Seed ferns from the late Paleozoic and Mesozoic: Any angiosperm ancestors lurking there?

Evolution and natural selection of ribosome-inactivating proteins in bacteria, fungi, and plants

Ribosome-inactivating proteins (RIPs) are found in bacteria, fungi, and plants, with a wide range of biological resistances such as anti-fungal, anti-viral, anti-insect, and anti-tumor. They can be roughly divided into proactive defense bacterial or fungal types and passive defense plant types. We identified 1592 RIP genes in bacteria, fungi, and plants. Approximately 88 % of the 764 bacterial RIPs were Shiga or Shiga-like toxins which were exotoxins and could rapidly enter cells to possess strong biotoxicity, and about 98 % of fungal RIPs were predicted as secreted proteins. RIPs were not detected in non-seed plants such as algae, bryophytes, and ferns. However, we found RIPs in some flowering and non-flowering seed plants. The existence of plant RIPs might be related to the structure of seeds or fruits, which might be associated with whether seeds are easy to survive and spread. The evolutionary characteristics of RIPs were different between dicotyledons and monocotyledons. In addition, we also found that RIP2 genes might emerge very early and be plant-specific. Some plant RIP1 genes might evolve from RIP2 genes. This study provides new insights into the evolution of RIPs.

Cretaceous pollen cone with three-dimensional preservation sheds light on the morphological evolution of cycads in deep time

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.

A novel cupulate seed plant, Xadzigacalix quatsinoensis gen. et sp. nov., provides new insight into the Mesozoic radiation of gymnosperms

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.

Constraining uncertainty in the timescale of angiosperm evolution and the veracity of a Cretaceous Terrestrial Revolution

Through the lens of the fossil record, angiosperm diversification precipitated a Cretaceous Terrestrial Revolution (KTR) in which pollinators, herbivores and predators underwent explosive co-diversification. Molecular dating studies imply that early angiosperm evolution is not documented in the fossil record. This mismatch remains controversial. We used a Bayesian molecular dating method to analyse a dataset of 83 genes from 644 taxa and 52 fossil calibrations to explore the effect of different interpretations of the fossil record, molecular clock models, data partitioning, among other factors, on angiosperm divergence time estimation. Controlling for different sources of uncertainty indicates that the timescale of angiosperm diversification is much less certain than previous molecular dating studies have suggested. Discord between molecular clock and purely fossil-based interpretations of angiosperm diversification may be a consequence of false precision on both sides. We reject a post-Jurassic origin of angiosperms, supporting the notion of a cryptic early history of angiosperms, but this history may be as much as 121 Myr, or as little as 23 Myr. These conclusions remain compatible with palaeobotanical evidence and a more general KTR in which major groups of angiosperms diverged later within the Cretaceous, alongside the diversification of pollinators, herbivores and their predators.

Was Charles Darwin right in his explanation of the ‘abominable mystery’?

The site and time of origin of angiosperms are still debated. The co-occurrence of many of the early branching lineages of flowering plants in a region somewhere between Australia and the SW Pacific islands suggests a possible Gondwanan origin of angiosperms. The recent recognition of Zealandia, a 94% submerged continent in the east of Australia, could explain the discrepancy between molecular clocks and fossil records about the age of angiosperms, supporting the old Darwinian hypothesis of a “lost continent” to explain the “abominable mystery” regarding the origin and rapid radiation of flowering plants.

Was Charles Darwin right in his explanation of the ‘abominable mystery’?

The site and time of origin of angiosperms are still debated. The co-occurrence of many of the early branching lineages of flowering plants in a region somewhere between Australia and the SW Pacific islands suggests a possible Gondwanan origin of angiosperms. The recent recognition of Zealandia, a 94% submerged continent in the east of Australia, could explain the discrepancy between molecular clocks and fossil records about the age of angiosperms, supporting the old Darwinian hypothesis of a “lost continent” to explain the “abominable mystery” regarding the origin and rapid radiation of flowering plants.

