryophyte and angiosperm models. We conclude with a perspective on research trends that promise to deliver a deeper understanding of the evolutionary and developmental mechanisms of male gametogenesis in plants.

Overlapping Patterns of Gene Expression Between Gametophyte and Sporophyte Phases in the Fern Polypodium amorphum (Polypodiales)

Ferns are unique among land plants in having sporophyte and gametophyte phases that are both free living and fully independent. Here, we examine patterns of sporophytic and gametophytic gene expression in the fern Polypodium amorphum, a member of the homosporous polypod lineage that comprises 80% of extant fern diversity, to assess how expression of a common genome is partitioned between two morphologically, ecologically, and nutritionally independent phases. Using RNA-sequencing, we generated transcriptome profiles for three replicates of paired samples of sporophyte leaf tissue and whole gametophytes to identify genes with significant differences in expression between the two phases. We found a nearly 90% overlap in the identity and expression levels of the genes expressed in both sporophytes and gametophytes, with less than 3% of genes uniquely expressed in either phase. We compare our results to those from similar studies to establish how phase-specific gene expression varies among major land plant lineages. Notably, despite having greater similarity in the identity of gene families shared between P. amorphum and angiosperms, P. amorphum has phase-specific gene expression profiles that are more like bryophytes and lycophytes than seed plants. Our findings suggest that shared patterns of phase-specific gene expression among seed-free plants likely reflect having relatively large, photosynthetic gametophytes (compared to the gametophytes of seed plants that are highly reduced). Phylogenetic analyses were used to further investigate the evolution of phase-specific expression for the phototropin, terpene synthase, and MADS-box gene families.

The Huperzia selago Shoot Tip Transcriptome Sheds New Light on the Evolution of Leaves

Lycopodiophyta—consisting of three orders, Lycopodiales, Isoetales and Selaginellales, with different types of shoot apical meristems (SAMs)—form the earliest branch among the extant vascular plants. They represent a sister group to all other vascular plants, from which they differ in that their leaves are microphylls—that is, leaves with a single, unbranched vein, emerging from the protostele without a leaf gap—not megaphylls. All leaves represent determinate organs originating on the flanks of indeterminate SAMs. Thus, leaf formation requires the suppression of indeterminacy, that is, of KNOX transcription factors. In seed plants, this is mediated by different groups of transcription factors including ARP and YABBY.

We generated a shoot tip transcriptome of Huperzia selago (Lycopodiales) to examine the genes involved in leaf formation. Our H. selago transcriptome does not contain any ARP homolog, although transcriptomes of Selaginella spp. do. Surprisingly, we discovered a YABBY homolog, although these transcription factors were assumed to have evolved only in seed plants.

The existence of a YABBY homolog in H. selago suggests that YABBY evolved already in the common ancestor of the vascular plants, and subsequently was lost in some lineages like Selaginellales, whereas ARP may have been lost in Lycopodiales. The presence of YABBY in the common ancestor of vascular plants would also support the hypothesis that this common ancestor had a simplex SAM. Furthermore, a comparison of the expression patterns of ARP in shoot tips of Selaginella kraussiana (Harrison CJ, etal. 2005. Independent recruitment of a conserved developmental mechanism during leaf evolution. Nature 434(7032):509–514.) and YABBY in shoot tips of H. selago implies that the development of microphylls, unlike megaphylls, does not seem to depend on the combined activities of ARP and YABBY. Altogether, our data show that Lycopodiophyta are a diverse group; so, in order to understand the role of Lycopodiophyta in evolution, representatives of Lycopodiales, Selaginellales, as well as of Isoetales, have to be examined.

