How deep is the conflict between molecular and fossil evidence on the age of angiosperms?

Pan-genome and phylogenomic analyses highlight Hevea species delineation and rubber trait evolution

The para rubber tree (Hevea brasiliensis) is the world's sole commercial source of natural rubber, a vital industrial raw material. However, the narrow genetic diversity of this crop poses challenges for rubber breeding. Here, we generate high-quality de novo genome assemblies for three H. brasiliensis cultivars, two H. brasiliensis wild accessions, and three other Hevea species (H. nitida, H. pauciflora, and H. benthamiana). Through analyzing genomes of 94 Hevea accessions, we identify five distinct lineages that do not align with their previous species delineations. We discover multiple accessions with hybrid origins between these lineages, indicating incomplete reproductive isolation between them. Only two out of four wild lineages have been introduced to commercial rubber cultivars. Furthermore, we reveal that the rubber production traits emerged following the development of a large REF/SRPP gene cluster and its functional specialization in rubber-producing laticifers within this genus. These findings would enhance rubber breeding and benefit research communities.

The meaning of mass extinctions and what the fossil record tells us about angiosperm survival at K-Pg: a reply to Hagen (2024)

Last year, we published research using phylogenetic comparative methods (PCMs) to reveal no phylogenetic evidence for elevated lineage-level extinction rates in angiosperms across K-Pg (Thompson JB, Ramírez-Barahona S. 2023 No phylogenetic evidence for angiosperm mass extinction at the Cretaceous-Palaeogene (K-Pg) boundary. Biol. Lett. 19, 20230314. (doi:10.1098/rsbl.2023.0314)), results that are in step with the global angiosperm fossil record. In a critique of our paper (Hagen ER. 2024 A critique of Thompson and Ramírez-Barahona (2023) or: how I learned to stop worrying and love the fossil record. EcoEvoRxiv. (doi:10.32942/X2631W)), simulation work is presented to argue we erred in our methodological choices and interpretations, and that we should have deferred to fossil evidence. In our opinion, underlying this critique are poor methodological choices on simulations and philosophical problems surrounding the definition of a mass extinction event, which leads to incorrect interpretations of both the fossil record and PCMs. We further argue that deferring to one source of evidence in favour of the other shuts the door to important evolutionary and philosophical questions.

A critique of Thompson and Ramírez-Barahona (2023) or: how I learned to stop worrying and love the fossil record

A recent study published in Biology Letters by Thompson and Ramírez-Barahona (2023) argued that, according to analyses of diversification on two massive molecular phylogenies comprising thousands of species, there is no evidence that angiosperms (i.e. flowering plants) were affected by the Cretaceous-Paleogene mass extinction. Here, I critique these conclusions from both methodological and philosophical perspectives. I demonstrate that the methods used in their study possess statistical limitations that strongly reduce the power to detect a true mass extinction event using data similar to those analysed by Thompson and Ramírez-Barahona (2023). Additionally, I use their study as a springboard to examine the relationship between phylogenetic and fossil evidence in diversification studies.

Phylogenomics and the rise of the angiosperms

Angiosperms are the cornerstone of most terrestrial ecosystems and human livelihoods1,2. A robust understanding of angiosperm evolution is required to explain their rise to ecological dominance. So far, the angiosperm tree of life has been determined primarily by means of analyses of the plastid genome3,4. Many studies have drawn on this foundational work, such as classification and first insights into angiosperm diversification since their Mesozoic origins5-7. However, the limited and biased sampling of both taxa and genomes undermines confidence in the tree and its implications. Here, we build the tree of life for almost 8,000 (about 60%) angiosperm genera using a standardized set of 353 nuclear genes8. This 15-fold increase in genus-level sampling relative to comparable nuclear studies9 provides a critical test of earlier results and brings notable change to key groups, especially in rosids, while substantiating many previously predicted relationships. Scaling this tree to time using 200 fossils, we discovered that early angiosperm evolution was characterized by high gene tree conflict and explosive diversification, giving rise to more than 80% of extant angiosperm orders. Steady diversification ensued through the remaining Mesozoic Era until rates resurged in the Cenozoic Era, concurrent with decreasing global temperatures and tightly linked with gene tree conflict. Taken together, our extensive sampling combined with advanced phylogenomic methods shows the deep history and full complexity in the evolution of a megadiverse clade.

Disparity of cycad leaves dispels the living fossil metaphor

The living fossil metaphor is tightly linked with the cycads. This group of gymnosperms is supposed to be characterised by long-term morphological stasis, particularly after their peak of diversity and disparity in the Jurassic. However, no formal test of this hypothesis exists. Here, we use a recent phylogenetic framework and an improved character matrix to reconstruct the Disparity Through Time for cycad leaves using a Principal Coordinate Analysis and employing Pre-Ordination Ancestral State Reconstruction to test the impact of sampling on the results. Our analysis shows that the cycad leaf morsphospace expanded up to the present, with numerous shifts in its general positioning, independently of sampling biases. Moreover, they also show that Zamiaceae expanded rapidly in the Early Cretaceous and continued to expand up to the present, while now-extinct clades experienced a slow contraction from their peak in the Triassic. We also show that rates of evolution were constantly high up to the Early Cretaceous, and then experienced a slight decrease in the Paleogene, followed by a Neogene acceleration. These results show a much more dynamic history for cycads, and suggest that the 'living fossil' metaphor is actually a hindrance to our understanding of their macroevolution.

Morpho Evo-Devo of the Gynoecium: Heterotopy, Redefinition of the Carpel, and a Topographic Approach

Since the 19th century, we have had countless debates, sometimes acrimonious, about the nature of the gynoecium. A pivotal question has been whether all angiosperms possess carpels or if some or all angiosperms are acarpellate. We can resolve these debates if we do not define the carpel as a closed megasporophyll but simply as an appendage that encloses the placenta or a single ovule. This redefinition may, however, lead to confusion because often it may not be clear whether the traditional (classical) definition of the carpel or the redefinition is implied. Therefore, a topographic approach is proposed that is compatible with the redefinition. According to this approach, gynoecia comprise one or more gynoecial appendages and placentas or single ovules that may be formed in different positions. Heterotopy refers to these different positions. In the context of evo-devo, which explores evolutionary changes in development, morpho evo-devo delves into spatial shifts of the placentas and ovules leading to heterotopy. Furthermore, it considers shifts in timing (heterochrony) and other processes leading to heteromorphy. Recognizing spatial shifting of the placentas or a single ovule and other evolutionary processes opens up new vistas in the search for the ancestor(s) of angiosperms and their gynoecia.