Early Cretaceous Umkomasia from Mongolia: implications for homology of corystosperm cupules

Corystosperms, a key extinct group of Late Permian to Early Cretaceous plants, are important for understanding seed plant phylogeny, including the evolution of the angiosperm carpel and anatropous bitegmic ovule. Here, we describe a new species of corystosperm seed-bearing organ, Umkomasia mongolica sp. nov., based on hundreds of three-dimensionally preserved mesofossils from the Early Cretaceous of Mongolia. Individual seed-bearing units of U. mongolica consist of a bract subtending an axis that bifurcates, with each fork (cupule stalk) bearing a cupule near the tip. Each cupule is formed by the strongly reflexed cupule stalk and two lateral flaps that partially enclose an erect seed. The seed is borne at, or close to, the tip of the reflexed cupule stalk, with the micropyle oriented towards the stalk base. The corystosperm cupule is generally interpreted as a modified leaf that bears a seed on its abaxial surface. However, U. mongolica suggests that an earlier interpretation, in which the seed is borne directly on an axis (shoot), is equally likely. The 'axial' interpretation suggests a possible relationship of corystosperms to Ginkgo. It also suggests that the cupules of corystosperms may be less distinct from those of Caytonia than has previously been supposed.

Phylogenetic diversification of Early Cretaceous seed plants: The compound seed cone of Doylea tetrahedrasperma

PREMISE OF THE STUDY

Discovery of cupulate ovules of Doylea tetrahedrasperma within a compact, compound seed cone highlights the rich diversity of fructification morphologies, pollination biologies, postpollination enclosure of seeds, and systematic diversity of Early Cretaceous gymnosperms.

METHODS

Specimens were studied using the cellulose acetate peel technique, three-dimensional reconstructions (in AVIZO), and morphological phylogenetic analyses (in TNT).

KEY RESULTS

Doylea tetrahedrasperma has bract/fertile short shoot complexes helically arranged within a compact, compound seed cone. Complexes diverge from the axis as a single unit and separate distally into a free bract tip and two sporophylls. Each sporophyll bears a single, abaxial seed, recurved toward the cone axis, that is enveloped after pollinaton by sporophyll tissue, forming a closed cupule. Ovules are pollinated by bisaccate grains captured by micropylar pollination horns.

CONCLUSIONS

The unique combination of characters shown by D. tetrahedrasperma includes the presence of cupulate seeds borne in conifer-like compound seed cones, an ovuliferous scale analogue structurally equivalent to the ovulate stalk of Ginkgo biloba, gymnospermous pollination, and nearly complete enclosure of mature seeds. These features characterize the Doyleales ord. nov., clearly distinguish it from the seed fern order Corystospermales, and allow for recognition of another recently described Early Cretaceous seed plant as a second species in genus Doylea. A morphological phylogenetic analysis highlights systematic relationships of the Doyleales ord. nov. and emphasizes the explosive phylogenetic diversification of gymnosperms that was underway at the time when flowering plants may have originated and/or first began to radiate.

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.

Angiosperm ovules: diversity, development, evolution

BACKGROUND

Ovules as developmental precursors of seeds are organs of central importance in angiosperm flowers and can be traced back in evolution to the earliest seed plants. Angiosperm ovules are diverse in their position in the ovary, nucellus thickness, number and thickness of integuments, degree and direction of curvature, and histological differentiations. There is a large body of literature on this diversity, and various views on its evolution have been proposed over the course of time. Most recently evo-devo studies have been concentrated on molecular developmental genetics in ovules of model plants.

SCOPE

The present review provides a synthetic treatment of several aspects of the sporophytic part of ovule diversity, development and evolution, based on extensive research on the vast original literature and on experience from my own comparative studies in a broad range of angiosperm clades.

CONCLUSIONS

In angiosperms the presence of an outer integument appears to be instrumental for ovule curvature, as indicated from studies on ovule diversity through the major clades of angiosperms, molecular developmental genetics in model species, abnormal ovules in a broad range of angiosperms, and comparison with gymnosperms with curved ovules. Lobation of integuments is not an atavism indicating evolution from telomes, but simply a morphogenetic constraint from the necessity of closure of the micropyle. Ovule shape is partly dependent on locule architecture, which is especially indicated by the occurrence of orthotropous ovules. Some ovule features are even more conservative than earlier assumed and thus of special interest in angiosperm macrosystematics.