The adaptive value of heterospory: Evidence from Selaginella

Heterospory was a pivotal evolutionary innovation for land plants, but it has never been clear why it evolved. We used the geographic distributions of 114 species of the heterosporous lycophyte Selaginella to explore the functional ecology of microspore and megaspore size, traits that would be correlated with many aspects of a species' regeneration niche. We characterized habitats at a global scale using leaf area index (LAI), a measure of foliage density and thus shading, and net primary productivity (NPP), a measure of growth potential. Microspore size tends to decrease as habitat LAI and NPP increase, a trend that could be related to desiccation resistance or to filtration of wind-borne particles by leaf surfaces. Megaspore size tends to increase among species that inhabit regions of high LAI, but there is an important interaction with NPP. This geographical pattern suggests that larger megaspores provide an establishment advantage in shaded habitats, although in open habitats, where light is less limiting, higher productivity of the environment seems to give an advantage to species with smaller megaspores. These results support previous theoretical arguments that heterospory was originally an adaptation to the increasing height and density of Devonian vegetative canopies that accompanied the diversification of vascular plants with leaves.

The Paleobiology of Pollination and its Precursors

Perhaps the most conspicuous of associations between insects and plants is pollination. Pollinating insects are typically the first and most obvious of interactions between insects and plants when one encounters a montane meadow or a tropical woodland. The complex ecological structure of insect pollinators and their host plants is a central focus within the ever-expanding discipline of plant-insect interactions. The relationships between plants and insects have provided the empirical documentation of many case-studies that have resulted in the formulation of biological principles and construction of theoretical models, such as the role of foraging strategy on optimal plant-resource use, the advantages of specialized versus generalized host preferences as viable feeding strategies, and whether “pollination syndromes” are meaningful descriptions that relate flower type to insect mouthpart structure and behavior (Roubik, 1989; Ollerton, 1996; Waser et al., 1996; Johnson and Steiner, 2000). Much of the recent extensive discussion of plant-insect associations has centered on understanding the origin, maintenance, and evolutionary change in plant/pollinator associations at ecological time scales and increasingly at longer-term macroevolutionary time intervals (Armbruster, 1992; Pellmyr and Leebens-Mack, 1999). Such classical plant-insect association studies—cycads and cycad weevils, figs and fig wasps, and yuccas and yucca moths—were explored at modern time scales and currently are being examined through a long-term geologic component that involves colonization models based on cladogenetic events of plant and insect associates, buttressed by the fossil record (Farrell, 1998; Pellmyr and Leebens-Mack, 1999; A. Herre,pers. comm.). In addition to tracing modern pollination to the earlier Cenozoic and later Mesozoic, there is a resurgence in understanding the evolutionary history of earlier palynivore taxa (spore, prepollen and pollen consumers), which led toward pollination as a mutualism (Scott et al., 1992).

The Modernization of Landscapes during the Late Paleozoic-Early Mesozoic

Since their first appearance in the Middle-Late Silurian, land plants have played an increasingly important role in shaping terrestrial ecosystems and landscapes. It is difficult to overestimate their role because they form the framework for terrestrial ecosystems, provide habitats for terrestrial animals, form an important part of the food chain, affect weathering processes and have a direct impact on soil formation, and, last but not least, play a primary role in the oxygen/carbon cycles.

On the widespread capacity for, and functional significance of, extreme inbreeding in ferns

Homosporous vascular plants utilize three different mating systems, one of which, gametophytic selfing, is an extreme form of inbreeding only possible in homosporous groups. This mating system results in complete homozygosity in all progeny and has important evolutionary and ecological implications. Ferns are the largest group of homosporous land plants, and the significance of extreme inbreeding for fern evolution has been a subject of debate for decades. We cultured gametophytes in the laboratory and quantified the relative frequencies of sporophyte production from isolated and paired gametophytes, and examined associations between breeding systems and several ecological and evolutionary traits. The majority of fern species studied show a capacity for gametophytic selfing, producing sporophytes from both isolated and paired gametophytes. While we did not follow sporophytes to maturity to investigate potential detrimental effects of homozygosity at later developmental stages, our results suggest that gametophytic selfing may have greater significance for fern evolution and diversification than has previously been realized. We present evidence from the largest study of mating behavior in ferns to date that the capacity for extreme inbreeding is prevalent in this lineage, and we discuss its implications and relevance and make recommendations for future studies of fern mating systems.