Genomic evidence for rediploidization and adaptive evolution following the whole-genome triplication

Whole-genome duplication (WGD), or polyploidy, events are widespread and significant in the evolutionary history of angiosperms. However, empirical evidence for rediploidization, the major process where polyploids give rise to diploid descendants, is still lacking at the genomic level. Here we present chromosome-scale genomes of the mangrove tree Sonneratia alba and the related inland plant Lagerstroemia speciosa. Their common ancestor has experienced a whole-genome triplication (WGT) approximately 64 million years ago coinciding with a period of dramatic global climate change. Sonneratia, adapting mangrove habitats, experienced extensive chromosome rearrangements post-WGT. We observe the WGT retentions display sequence and expression divergence, suggesting potential neo- and sub-functionalization. Strong selection acting on three-copy retentions indicates adaptive value in response to new environments. To elucidate the role of ploidy changes in genome evolution, we improve a model of the polyploidization-rediploidization process based on genomic evidence, contributing to the understanding of adaptive evolution during climate change.

The angiosperm radiation played a dual role in the diversification of insects and insect pollinators

Interactions with angiosperms have been hypothesised to play a crucial role in driving diversification among insects, with a particular emphasis on pollinator insects. However, support for coevolutionary diversification in insect-plant interactions is weak. Macroevolutionary studies of insect and plant diversities support the hypothesis that angiosperms diversified after a peak in insect diversity in the Early Cretaceous. Here, we used the family-level fossil record of insects as a whole, and insect pollinator families in particular, to estimate diversification rates and the role of angiosperms on insect macroevolutionary history using a Bayesian process-based approach. We found that angiosperms played a dual role that changed through time, mitigating insect extinction in the Cretaceous and promoting insect origination in the Cenozoic, which is also recovered for insect pollinator families only. Although insects pollinated gymnosperms before the angiosperm radiation, a radiation of new pollinator lineages began as angiosperm lineages increased, particularly significant after 50 Ma. We also found that global temperature, increases in insect diversity, and spore plants were strongly correlated with origination and extinction rates, suggesting that multiple drivers influenced insect diversification and arguing for the investigation of different explanatory variables in further studies.

Diversification of flowering plants in space and time

The rapid diversification and high species richness of flowering plants is regarded as 'Darwin's second abominable mystery'. Today the global spatiotemporal pattern of plant diversification remains elusive. Using a newly generated genus-level phylogeny and global distribution data for 14,244 flowering plant genera, we describe the diversification dynamics of angiosperms through space and time. Our analyses show that diversification rates increased throughout the early Cretaceous and then slightly decreased or remained mostly stable until the end of the Cretaceous-Paleogene mass extinction event 66 million years ago. After that, diversification rates increased again towards the present. Younger genera with high diversification rates dominate temperate and dryland regions, whereas old genera with low diversification dominate the tropics. This leads to a negative correlation between spatial patterns of diversification and genus diversity. Our findings suggest that global changes since the Cenozoic shaped the patterns of flowering plant diversity and support an emerging consensus that diversification rates are higher outside the tropics.

Jurassic NLR: Conserved and dynamic evolutionary features of the atypically ancient immune receptor ZAR1

Plant nucleotide-binding leucine-rich repeat (NLR) immune receptors generally exhibit hallmarks of rapid evolution, even at the intraspecific level. We used iterative sequence similarity searches coupled with phylogenetic analyses to reconstruct the evolutionary history of HOPZ-ACTIVATED RESISTANCE1 (ZAR1), an atypically conserved NLR that traces its origin to early flowering plant lineages ∼220 to 150 million yrs ago (Jurassic period). We discovered 120 ZAR1 orthologs in 88 species, including the monocot Colocasia esculenta, the magnoliid Cinnamomum micranthum, and most eudicots, notably the Ranunculales species Aquilegia coerulea, which is outside the core eudicots. Ortholog sequence analyses revealed highly conserved features of ZAR1, including regions for pathogen effector recognition and cell death activation. We functionally reconstructed the cell death activity of ZAR1 and its partner receptor-like cytoplasmic kinase (RLCK) from distantly related plant species, experimentally validating the hypothesis that ZAR1 evolved to partner with RLCKs early in its evolution. In addition, ZAR1 acquired novel molecular features. In cassava (Manihot esculenta) and cotton (Gossypium spp.), ZAR1 carries a C-terminal thioredoxin-like domain, and in several taxa, ZAR1 duplicated into 2 paralog families, which underwent distinct evolutionary paths. ZAR1 stands out among angiosperm NLR genes for having experienced relatively limited duplication and expansion throughout its deep evolutionary history. Nonetheless, ZAR1 also gave rise to noncanonical NLRs with integrated domains and degenerated molecular features.

Fluctuation in the diversity of mayflies (Insecta, Ephemerida) as documented in the fossil record

Due to their aquatic larvae, the evolution of mayflies is intricately tied to environmental changes affecting lakes and rivers. Despite a rich fossil record, little is known about the factors shaping the pattern of diversification of mayflies in deep time. We assemble an unprecedented dataset encompassing all fossil occurrences of mayflies and perform a Bayesian analysis to identify periods of increased origination or extinction. We provide strong evidence for a major extinction of mayflies in the mid-Cretaceous. This extinction and subsequent faunal turnover were probably connected with the rise of angiosperms. Their dominance caused increased nutrient input and changed the chemistry of the freshwater environments, a trend detrimental mainly to lacustrine insects. Mayflies underwent a habitat shift from hypotrophic lakes to running waters, where most of their diversity has been concentrated from the Late Cretaceous to the present.

Intra-gastric phytoliths provide evidence for folivory in basal avialans of the Early Cretaceous Jehol Biota

Angiosperms became the dominant plant group in early to middle Cretaceous terrestrial ecosystems, coincident with the timing of the earliest pulse of bird diversification. While living birds and angiosperms exhibit strong interactions across pollination/nectivory, seed dispersal/frugivory, and folivory, documentation of the evolutionary origins and construction of that ecological complexity remains scarce in the Mesozoic. Through the first study of preserved in situ dietary derived phytoliths in a nearly complete skeleton of the early diverging avialan clade Jeholornithidae, we provide direct dietary evidence that Jeholornis consumed leaves likely from the magnoliid angiosperm clade, and these results lend further support for early ecological connections among the earliest birds and angiosperms. The broad diet of the early diverging avialan Jeholornis including at least fruits and leaves marks a clear transition in the early evolution of birds in the establishment of an arboreal (angiosperm) herbivore niche in the Early Cretaceous occupied largely by birds today. Morphometric reanalysis of the lower jaw of Jeholornis further supports a generalized morphology shared with other herbivorous birds, including an extant avian folivore, the hoatzin.

