Eocene lantern fruits from Gondwanan Patagonia and the early origins of Solanaceae

Osmoxylon-like fossils from early Eocene South America: West Gondwana-Malesia connections in Araliaceae

PREMISE

Araliaceae comprise a moderately diverse, predominantly tropical angiosperm family with a limited fossil record. Gondwanan history of Araliaceae is hypothesized in the literature, but no fossils have previously been reported from the former supercontinent.

METHODS

I describe large (to macrophyll size), palmately compound-lobed leaf fossils and an isolated umbellate infructescence from the early Eocene (52 Ma), late-Gondwanan paleorainforest flora at Laguna del Hunco in Argentine Patagonia.

RESULTS

The leaf fossils are assigned to Caffapanax canessae gen. et sp. nov. (Araliaceae). Comparable living species belong to five genera that are primarily distributed from Malesia to South China. The most similar genus is Osmoxylon, which is centered in east Malesia and includes numerous threatened species. The infructescence is assigned to Davidsaralia christophae gen. et sp. nov. (Araliaceae) and is also comparable to Osmoxylon.

CONCLUSIONS

The Caffapanax leaves and Davidsaralia infructescence, potentially representing the same source taxon, are the oldest araliaceous macrofossils and provide direct evidence of Gondwanan history in the family. The new fossils and their large leaves enrich the well-established biogeographic and climatic affinities of the fossil assemblage with imperiled Indo-Pacific, everwet tropical rainforests. The fossils most likely represent shrubs or small trees, adding to the rich record of understory vegetation recovered from Laguna del Hunco.

Blooming balloons: Searching for mechanisms of the inflated calyx

Studying morphological novelties offers special insights into developmental biology and evolution. The inflated calyx syndrome (ICS) is a largely unrecognized but fascinating feature of flower development, where sepals form balloon-like husks that encapsulate fruits. Despite its independent emergence in many lineages of flowering plants, the genetic and molecular mechanisms of ICS remain unknown. Early studies in the Solanaceae genus Physalis put forth key roles of MADS-box genes in ICS. However, recent work suggests these classical floral identity transcription factors were false leads. With newfound capabilities that allow rapid development of genetic systems through genomics and genome editing, Physalis has re-emerged as the most tractable model species for dissecting ICS. This review revisits current understanding of ICS and highlights how recent advancements enable a reset in the search for genetic and molecular mechanisms using unbiased, systematic approaches.

Deciphering the evolutionary development of the "Chinese lantern" within Solanaceae

MAIN CONCLUSION

The key genetic variation underlying the evo-devo of ICS in Solanaceae may be further pinpointed using an integrated strategy of forward and reverse genetics studies under the framework of phylogeny. The calyx of Physalis remains persistent throughout fruit development. Post-flowering, the fruiting calyx is inflated rapidly to encapsulate the berry, giving rise to a "Chinese lantern" structure called inflated calyx syndrome (ICS). It is unclear how this novelty arises. Over the past 2 decades, the role of MADS-box genes in the evolutionary development (evo-devo) of ICS has mainly been investigated within Solanaceae. In this review, we analyze the main achievements, challenges, and new progress. ICS acts as a source for fruit development, provides a microenvironment to protect fruit development, and assists in long-distance fruit dispersal. ICS is a typical post-floral trait, and the onset of its development is triggered by specific developmental signals that coincide with fertilization. These signals can be replaced by exogenous gibberellin and cytokinin application. MPF2-like heterotopic expression and MBP21-like loss have been proposed to be two essential evolutionary events for ICS origin, and manipulating the related MADS-box genes has been shown to affect the ICS size, sepal organ identity, and/or male fertility, but not completely disrupt ICS. Therefore, the core genes or key links in the ICS biosynthesis pathways may have undergone secondary mutations during evolution, or they have not yet been pinpointed. Recently, we have made some encouraging progress in acquiring lantern mutants in Physalis floridana. In addition to technological innovation, we propose an integrated strategy to further analyze the evo-devo mechanisms of ICS in Solanaceae using forward and reverse genetics studies under the framework of phylogeny.