Stratigraphy, palaeoenvironments and palaeoecology of the Loch Humphrey Burn lagerstätte and other Mississippian palaeobotanical localities of the Kilpatrick Hills, southwest Scotland

Background and Aims. The largely Mississippian strata of the Kilpatrick Hills, located at the western end of the Scottish Midland Valley, enclose several macrofossil floras that together contain ca 21 organ-species of permineralised plants and ca 44 organ-species of compressed plants, here estimated to represent 25 whole-plant species (Glenarbuck = nine, Loch Humphrey Burn Lower = 11, Upper = seven). The most significant locality is the internationally important volcanigenic sequence that is reputedly intercalated within the Clyde Plateau Lava Formation at Loch Humphrey Burn, where ca 30 m of reworked tuffs and other clastic sediments enclose one of the world’s most important terrestrial lagerstätten of this period. We here explore the palaeoecology and palaeoenvironments of the locality, and elucidate its controversial age.

Methods. Repeated re-excavation of key exposures allowed recognition of five main depositional units, differing in thickness from 4 m to 12 m. It also permitted detailed sampling for plant macrofossils and microfossils throughout the succession. Several approaches are integrated to re-assess the taphonomy and preservation of these exceptional plant fossils.

Key Results. The deposits are rich in taxonomically diverse miospores and in toto contain at least six well-developed compression floras, together with two beds yielding nodules that enclose well-researched anatomically preserved plants permineralised in calcite. Bulk geochemistry shows that the upper nodules formed by migration of Ca with subordinate Mn and Na. Some phylogenetically important plant fossils recovered in the early 20th century have been traced to their source horizons. Trends in relative proportions of macrofossil and microfossil taxa through the sequence are only moderately congruent, perhaps reflecting the likelihood that microfossils sample the regional rather than the local flora.

Conclusions. The Loch Humphrey Burn sequence encompasses a wide range of depositional environments that intercalates high-energy fluvial channels (possibly developed during flash floods in a seasonally arid environment) with lower energy flood plains and a brief lacustrine interval; all yield macrofloras typically dominated by allochthonous pteridosperms. The uppermost unit represents clastic swamps dominated by (hypo)autochthonous lycopsids and ferns s.l., and is tentatively correlated with the entire—reputedly mid-Visean—exposure at nearby Glenarbuck. Other nearby localities with rooted tree-lycopsids appear to have immediately pre-dated the onset of regional volcanism. These interpretations allow revised provenancing and dating of historical collections of key plant fossils. The late Tournaisian date previously attributed on palynological evidence to the lowest unit at Loch Humphrey Burn appears increasingly improbable when our re-appraisal of the macrofloras and microfloras is placed in the context of (a) statistical comparison with other permineralised Mississippian assemblages and (b) recent stratigraphic and geochronologic studies in the region; rather, we ascribe the entire Kilpatrick Hills sequence to the mid-Visean. Stratigraphic and palaeoenvironmental interpretations of the Mississippian rocks of the Kilpatrick Hills have especially profound implications for our understanding of the physical evolution of Scotland during the Variscan orogeny and formation of Pangea.

The impact of fire on the Late Paleozoic Earth system

Analyses of bulk petrographic data indicate that during the Late Paleozoic wildfires were more prevalent than at present. We propose that the development of fire systems through this interval was controlled predominantly by the elevated atmospheric oxygen concentration (p(O2)) that mass balance models predict prevailed. At higher levels of p(O2), increased fire activity would have rendered vegetation with high-moisture contents more susceptible to ignition and would have facilitated continued combustion. We argue that coal petrographic data indicate that p(O2) rather than global temperatures or climate, resulted in the increased levels of wildfire activity observed during the Late Paleozoic and can, therefore, be used to predict it. These findings are based upon analyses of charcoal volumes in multiple coals distributed across the globe and deposited during this time period, and that were then compared with similarly diverse modern peats and Cenozoic lignites and coals. Herein, we examine the environmental and ecological factors that would have impacted fire activity and we conclude that of these factors p(O2) played the largest role in promoting fires in Late Paleozoic peat-forming environments and, by inference, ecosystems generally, when compared with their prevalence in the modern world.