A new remarkable Early Cretaceous nelumbonaceous fossil bridges the gap between herbaceous aquatic and woody protealeans

Dating back to the late Early Cretaceous, the macrofossil record of the iconic lotus family (Nelumbonaceae) is one of the oldest of flowering plants and suggests that their unmistakable leaves and nutlets embedded in large pitted receptacular fruits evolved relatively little in the 100 million years since their first known appearance. Here we describe a new fossil from the late Barremian/Aptian Crato Formation flora (NE Brazil) with both vegetative and reproductive structures, Notocyamus hydrophobus gen. nov. et sp. nov., which is now the oldest and most complete fossil record of Nelumbonaceae. In addition, it displays a unique mosaic of ancestral and derived macro- and micromorphological traits that has never been documented before in this family. This new Brazilian fossil-species also provides a rare illustration of the potential morphological and anatomical transitions experienced by Nelumbonaceae prior to a long period of relative stasis. Its potential plesiomorphic and apomorphic features shared with Proteaceae and Platanaceae not only fill a major morphological gap within Proteales but also provide new support for their unexpected relationships first suggested by molecular phylogenies.

Uncertainties surrounding the oldest fossil record of diatoms

Molecular clocks estimate that diatom microalgae, one of Earth's foremost primary producers, originated near the Triassic-Jurassic boundary (200 Ma), which is close in age to the earliest, generally accepted diatom fossils of the genus Pyxidicula. During an extensive search for Jurassic diatoms from twenty-five sites worldwide, three sites yielded microfossils initially recognized as diatoms. After applying stringent safeguards and evaluation criteria, however, the fossils found at each of the three sites were rejected as new diatom records. This led us to systematically reexamine published evidence in support of Lower- and Middle-Jurassic Pyxidicula fossils. Although Pyxidicula resembles some extant radial centric diatoms and has character states that may have been similar to those of ancestral diatoms, we describe numerous sources of uncertainty regarding the reliability of these records. We conclude that the Lower Jurassic Pyxidicula fossils were most likely calcareous nannofossils, whereas the Middle Jurassic Pyxidicula species has been reassigned to the Lower Cretaceous and is likely a testate amoeba, not a diatom. Excluding the Pyxidicula fossils widens the gap between the estimated time of origin and the oldest abundant fossil diatom record to 75 million years. This study underscores the difficulties in discovering and validating ancient microfossils.

Advances in the understanding of Blattodea evolution: Insights from phylotranscriptomics and spermathecae

Cockroaches, an ancient and diverse group of insects on earth that originated in the Carboniferous, displays a wide array of morphology or biology diversity. The spermatheca is an organ of the insect reproductive system; the diversity of spermathecae might be the adaption to different mating and sperm storage strategies. Yet a consensus about the phylogenetic relationships among the main lineages of Blattodea and the evolution of spermatheca has not been reached until now. Here we added the transcriptome data of Anaplectidae for the first time and supplemented other family level groups (such as Blaberidae, Corydiidae) to address the pending issues. Our results showed that Blattoidea was recovered as sister to Corydioidea, which was strongly supported by molecular evidence. In Blattoidea, (Lamproblattidae + Anaplectidae) + (Cryptocercidae + Termitoidae) was strongly supported by our molecular data. In Blaberoidea, Pseudophyllodromiidae and Blaberidae were recovered to be monophyletic, while Blattellidae was found to be paraphyletic with respect to Malaccina. Ectobius sylvestris + Malaccina discoidalis formed the sister group to other Blaberoidea; Blattellidae (except Malaccina discoidalis) + Nyctiboridae was found as the sister of Blaberidae. Corydiidae was recovered to be non-monophyletic due to the embedding of Nocticola sp. Our ASR analysis of spermatheca suggested that primary spermathecae were present in the common ancestor, and it transformed at least six times during the evolutionary history of Blattodea. The evolution of spermatheca could be described as a unidirectional trend: the increased size to accommodate more sperm. Furthermore, major splits within the existing genera of cockroaches occurred in the Upper Paleogene to Neogene. Our study provides strong support for the relationship among three superfamilies and offers some new insights into the phylogeny of cockroaches. Meanwhile, this study also provides basic knowledge on the evolution of spermathecae and reproductive patterns.

Is Santaniella a ranunculid? Reassessment of this enigmatic fossil angiosperm from the Lower Cretaceous (Aptian, Crato Konservat-Lagerstätte, Brazil) provides a new interpretation

PREMISE

The Lower Cretaceous Crato Konservat-Lagerstätte (CKL) preserves a rich flora that includes early angiosperms from northern Gondwana. From this area, the recently described fossil genus Santaniella was interpreted as a ranunculid (presumably Ranunculaceae). However, based on our examination of an additional specimen and a new phylogenetic analysis, we offer an alternative interpretation.

METHODS

The new fossil was collected from an active quarry for paving stones in the state of Ceará, northeastern Brazil. We assessed support for alternative phylogenetic hypotheses using a combined analysis of morphological data and DNA sequence data using Bayesian inference. We used a consensus network to visualize the posterior distribution of trees, and we used RoguePlot to illustrate the support for alternative positions on a scaffold tree.

RESULTS

The new material includes a flower-like structure not present in the original material and also includes follicles preserved at early stages of development. The flower-like structure is a compact terminal cluster of elliptical sterile laminar organs surrounding internal filamentous structures that occur on flexuous axes. Phylogenetic analyses did not support the fossil placement among eudicots. Instead, Santaniella appears to belong in the magnoliid clade.

CONCLUSIONS

The presence of seeds in a marginal-linear placentation and enclosed in a follicle supports the fossil as an angiosperm. However, even though most characters are clearly recognizable, its combination of characters does not provide strong support for a close relationship to any extant order of flowering plants. Its position in the magnoliid clade is intriguing and, based on plicate carpels, it is definitely a mesangiosperm.

New Fossil Evidence Suggests That Angiosperms Flourished in the Middle Jurassic

Angiosperms are a group of plants with the highest rate of evolution, the largest number of species, the widest distribution and the strongest adaptability. Needless to say, angiosperms are the most important group for the humans. The studies on the origin, evolution and systematics of angiosperms have been the major challenges in plant sciences. However, the origin and early history of angiosperms remains poorly understood and controversial among paleobotanists. Some paleobotanists insist that there were no angiosperms in the pre-Cretaceous age. However, this conclusion is facing increasing challenges from fossil evidence, especially Early Jurassic Nanjinganthus, which is based on over two hundred specimens of fossil flowers. Studying more fossil plants is the only reliable way to elucidate the origin and early evolution of angiosperms. Here, we document a new species of angiosperms, Qingganninginfructus formosa gen. et sp. nov, and provide the first detailed three-dimensional morphology of Qingganninginfructus gen. nov from the Middle Jurassic of Northwest China. A Micro-CT examination shows that the best-preserved fossil infructescence has eleven samaroid fruits, each with a single basal ovule. Since these fossils are distinct in morphology and organization from all organs of known gymnosperms and angiosperms (the latter are defined by their enclosed ovules), we interpret Qingganninginfructus as a new genus of angiosperms including a new species, Q. formosa gen. et sp. nov., and an unspecified species from the Middle Jurassic of Northwest China. The discovery of this new genus of angiosperms from the Middle Jurassic, in addition to the existing records, undermines the "no angiosperms until the Cretaceous" stereotype and updates the perspective on the origin and early history of angiosperms.