The evolution of seeds

The evolution of the seed represents a remarkable life-history transition for photosynthetic organisms. Here, we review the recent literature and historical understanding of how and why seeds evolved. Answering the 'how' question involves a detailed understanding of the developmental morphology and anatomy of seeds, as well as the genetic programs that determine seed size. We complement this with a special emphasis on the evolution of dormancy, the characteristic of seeds that allows for long 'distance' time travel. Answering the 'why' question involves proposed hypotheses of how natural selection has operated to favor the seed life-history phenomenon. The recent flurry of research describing the comparative biology of seeds is discussed. The review will be divided into sections dealing with: (1) the development and anatomy of seeds; (2) the endosperm; (3) dormancy; (4) early seed-like structures and the transition to seeds; and (5) the evolution of seed size (mass). In many cases, a special distinction is made between angiosperm and gymnosperm seeds. Finally, we make some recommendations for future research in seed biology.

A duplicate gene rooting of seed plants and the phylogenetic position of flowering plants

Flowering plants represent the most significant branch in the tree of land plants, with respect to the number of extant species, their impact on the shaping of modern ecosystems and their economic importance. However, unlike so many persistent phylogenetic problems that have yielded to insights from DNA sequence data, the mystery surrounding the origin of angiosperms has deepened with the advent and advance of molecular systematics. Strong statistical support for competing hypotheses and recent novel trees from molecular data suggest that the accuracy of current molecular trees requires further testing. Analyses of phytochrome amino acids using a duplicate gene-rooting approach yield trees that unite cycads and angiosperms in a clade that is sister to a clade in which Gingko and Cupressophyta are successive sister taxa to gnetophytes plus Pinaceae. Application of a cycads + angiosperms backbone constraint in analyses of a morphological dataset yields better resolved trees than do analyses in which extant gymnosperms are forced to be monophyletic. The results have implications both for our assessment of uncertainty in trees from sequence data and for our use of molecular constraints as a way to integrate insights from morphological and molecular evidence.

Nystroemiaceae, a new family of Permian gymnosperms from China with an unusual combination of features

Nystroemiaceae is proposed as a new family of gymnosperms from the Permian of Cathaysia that adds to the diversity of gymnosperms known from this critical time in seed plant evolution. This family is characterized by bifurcating and highly branched pinnate ovuliferous organs bearing bicornute ovules (seeds) and entire leaves with anastomozing veins that are born on complex and modern-looking branching systems with clear axillary branching. The reconstruction is based on numerous large specimens from two localities in North China, in which the different plant parts are attached to each other. The ovulate structures show some apparently plesiomorphic (primitive) character states more typical of early seed plants, whereas the leaves and branches show the clearly apomorphic (derived) character states of broad-leaved gymnosperms.

Distinguishing angiophytes from the earliest angiosperms: A Lower Cretaceous (Valanginian-Hauterivian) fruit-like reproductive structure

A remarkably diverse Lower Cretaceous (Valanginian-Hauterivian) flora at Apple Bay, Vancouver Island, preserves seed plants at an important time of floristic evolutionary transition, about the same time as the earliest flowering plant megafossils. The fossils are permineralized in carbonate concretions and include tetrahedral seeds within cupule- or carpel-like structures. These enclosing structures, composed of elongate sclerenchyma cells with spiral thickenings that grade externally to a few layers of parenchyma, are vascularized by one collateral vascular bundle and lack trichomes. They apparently broke open to release the tightly enclosed seeds by valves. Seeds are similar to those of the Triassic seed fern Petriellaea, but are about 100 million years younger and differ in size, vascularization, integumentary anatomy, seed attachment, and number of seeds/cupule. These new seeds are described as Doylea tetrahedrasperma gen. et sp. nov., tentatively assigned to Corystospermales. Inverted cupules are reminiscent of an outer angiosperm integument rather than a carpel. Like fruits, cupules opened to release seeds at maturity, thereby foretelling several aspects of angiospermy. They show that nearly total ovule enclosure, a level of organization approaching angiospermy, was achieved by advanced seed ferns during the Mesozoic.