The relative and absolute frequencies of angiosperm sexual systems: dioecy, monoecy, gynodioecy, and an updated online database

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PREMISE OF THE STUDY

Separating sexual function between different individuals carries risks, especially for sedentary organisms. Nevertheless, many land plants have unisexual gametophytes or sporophytes. This study brings together data and theoretical insights from research over the past 20 yr on the occurrence and frequency of plant sexual systems, focusing on the flowering plants.•

METHODS

A list of genera with dioecious species, along with other information, is made available (http://www.umsl.edu/∼renners/). Frequencies of other sexual systems are tabulated, and data on the genetic regulation, ecological context, and theoretical benefits of dioecy reviewed.•

KEY RESULTS

There are 15600 dioecious angiosperms in 987 genera and 175 families, or 5-6% of the total species (7% of genera, 43% of families), with somewhere between 871 to 5000 independent origins of dioecy. Some 43% of all dioecious angiosperms are in just 34 entirely dioecious clades, arguing against a consistent negative influence of dioecy on diversification. About 31.6% of the dioecious species are wind-pollinated, compared with 5.5-6.4% of nondioecious angiosperms. Also, 1.4% of all angiosperm genera contain dioecious and monoecious species, while 0.4% contain dioecious and gynodioecious species. All remaining angiosperm sexual systems are rare. Chromosomal sex determination is known from 40 species; environmentally modulated sex allocation is common. Few phylogenetic studies have focused on the evolution of dioecy.•

CONCLUSIONS

The current focus is on the genetic mechanisms underlying unisexual flowers and individuals. Mixed strategies of sexual and vegetative dispersal, together with plants' sedentary life style, may often favor polygamous systems in which sexually inconstant individuals can persist. Nevertheless, there are huge entirely dioecious clades of tropical woody plants.

Between two fern genomes

Ferns are the only major lineage of vascular plants not represented by a sequenced nuclear genome. This lack of genome sequence information significantly impedes our ability to understand and reconstruct genome evolution not only in ferns, but across all land plants. Azolla and Ceratopteris are ideal and complementary candidates to be the first ferns to have their nuclear genomes sequenced. They differ dramatically in genome size, life history, and habit, and thus represent the immense diversity of extant ferns. Together, this pair of genomes will facilitate myriad large-scale comparative analyses across ferns and all land plants. Here we review the unique biological characteristics of ferns and describe a number of outstanding questions in plant biology that will benefit from the addition of ferns to the set of taxa with sequenced nuclear genomes. We explain why the fern clade is pivotal for understanding genome evolution across land plants, and we provide a rationale for how knowledge of fern genomes will enable progress in research beyond the ferns themselves.

Correlates of monoicy and dioicy in hornworts, the apparent sister group to vascular plants

Background

Whether male and female gametes are produced by single or separate individuals shapes plant mating and hence patterns of genetic diversity among and within populations. Haploid-dominant plants (“bryophytes”: liverworts, mosses and hornworts) can have unisexual (dioicous) or bisexual (monoicous) gametophytes, and today, 68% of liverwort species, 57% of moss species, and 40% of hornwort species are dioicous. The transitions between the two sexual systems and possible correlations with other traits have been studied in liverworts and mosses, but not hornworts. Here we use a phylogeny for 98 of the 200 species of hornworts, the sister group to vascular plants, representing roughly equal proportions of all monoicous and all dioicous species, to test whether transitions in sexual systems are predominantly from monoicy to dioicy as might be expected based on studies of mosses. We further investigate possible correlations between sexual system and spore size, antheridium number, ploidy level, and diversification rate, with character selection partly based on findings in mosses and liverworts.