Biodiversity of ecosystems in an arid setting: The late Albian plant communities and associated biota from eastern Iberia

Deserts are stressful environments where the living beings must acquire different strategies to survive due to the water stress conditions. From the late Albian to the early Cenomanian, the northern and eastern parts of Iberia were the location of the desert system represented by deposits assigned to the Utrillas Group, which bear abundant amber with numerous bioinclusions, including diverse arthropods and vertebrate remains. In the Maestrazgo Basin (E Spain), the late Albian to early Cenomanian sedimentary succession represents the most distal part of the desert system (fore-erg) that was characterised by an alternation of aeolian and shallow marine sedimentary environments in the proximity of the Western Tethys palaeo-coast, with rare to frequent dinoflagellate cysts. The terrestrial ecosystems from this area were biodiverse, and comprised plant communities whose fossils are associated with sedimentological indicators of aridity. The palynoflora dominated by wind-transported conifer pollen is interpreted to reflect various types of xerophytic woodlands from the hinterlands and the coastal settings. Therefore, fern and angiosperm communities abundantly grew in wet interdunes and coastal wetlands (temporary to semi-permanent freshwater/salt marshes and water bodies). In addition, the occurrence of low-diversity megafloral assemblages reflects the existence of coastal salt-influenced settings. The palaeobotanical study carried out in this paper which is an integrative work on palynology and palaeobotany, does not only allow the reconstruction of the vegetation that developed in the mid-Cretaceous fore-erg from the eastern Iberia, in addition, provides new biostratigraphic and palaeogeographic data considering the context of angiosperm radiation as well as the biota inferred in the amber-bearing outcrops of San Just, Arroyo de la Pascueta and La Hoya (within Cortes de Arenoso succesion). Importantly, the studied assemblages include Afropollis, Dichastopollenites, Cretacaeiporites together with pollen produced by Ephedraceae (known for its tolerance to arid conditions). The presence of these pollen grains, typical for northern Gondwana, associates the Iberian ecosystems with those characterising the mentioned region.

Plant biology: Insect herbivory on fossil leaves provides the oldest evidence of sleep movements in plants

Only a few groups of plants can move their leaves at night. A new study documents sleep movements in fossil leaves that are older than the dinosaurs, suggesting that this behavior is much more ancient than previously appreciated.

Micro-CT results exhibit ovules enclosed in the ovaries of Nanjinganthus

The Early Jurassic angiosperm Nanjinganthus has triggered a heated debate among botanists, partially due to the fact that the enclosed ovules were visible to naked eyes only when the ovary is broken but not visible when the closed ovary is intact. Although traditional technologies cannot confirm the existence of ovules in a closed ovary, newly available Micro-CT can non-destructively reveal internal features of fossil plants. Here, we performed Micro-CT observations on three dimensionally preserved coalified compressions of Nanjinganthus. Our outcomes corroborate the conclusion given by Fu et al., namely, that Nanjinganthus is an Early Jurassic angiosperm.

An Anatomically Preserved Cone-like Flower from the Lower Cretaceous of China

Although diverse fossil angiosperms (including their reproductive organs) have been reported from the Early Cretaceous, few of them are well-documented due to poor preservation and limited technologies available to apply. For example, paraffin sectioning, a routine technology applied to reveal the anatomical details of extant plants, was hitherto at most rarely applied to fossil plants. This undermines the comparability between the outcomes of studies on fossil and extant plants, and makes our understanding on plants incomplete and biased. Here, we applied paraffin sectioning technology, in addition to light microscopy, SEM, and TEM, to document a fossil reproductive organ, Xilinia gen. nov., from the Early Cretaceous in Inner Mongolia, China. The anatomical details of this new reproductive organ were documented. Xilinia bears a remarkable resemblance to conifer cones, although its ovules are enclosed in carpels. The paradoxical cone-like morphology of Xilinia appears to represent a transitional snapshot of plant evolution that is absent in extant plants.

Model Species to Investigate the Origin of Flowers

The angiosperms, or flowering plants, arose at least 135 million years ago (Ma) and rapidly diversified to form over 300,000 species alive today. This group appears, however, to have separated from its closest living relatives, the extant gymnosperms, much earlier: over 300 Ma. Representatives of basally-diverging angiosperm lineages are of key importance to studies aimed at reconstructing the most recent common ancestor of living angiosperms, including its morphological, anatomical, eco-physiological and molecular aspects. Furthermore, evo-devo comparisons of angiosperms with living gymnosperms may help to determine how the many novel aspects of angiosperms, including those of the flower, first came about. This chapter reviews literature on the origin of angiosperms and focusses on basally-diverging angiosperms and gymnosperms that show advantages as potential experimental models, reviewing information and protocols for the use of these species in an evo-devo context. The final section suggests a means by which data from living and fossil groups could be integrated to better elucidate evolutionary events that took place on the long stem-lineage that apparently preceded the radiation of living angiosperms.

Illusion of flight? Absence, evidence and the age of winged insects

The earliest fossils of winged insects (Pterygota) are mid-Carboniferous (latest Mississippian, 328–324 Mya), but estimates of their age based on fossil-calibrated molecular phylogenetic studies place their origin at 440–370 Mya during the Silurian or Devonian. This discrepancy would require that winged insects evaded fossilization for at least the first ~50 Myr of their history. Here, we examine the plausibility of such a gap in the fossil record, and possible explanations for it, based on comparisons with the fossil records of other arthropod groups, the distribution of first occurrence dates of pterygote families, phylogenetically informed simulations of the fossilization of Palaeozoic insects, and re-analysis of data presented by Misof and colleagues using updated fossil calibrations under a variety of prior probability settings. We do not find support for the mechanisms previously suggested to account for such an extended gap in the pterygote fossil record, including sampling bias, preservation bias, and body size. We suggest that inference of an early origin of Pterygota long prior to their first appearance in the fossil record is probably an analytical artefact of taxon sampling and choice of fossil calibration points, possibly compounded by heterogeneity in rates of sequence evolution or speciation, including radiations or ‘bursts’ during their early history.

Cutting the long branches: Consilience as a path to unearth the evolutionary history of Gnetales

The Gnetales are one of the most fascinating groups within seed plants. Although the advent of molecular phylogenetics has generated some confidence in their phylogenetic placement of Gnetales within seed plants, their macroevolutionary history still presents many unknowns. Here, we review the reasons for such unknowns, and we focus the discussion on the presence of “long branches” both in their molecular and morphological history. The increased rate of molecular evolution and genome instability as well as the numerous unique traits (both reproductive and vegetative) in the Gnetales have been obstacles to a better understanding of their evolution. Moreover, the fossil record of the Gnetales, though relatively rich, has not yet been properly reviewed and investigated using a phylogenetic framework. Despite these apparent blocks to progress we identify new avenues to enable us to move forward. We suggest that a consilience approach, involving different disciplines such as developmental genetics, paleobotany, molecular phylogenetics, and traditional anatomy and morphology might help to “break” these long branches, leading to a deeper understanding of this mysterious group of plants.

Pre-Carpels from the Middle Triassic of Spain

In stark contrast to the multitude of hypotheses on carpel evolution, there is little fossil evidence testing these hypotheses. The recent discovery of angiosperms from the Early Jurassic makes the search for precursors of angiosperm carpels in the Triassic more promising. Our light microscopic and SEM observations on Combina gen. nov., a cone-like organ from the Middle Triassic of Spain, indicate that its lateral unit includes an axillary anatropous ovule and a subtending bract, and the latter almost fully encloses the former. Such an observation not only favors one of the theoretical predictions but also makes some Mesozoic gymnosperms (especially conifers and Combina) comparable to some angiosperms. Combina gen. nov. appears to be an important chimeric fossil plant that may complete the evidence chain of the origin of carpels in geological history, partially narrowing the gap between angiosperms and gymnosperms.

A high-quality Buxus austro-yunnanensis (Buxales) genome provides new insights into karyotype evolution in early eudicots

Background

Eudicots are the most diverse group of flowering plants that compromise five well-defined lineages: core eudicots, Ranunculales, Proteales, Trochodendrales, and Buxales. However, the phylogenetic relationships between these five lineages and their chromosomal evolutions remain unclear, and a lack of high-quality genome analyses for Buxales has hindered many efforts to address this knowledge gap.

Results

Here, we present a high-quality chromosome-level genome of Buxus austro-yunnanensis (Buxales). Our phylogenomic analyses revealed that Buxales and Trochodendrales are genetically similar and classified as sisters. Additionally, both are sisters to the core eudicots, while Ranunculales was found to be the first lineage to diverge from these groups. Incomplete lineage sorting and hybridization were identified as the main contributors to phylogenetic discordance (34.33%) between the lineages. In fact, B. austro-yunnanensis underwent only one whole-genome duplication event, and collinear gene phylogeny analyses suggested that separate independent polyploidizations occurred in the five eudicot lineages. Using representative genomes from these five lineages, we reconstructed the ancestral eudicot karyotype (AEK) and generated a nearly gapless karyotype projection for each eudicot species. Within core eudicots, we recovered one common chromosome fusion event in asterids and malvids, respectively. Further, we also found that the previously reported fused AEKs in Aquilegia (Ranunculales) and Vitis (core eudicots) have different fusion positions, which indicates that these two species have different karyotype evolution histories.

Conclusions

Based on our phylogenomic and karyotype evolution analyses, we revealed the likely relationships and evolutionary histories of early eudicots. Ultimately, our study expands genomic resources for early-diverging eudicots.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12915-022-01420-1.

Early diversifications of angiosperms and their insect pollinators: were they unlinked?

The present-day ubiquity of angiosperm-insect pollination has led to the hypothesis that these two groups coevolved early in their evolutionary history. However, recent fossil discoveries and fossil-calibrated molecular dating analyses challenge the notion that early diversifications of angiosperms and insects were inextricably linked. In this article, we examine (i) the discrepancies between dates of emergence for angiosperms and major clades of insects; (ii) the long history of gymnosperm-insect pollination modes, which likely shaped early angiosperm-insect pollination mutualisms; and (iii) how the K-Pg (Cretaceous-Paleogene) mass extinction event was vital in propelling modern angiosperm-insect mutualisms. We posit that the early diversifications of angiosperms and their insect pollinators were largely decoupled until the end of the Cretaceous.

Climate windows of opportunity for plant expansion during the Phanerozoic

Earth's long-term climate may have profoundly influenced plant evolution. Local climatic factors, including water availability, light, and temperature, play a key role in plant physiology and growth, and have fluctuated substantially over geological time. However, the impact of these key climate variables on global plant biomass across the Phanerozoic has not yet been established. Linking climate and dynamic vegetation modelling, we identify two key 'windows of opportunity' during the Ordovician and Jurassic-Paleogene capable of supporting dramatic expansions of potential plant biomass. These conditions are driven by continental dispersion, paleolatitude of continental area and a lack of glaciation, allowing for an intense hydrological cycle and greater water availability. These windows coincide with the initial expansion of land plants and the later angiosperm radiation. Our findings suggest that the timing and expansion of habitable space for plants played an important role in plant evolution and diversification.

What is the age of flowering plants?

The origin of flowering plants (angiosperms) was one of the most transformative events in the history of our planet. Despite considerable interest from multiple research fields, numerous questions remain, including the age of the group as a whole. Recent studies have reported a perplexing range of estimates for the crown-group age of angiosperms, from ~140 million years (Ma; Early Cretaceous) to 270 Ma (Permian). Both ends of the spectrum are now supported by both macroevolutionary analyses of the fossil record and fossil-calibrated molecular dating analyses. Here, we first clarify and distinguish among the three ages of angiosperms: the age of their divergence with acrogymnosperms (stem age); the age(s) of emergence of their unique, distinctive features including flowers (morphological age); and the age of the most recent common ancestor of all their living species (crown age). We then demonstrate, based on recent studies, that fossil-calibrated molecular dating estimates of the crown-group age of angiosperms have little to do with either the amount of molecular data or the number of internal fossil calibrations included. Instead, we argue that this age is almost entirely conditioned by its own prior distribution (typically a calibration density set by the user in Bayesian analyses). Lastly, we discuss which future discoveries or novel types of analyses are most likely to bring more definitive answers. In the meantime, we propose that the age of angiosperms is best described as largely unknown (140-270 Ma) and that contrasting age estimates in the literature mostly reflect conflicting prior distributions. We also suggest that future work that depends on the time scale of flowering plant diversification be designed to integrate over this vexing uncertainty.

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.

Pollen in water of unstable salinity: Evolution and function of dynamic apertures in monocot aquatics

PREMISE

The sporoderm of seed-plant pollen grains typically has apertures in which the outer sporopollenin-bearing layer is relatively sparse. The apertures allow regulation of the internal volume of the pollen grain during desiccation and rehydration (harmomegathy) and also serve as sites of pollen germination. A small fraction of angiosperms undergo pollination in water or at the water surface, where desiccation is unlikely. Their pollen grains commonly lack apertures, though with some notable exceptions. We tested a hypothesis that in some angiosperm aquatics that inhabit water of unstable salinity, the pollen apertures accommodate osmotic effects that occur during pollination in such conditions.

METHODS

Pollen grains of the tepaloid clade of the monocot order Alismatales, which contains ecologically diverse aquatic and marshy plants, were examined using light microscopy and scanning electron microscopy. We used Ruppia as a model to test pollen grain response in water of various salinities. Pollen aperture evolution was also analyzed using molecular tree topologies.