Results

Hornworts underwent numerous transitions between monoicy and dioicy. The transition rate from dioicy to monoicy was 2× higher than in the opposite direction, but monoicous groups have higher extinction rates; diversification rates do not correlate with sexual system. A correlation important in mosses, that between monoicy and polyploidy, apparently plays a small role: of 20 species with chromosome counts, only one is polyploid, the monoicous Anthoceros punctatus. A contingency test revealed that transitions to dioicy were more likely in species with small spores, supporting the hypothesis that small but numerous spores may be advantageous for dioicous species that depend on dense carpets of gametophytes for reproductive assurance. However, we found no evidence for increased antheridium-per-chamber numbers in dioicous species.

Conclusions

Sexual systems in hornworts are labile, and the higher number of extant monoicous species (60%) may be largely due to frequent transitions to monoicy.

LEAFY COTYLEDON1, a key regulator of seed development, is expressed in vegetative and sexual propagules of Selaginella moellendorffii

LEAFY COTYLEDON1 (LEC1) is a central regulator of seed development that plays a key role in controlling the maturation phase during which storage macromolecules accumulate and the embryo becomes tolerant of desiccation. We queried the genomes of seedless plants and identified a LEC1 homolog in the lycophyte, Selaginella moellendorffii, but not in the bryophyte, Physcomitrella patens. Genetic suppression experiments indicated that Selaginella LEC1 is the functional ortholog of Arabidopsis LEC1. Together, these results suggest that LEC1 originated at least 30 million years before the first seed plants appeared in the fossil record. The accumulation of Selaginella LEC1 RNA primarily in sexual and asexual reproductive structures suggests its involvement in cellular processes similar to those that occur during the maturation phase of seed development.

Unisexual cucumber flowers, sex and sex differentiation

Sex is a universal phenomenon in the world of eukaryotes. Attempts have been made to understand regulatory mechanisms for plant sex determination by investigating unisexual flowers. The cucumber plant is one of the model systems for studying how sex determination is regulated by phytohormones. A systematic investigation of the development of unisexual cucumber flowers is summarized here, and it is suggested that the mechanism of the unisexual flower can help us to understand how the process leading to one type of gametogenesis is prevented. Based on these findings, we concluded that the unisexual cucumber flowers is not an issue of sex differentiation, but instead a mechanism for avoiding self-pollination. Sex differentiation is essentially the divergent point(s) leading to heterogametogenesis. On the basis of analyses of sex differentiation in unicellular organisms and animals as well as the core process of plant life cycle, a concept of "sexual reproduction cycle" is proposed for understanding the essential role of sex and a "progressive model" for future investigations of sex differentiation in plants.

The evolutionary diversification of seed size: using the past to understand the present

The Devonian origin of seed plants and subsequent morphological diversification of seeds during the late Paleozoic represents an adaptive radiation into unoccupied ecological niche space. A plant's seed size is correlated with its life-history strategy, growth form, and seed dispersal syndrome. The fossil record indicates that the oldest seed plants had relatively small seeds, but the Mississippian seed size envelope increased significantly with the diversification of larger seeded lineages. Fossil seeds equivalent to the largest extant gymnosperm seeds appeared by the Pennsylvanian, concurrent with morphological diversification of growth forms and dispersal syndromes as well as the clade's radiation into new environments. Wang's Analysis of Skewness indicates that the evolutionary trend of increasing seed size resulted from primarily passive processes in Pennsylvanian seed plants. The distributions of modern angiosperms indicate a more diverse system of active and some passive processes, unbounded by Paleozoic limits; multiple angiosperm lineages independently evolved though the upper and lower bounds. Quantitative measures of preservation suggest that, although our knowledge of Paleozoic seeds is far from complete, the evolutionary trend in seed size is unlikely to be an artifact of taphonomy.