RESULTS

Phylogenetic optimizations demonstrated an evolutionary loss and two subsequent regains of the aperturate condition in the tepaloid clade of Alismatales. Both of the taxa that have reverted to aperturate pollen (Ruppia, Ruppiaceae; Althenia, Potamogetonaceae) are adapted to changeable water salinity. Direct experiments with Ruppia showed that the pollen apertures have a role in a harmomegathic response to differences in water salinity.

CONCLUSIONS

Our results showed that the inferred regain of pollen apertures represents an adaptation to changeable water salinity. We invoke a loss-and-regain scenario, prompting questions that are testable using developmental genetics and plant physiology.

Effectiveness of Two Universal Angiosperm Probe Sets Tested In Silico for Caryophyllids Taxa with Emphasis on Cacti Species

In angiosperms, huge advances in massive DNA sequencing technologies have impacted phylogenetic studies. Probe sets have been developed with the purpose of recovering hundreds of orthologous loci of targeted DNA sequences (TDS) across different plant lineages. We tested in silico the effectiveness of two universal probe sets in the whole available genomes of Caryophyllids, emphasizing phylogenetic issues in cacti species. A total of 870 TDS (517 TDS from Angiosperm v.1 and 353 from Angiosperms353) were individually tested in nine cacti species and Amaranthus hypochondriacus (external group) with ≥17 Gbp of available DNA data. The effectiveness was measured by the total number of orthologous loci recovered and their length, the percentage of loci discarded by paralogy, and the proportion of informative sites (PIS) in the alignments. The results showed that, on average, Angiosperms353 was better than Angiosperm v.1 for cacti species, since the former obtained an average of 275.6 loci that represent 123,687 bp, 2.48% of paralogous loci, and 4.32% of PIS in alignments, whereas the latter recovered 148.4 loci (37,683 bp), 10.38% of paralogous loci, and 3.49% of PIS. We recommend the use of predesigned universal probe sets for Caryophyllids, since these recover a high number of orthologous loci that resolve phylogenetic relationships.

Phylogenomic analyses of echinoid diversification prompt a re-evaluation of their fossil record

Echinoids are key components of modern marine ecosystems. Despite a remarkable fossil record, the emergence of their crown group is documented by few specimens of unclear affinities, rendering their early history uncertain. The origin of sand dollars, one of its most distinctive clades, is also unclear due to an unstable phylogenetic context. We employ 18 novel genomes and transcriptomes to build a phylogenomic dataset with a near-complete sampling of major lineages. With it, we revise the phylogeny and divergence times of echinoids, and place their history within the broader context of echinoderm evolution. We also introduce the concept of a chronospace - a multidimensional representation of node ages - and use it to explore methodological decisions involved in time calibrating phylogenies. We find the choice of clock model to have the strongest impact on divergence times, while the use of site-heterogeneous models and alternative node prior distributions show minimal effects. The choice of loci has an intermediate impact, affecting mostly deep Paleozoic nodes, for which clock-like genes recover dates more congruent with fossil evidence. Our results reveal that crown group echinoids originated in the Permian and diversified rapidly in the Triassic, despite the relative lack of fossil evidence for this early diversification. We also clarify the relationships between sand dollars and their close relatives and confidently date their origins to the Cretaceous, implying ghost ranges spanning approximately 50 million years, a remarkable discrepancy with their rich fossil record.

The Angiosperm Terrestrial Revolution and the origins of modern biodiversity

Biodiversity today has the unusual property that 85% of plant and animal species live on land rather than in the sea, and half of these live in tropical rainforests. An explosive boost to terrestrial diversity occurred from c. 100-50 million years ago, the Late Cretaceous and early Palaeogene. During this interval, the Earth-life system on land was reset, and the biosphere expanded to a new level of productivity, enhancing the capacity and species diversity of terrestrial environments. This boost in terrestrial biodiversity coincided with innovations in flowering plant biology and evolutionary ecology, including their flowers and efficiencies in reproduction; coevolution with animals, especially pollinators and herbivores; photosynthetic capacities; adaptability; and ability to modify habitats. The rise of angiosperms triggered a macroecological revolution on land and drove modern biodiversity in a secular, prolonged shift to new, high levels, a series of processes we name here the Angiosperm Terrestrial Revolution.

A global phylogenetic regionalization of vascular plants reveals a deep split between Gondwanan and Laurasian biotas

Existing global regionalization schemes for plants consider the compositional affinities among biotas, but these have not explicitly considered phylogenetic information. Here, we present for the first time, a phytogeographical delineation of the global vascular flora based on species-level evolutionary relationships. We analysed 8737 820 geographical occurrence records for vascular plants together with a time-calibrated phylogeny including 67 269 species. We constructed a global phylogenetic regionalization by estimating species composition and phylogenetic beta diversity among 200 km × 200 km grid cells across the world. We identified de novo 16 phytogeographical units that are deeply split into two clusters: Laurasian and Gondwanan. Our regionalization broadly matches previous schemes, but also highlights the separation of the Gondwanan biota into an Holotropical cluster and an Australian-Neozealandic-Patagonian cluster. In contrast, no clear split among Laurasian and Gondwanan biotas was retrieved when omitting phylogenetic information. The integration of phylogenetic and geographical information provides new insights into the delineation of phytogeographical areas and their historical relationships, enabling the identification of three large, clearly differentiated biotas, here referred to as kingdoms: Holarctic, Holotropical, and Austral. Our results provide further evidence for delineating transition zones and show a clear latitudinal pattern of increasing evolutionary distinctiveness towards the poles.

An exceptionally well-preserved herbaceous eudicot from the Early Cretaceous (late Aptian-early Albian) of Northwest China

A fossil eudicot, Gansufructus saligna gen. et sp. nov., is reported from the Early Cretaceous (late Aptian-early Albian) of the Gansu Province, Northwest China, based on numerous well-preserved axes with attached leaves and infructescences. The leaves are alternate, short petiolate and linear-lanceolate with low rank pinnate to reticulate venation. The infructescences are loose panicles bearing fruits in different stages of maturity, each containing four partly free carpels borne in a whorled arrangement. Each carpel has three to five seeds borne along its ventral margin. The nature of the leaves and axes indicates a terrestrial, herbaceous habit. In general organization, Gansufructus is closely similar to the fruit-bearing axes of Sinocarpus decussatus from the Early Cretaceous Jehol Biota, as well as other more or less contemporaneous angiosperms from the Far East, which together provide evidence of diverse eudicot angiosperms of low stature colonizing areas close to environments of deposition.

Evolution and diversity of the angiosperm anther: trends in function and development

Anther development and dehiscence is considered from an evolutionary perspective to identify drivers for differentiation, functional conservation and to identify key questions for future male reproduction research. Development of viable pollen and its timely release from the anther are essential for fertilisation of angiosperm flowers. The formation and subsequent dehiscence of the anther are under tight regulatory control, and these processes are remarkably conserved throughout the diverse families of the angiosperm clade. Anther development is a complex process, which requires timely formation and communication between the multiple somatic anther cell layers (the epidermis, endothecium, middle layer and tapetum) and the developing pollen. These layers go through regulated development and selective degeneration to facilitate the formation and ultimate release of the pollen grains. Insight into the evolution and divergence of anther development and dehiscence, especially between monocots and dicots, is driving greater understanding of the male reproductive process and increased, resilient crop yields. This review focuses on anther structure from an evolutionary perspective by highlighting their diversity across plant species. We summarise new findings that illustrate the complexities of anther development and evaluate how they challenge established models of anther form and function, and how they may help to deliver future sustainable crop yields.

A eudicot leaf from the Lower Cretaceous (Aptian, Araripe Basin) Crato Konservat-Lagerstätte

PREMISE

The Crato Konservat-Lagerstätte in Brazil preserves an exceptionally rich assemblage of plant macrofossils from the Early Cretaceous (late Aptian), including rare early angiosperm fossils related to Nymphaeales, monocots, and magnoliids, and a variety of angiosperms of uncertain affinities. Macrofossils of eudicot angiosperms have not been described previously, despite the presence of tricolpate pollen. We describe a fossil leaf with morphology characteristic of eudicot angiosperms.

METHODS

The fossil was collected from a quarry in the Lower Cretaceous (late Aptian) Crato Formation of northeastern Brazil in the state of Ceará. We compared the leaf architecture with that of ferns, gymnosperms, and similar living and fossil angiosperms.

RESULTS

The leaf of Baderadea pinnatissecta gen. et sp. nov. is simple and petiolate, with leaf architecture similar to that of some herbaceous Ranunculales. The blade is 5 cm long and the margin is untoothed and twice pinnately lobed with narrow lobes (pinnatisect). The primary vein framework is pinnate and there are multiple orders of reticulate venation.

CONCLUSIONS

The combination of characters preserved in the fossil supports the interpretation that B. pinnatissecta was an herbaceous eudicot similar to some members of Ranunculales and distinguished from other lobate Aptian angiosperms by leaf shape, presence of multiple orders of reticulate venation, and the absence of glandular teeth. The presence of eudicots in the flora of the Crato was already supported by pollen; the discovery of macrofossils like these provides additional information about their morphology and ecological role in low-latitude Early Cretaceous plant communities.

Expression and Functional Analyses of Nymphaea caerulea MADS-Box Genes Contribute to Clarify the Complex Flower Patterning of Water Lilies

Nymphaeaceae are early diverging angiosperms with large flowers characterized by showy petals and stamens not clearly whorled but presenting a gradual morphological transition from the outer elements to the inner stamens. Such flower structure makes these plant species relevant for studying flower evolution. MADS-domain transcription factors are crucial components of the molecular network that controls flower development. We therefore isolated and characterized MADS-box genes from the water lily Nymphaea caerulea. RNA-seq experiments on floral buds have been performed to obtain the transcript sequences of floral organ identity MADS-box genes. Maximum Likelihood phylogenetic analyses confirmed their belonging to specific MADS-box gene subfamilies. Their expression was quantified by RT-qPCR in all floral organs at two stages of development. Protein interactions among these transcription factors were investigated by yeast-two-hybrid assays. We found especially interesting the involvement of two different AGAMOUS-like genes (NycAG1 and NycAG2) in the water lily floral components. They were therefore functionally characterized by complementing Arabidopsis ag and shp1 shp2 mutants. The expression analysis of MADS-box genes across flower development in N. caerulea described a complex scenario made of numerous genes in numerous floral components. Their expression profiles in some cases were in line with what was expected from the ABC model of flower development and its extensions, while in other cases presented new and interesting gene expression patterns, as for instance the involvement of NycAGL6 and NycFL. Although sharing a high level of sequence similarity, the two AGAMOUS-like genes NycAG1 and NycAG2 could have undergone subfunctionalization or neofunctionalization, as only one of them could partially restore the euAG function in Arabidopsis ag-3 mutants. The hereby illustrated N. caerulea MADS-box gene expression pattern might mirror the morphological transition from the outer to the inner floral organs, and the presence of transition organs such as the petaloid stamens. This study is intended to broaden knowledge on the role and evolution of floral organ identity genes and the genetic mechanisms causing biodiversity in angiosperm flowers.

Hagenia from the early Miocene of Ethiopia: Evidence for possible niche evolution?

Fossil pollen believed to be related to extant Hagenia abyssinica were discovered in the early Miocene (21.73 Ma) Mush Valley paleoflora, Ethiopia, Africa. Both the fossil and extant pollen grains of H. abyssinica were examined with combined light microscopy, scanning electron microscopy, and transmission electron microscopy to compare the pollen and establish their relationships. Based on this, the fossil pollen grains were attributed to Hagenia. The presence of Hagenia in the fossil assemblage raises the questions if its habitat has changed over time, and if the plants are/were wind pollinated. To shed light on these questions, the morphology of extant anthers was also studied, revealing specialized hairs inside the anthers, believed to aid in insect pollination. Pollen and anther morphology are discussed in relation to the age and origin of the genus within a molecular dated phylogenetic framework, the establishment of complex topography in East Africa, other evidence regarding pollination modes, and the palynological record. The evidence presented herein, and compiled from the literature, suggests that Hagenia was an insect-pollinated lowland rainforest element during the early Miocene of the Mush Valley. The current Afromontane habitat and ambophilous (insect and wind) pollination must have evolved in post-mid-Miocene times.

Fossil data support a pre-Cretaceous origin of flowering plants

Flowering plants (angiosperms) are the most diverse of all land plants, becoming abundant in the Cretaceous and achieving dominance in the Cenozoic. However, the exact timing of their origin remains a controversial topic, with molecular clocks generally placing their origin much further back in time than the oldest unequivocal fossils. To resolve this discrepancy, we developed a Bayesian method to estimate the ages of angiosperm families on the basis of the fossil record (a newly compiled dataset of ~15,000 occurrences in 198 families) and their living diversity. Our results indicate that several families originated in the Jurassic, strongly rejecting a Cretaceous origin for the group. We report a marked increase in lineage accumulation from 125 to 72 million years ago, supporting Darwin's hypothesis of a rapid Cretaceous angiosperm diversification. Our results demonstrate that a pre-Cretaceous origin of angiosperms is supported not only by molecular clock approaches but also by analyses of the fossil record that explicitly correct for incomplete sampling.

Angiosperm pollinivory in a Cretaceous beetle

Despite the crucial importance of flower-visiting insects in modern ecosystems, there is little fossil evidence on the origins of angiosperm pollination. Most reports of pollination in the Mesozoic fossil record have been based on the co-occurrence of the purported pollinators with pollen grains and assumed morphological adaptations for vectoring pollen. Here, we describe an exceptionally preserved short-winged flower beetle (Cucujoidea: Kateretidae) from mid-Cretaceous amber, Pelretes vivificus gen. et sp. nov., associated with pollen aggregations and coprolites consisting mainly of pollen, providing direct evidence of pollen-feeding in a Cretaceous beetle and confirming that diverse beetle lineages visited early angiosperms in the Cretaceous. The exquisite preservation of our fossil permits the identification of the pollen grains as Tricolpopollenites (Asteridae or Rosidae), representing a record of flower beetle pollination of a group of derived angiosperms in the Mesozoic and suggesting that potentially diverse beetle lineages visited early angiosperms by the mid-Cretaceous.