Terrestrialization in the Late Devonian: a palaeoecological overview of the Red Hill site, Pennsylvania, USA

Alluvial floodplains were a critical setting during the Late Devonian for the evolution of terrestriality among plants, invertebrate and vertebrates. The Red Hill site in Pennsylvania, US, provides a range of information about the physical and biotic setting of a floodplain ecosystem along the southern margin of the Euramerican landmass during the late Famennian age. An avulsion model for floodplain sedimentation is favoured in which a variety of inter-channel depositional settings formed a wide range of aquatic and terrestrial habitats. The Red Hill flora demonstrates ecological partitioning of the floodplain landscape at a high taxonomic level. In addition to progymnosperm forests, lycopsid wetlands and zygopterid fern glades, the flora includes patches of early spermatophytes occupying sites disturbed by fires. The Red Hill fauna illustrates the development of a diverse penecontemporaneous community including terrestrial invertebrates and a wide range of vertebrates that were living within aquatic habitats. Among the vertebrates are several limbed tetrapodomorphs that inhabited the burgeoning shallow water habitats on the floodplain.

Evolution of tree nutrition

Using a broad definition of trees, the evolutionary origins of trees in a nutritional context is considered using data from the fossil record and molecular phylogeny. Trees are first known from the Late Devonian about 380 million years ago, originated polyphyletically at the pteridophyte grade of organization; the earliest gymnosperms were trees, and trees are polyphyletic in the angiosperms. Nutrient transporters, assimilatory pathways, homoiohydry (cuticle, intercellular gas spaces, stomata, endohydric water transport systems including xylem and phloem-like tissue) and arbuscular mycorrhizas preceded the origin of trees. Nutritional innovations that began uniquely in trees were the seed habit and, certainly (but not necessarily uniquely) in trees, ectomycorrhizas, cyanobacterial, actinorhizal and rhizobial (Parasponia, some legumes) diazotrophic symbioses and cluster roots.

MIKC* MADS-box proteins: conserved regulators of the gametophytic generation of land plants

Land plants (embryophytes) are characterized by an alternation of two generations, the haploid gametophyte and the diploid sporophyte. The development of the small and simple male gametophyte of the flowering plant Arabidopsis (Arabidopsis thaliana) critically depends on the action of five MIKC* group MCM1-AGAMOUS-DEFICIENS-SRF-box (MADS-box) proteins. In this study, these MIKC* MADS-box genes were isolated from land plants with relatively large and complex gametophyte bodies, namely the bryophytes. We found that although the gene family expanded in the mosses Sphagnum subsecundum, Physcomitrella patens, and Funaria hygrometrica, only a single homologue, Marchantia polymorpha MADS-box gene 1 (MpMADS1), has been retained in the liverwort M. polymorpha. Liverworts are the earliest diverging land plants, and so a comparison of MpMADS1 with its angiosperm homologues addresses the molecular evolution of an embryophyte-specific transcription factor over the widest phylogenetic distance. MpMADS1 was found to form a homodimeric DNA-binding complex, which is in contrast to the Arabidopsis proteins that are functional only as heterodimeric complexes. The M. polymorpha homodimer, nevertheless, recognizes the same DNA sequences as its angiosperm counterparts and can functionally replace endogenous MIKC* complexes to a significant extent when heterologously expressed in Arabidopsis pollen. The 11 MIKC* homologues from the moss F. hygrometrica are highly and almost exclusively expressed in the gametophytic generation. Taken together, these findings suggest that MIKC* MADS-box proteins have largely preserved molecular roles in the gametophytic generation of land plants.

Selaginella and 400 million years of separation

Selaginella (spikemoss) is an enigma in the plant kingdom. Although a fascination to botanists at the turn of the twentieth century, members of this genus are unremarkable in appearance, never flower, and are of no agronomic value. However, members of this genus are relicts from ancient times, and one has to marvel at how this genus has survived virtually unchanged in appearance for hundreds of millions of years. In light of the recent completion of the Selaginella moellendorffii genome sequence, this review is intended to survey what is known about Selaginella, with a special emphasis on recent inquiries into its unique biology and importance in understanding the early evolution of vascular plants.