A chromosome-level genome assembly for the tertiary relict plant Tetracentron sinense oliv. (trochodendraceae)

Tetracentron sinense and Trochodendron aralioides are two Tertiary relict species of large trees in the family Trochodendraceae with narrow distributions on the mainland and islands of eastern Asia. They belong to the order Trochodendrales, which is one of the four early-diverged eudicot lineages. These two relict species provide a good system in which to examine genomic changes that occurred as they survived during repeated climatic oscillations in the Quaternary. We sequenced the genome of Te. sinense and compared it with that of Tr. aralioides. We found that Te. sinense has a smaller genome size (986.3 Mb) than that of Tr. aralioides (1610 Mb). Repetitive elements made the major contribution to the contrasting genome sizes in the two species, with most bursts of repeats occurring within the past four million years when the climate oscillated greatly. These species share two rounds of whole-genome duplications. The mainland species Te. sinense had a larger effective population size than the island species Tr. aralioides after the largest glaciation during the Quaternary climatic oscillation. However, soon after this recovery stage, the effective population sizes of both species continued to decrease, although the current effective population size of Te. sinense is still larger than that of Tr. aralioides. We recovered three distinctly diverged clades through resequencing the genomes of 50 individuals across the distributional range of Te. sinense in China. Our results provide an important genomic resource with which to examine early trait evolution in the core eudicots and assist efforts to conserve this relict tree species.

The origin of Darwin's "abominable mystery"

The phrase "Darwin's abominable mystery" is frequently used with reference to a range of outstanding questions about the evolution of the plant group today known as the angiosperms. Here, I seek to more fully understand what prompted Darwin to coin the phrase in 1879, and the meaning he attached to it, by surveying the systematics, paleobotanical records, and phylogenetic hypotheses of his time. In the light of this historical research, I argue that Darwin was referring to the origin only of a subset of what are today called angiosperms: a (now obsolete) group equivalent to the "dicotyledons" of the Hooker and Bentham system. To Darwin and his contemporaries, the dicotyledons' fossil record began abruptly and with great diversity in the Cretaceous, whereas the gymnosperms and monocotyledons were thought to have fossil records dating back to the Carboniferous or beyond. Based on their morphology, the dicotyledons were widely seen by botanists in Darwin's time (unlike today) as more similar to the gymnosperms than to the monocotyledons. Thus, morphology seemed to point to gymnosperm progenitors of dicotyledons, but this hypothesis made the monocotyledons, given their (at the time) apparently longer fossil record, difficult to place. Darwin had friendly disagreements about the mystery of the dicotyledons' abrupt appearance in the fossil record with others who thought that their evolution must have been more rapid than his own gradualism would allow. But the mystery may have been made "abominable" to him because it was seen by some contemporary paleobotanists, most notably William Carruthers, the Keeper of Botany at the British Museum, as evidence for divine intervention in the history of life. Subsequent developments in plant systematics and paleobotany after 1879 meant that Darwin's letter was widely understood to be referring to the abrupt appearance of all angiosperms when it was published in 1903, a meaning that has been attached to it ever since.

The rise of angiosperms pushed conifers to decline during global cooling

Competition among species and entire clades can impact species diversification and extinction, which can shape macroevolutionary patterns. The fossil record shows successive biotic turnovers such that a dominant group is replaced by another. One striking example involves the decline of gymnosperms and the rapid diversification and ecological dominance of angiosperms in the Cretaceous. It is generally believed that angiosperms outcompeted gymnosperms, but the macroevolutionary processes and alternative drivers explaining this pattern remain elusive. Using extant time trees and vetted fossil occurrences for conifers, we tested the hypotheses that clade competition or climate change led to the decline of conifers at the expense of angiosperms. Here, we find that both fossil and molecular data show high congruence in revealing 1) low diversification rates, punctuated by speciation pulses, during warming events throughout the Phanerozoic and 2) that conifer extinction increased significantly in the Mid-Cretaceous (100 to 110 Ma) and remained high ever since. Their extinction rates are best explained by the rise of angiosperms, rejecting alternative models based on either climate change or time alone. Our results support the hypothesis of an active clade replacement, implying that direct competition with angiosperms increased the extinction of conifers by pushing their remaining species diversity and dominance out of the warm tropics. This study illustrates how entire branches on the Tree of Life may actively compete for ecological dominance under changing climates.

Genetic activity during early plant embryogenesis

Seeds are essential for human civilization, so understanding the molecular events underpinning seed development and the zygotic embryo it contains is important. In addition, the approach of somatic embryogenesis is a critical propagation and regeneration strategy to increase desirable genotypes, to develop new genetically modified plants to meet agricultural challenges, and at a basic science level, to test gene function. We briefly review some of the transcription factors (TFs) involved in establishing primary and apical meristems during zygotic embryogenesis, as well as TFs necessary and/or sufficient to drive somatic embryo programs. We focus on the model plant Arabidopsis for which many tools are available, and review as well as speculate about comparisons and contrasts between zygotic and somatic embryo processes.

Phylogenetic analysis of fossil flowers using an angiosperm-wide data set: proof-of-concept and challenges ahead

PREMISE

Significant paleobotanical discoveries in recent decades have considerably improved our understanding of the early evolution of angiosperms and their flowers. However, our ability to test the systematic placement of fossil flowers on the basis of phylogenetic analyses has remained limited, mainly due to the lack of an adequate, angiosperm-wide morphological data set for extant taxa. Earlier attempts to place fossil flowers phylogenetically were, therefore, forced to make prior qualitative assessments of the potential systematic position of fossils and to restrict phylogenetic analyses to selected angiosperm subgroups.

METHODS

We conduct angiosperm-wide molecular backbone analyses of 10 fossil flower taxa selected from the Cretaceous record. Our analyses make use of a floral trait data set built within the framework of the eFLOWER initiative. We provide an updated version of this data set containing data for 28 floral and two pollen traits for 792 extant species representing 372 angiosperm families.

RESULTS

We find that some fossils are placed congruently with earlier hypotheses while others are found in positions that had not been suggested previously. A few take up equivocal positions, including the stem branches of large clades.

CONCLUSIONS

Our study provides an objective approach to test for the phylogenetic position of fossil flowers across angiosperms. Such analyses may provide a complementary tool for paleobotanical studies, allowing for a more comprehensive understanding of fossil phylogenetic relationships in angiosperms. Ongoing work focused on extending the sampling of extant taxa and the number of floral traits will further improve the applicability and accuracy of our approach.