Early Eocene infructescences from Argentine Patagonia expand the biogeography of Malvoideae

PREMISE

Fossil infructescences and isolated fruits with characters of Malvoideae, a subfamily of Malvaceae (mallow family), were collected from early Eocene sediments in Chubut, Argentina. The main goals of this research are to describe and place these fossils systematically, and to explore their biogeographical implications.

METHODS

Fossils were collected at the Laguna del Hunco site, Huitrera Formation, Chubut, Patagonia, Argentina. They were prepared, photographed, and compared with extant and fossil infructescences and fruits of various families using herbarium material and literature.

RESULTS

The infructescences are panicles with alternate arrangement of fruits. They bear the fruits on short pedicels that are subtended by a bract; the fruits display an infracarpelar disk and split to the base into five ovate sections interpreted as mericarps. Each mericarp is characterized by an acute apex and the presence of a longitudinal ridge. The isolated fruits show the same features as those on the infructescences. The fossils share unique features with members of the cosmopolitan family Malvaceae, subfamily Malvoideae.

CONCLUSIONS

The fossils have a unique combination of characters that does not conform to any previously described genus, justifying the erection of a new genus and species, Uiher karuen. This new taxon constitutes the first known Malvoideae reproductive fossils of the Southern Hemisphere, expanding the distribution of Malvoideae during the early Eocene.

A highly resolved nuclear phylogeny uncovers strong phylogenetic conservatism and correlated evolution of fruit color and size in Solanum L

Mutualisms between plants and fruit-eating animals were key to the radiation of angiosperms. Still, phylogenetic uncertainties limit our understanding of fleshy-fruit evolution, as in the case of Solanum, a genus with remarkable fleshy-fruit diversity, but with unresolved phylogenetic relationships. We used 1786 nuclear genes from 247 species, including 122 newly generated transcriptomes/genomes, to reconstruct the Solanum phylogeny and examine the tempo and mode of the evolution of fruit color and size. Our analysis resolved the backbone phylogeny of Solanum, providing high support for its clades. Our results pushed back the origin of Solanum to 53.1 million years ago (Ma), with most major clades diverging between 35 and 27 Ma. Evolution of Solanum fruit color and size revealed high levels of trait conservatism, where medium-sized berries that remain green when ripe are the likely ancestral form. Our analyses revealed that fruit size and color are evolutionary correlated, where dull-colored fruits are two times larger than black/purple and red fruits. We conclude that the strong phylogenetic conservatism shown in the color and size of Solanum fruits could limit the influences of fruit-eating animals on fleshy-fruit evolution. Our findings highlight the importance of phylogenetic constraints on the diversification of fleshy-fruit functional traits.

Advances in Physalis molecular research: applications in authentication, genetic diversity, phylogenetics, functional genes, and omics

The plants of the genus Physalis L. have been extensively utilized in traditional and indigenous Chinese medicinal practices for treating a variety of ailments, including dermatitis, malaria, asthma, hepatitis, and liver disorders. The present review aims to achieve a comprehensive and up-to-date investigation of the genus Physalis, a new model crop, to understand plant diversity and fruit development. Several chloroplast DNA-, nuclear ribosomal DNA-, and genomic DNA-based markers, such as psbA-trnH, internal-transcribed spacer (ITS), simple sequence repeat (SSR), random amplified microsatellites (RAMS), sequence-characterized amplified region (SCAR), and single nucleotide polymorphism (SNP), were developed for molecular identification, genetic diversity, and phylogenetic studies of Physalis species. A large number of functional genes involved in inflated calyx syndrome development (AP2-L, MPF2, MPF3, and MAGO), organ growth (AG1, AG2, POS1, and CNR1), and active ingredient metabolism (24ISO, DHCRT, P450-CPL, SR, DUF538, TAS14, and 3β-HSB) were identified contributing to the breeding of novel Physalis varieties. Various omic studies revealed and functionally identified a series of reproductive organ development-related factors, environmental stress-responsive genes, and active component biosynthesis-related enzymes. The chromosome-level genomes of Physalis floridana Rydb., Physalis grisea (Waterf.) M. Martínez, and Physalis pruinosa L. have been recently published providing a valuable resource for genome editing in Physalis crops. Our review summarizes the recent progress in genetic diversity, molecular identification, phylogenetics, functional genes, and the application of omics in the genus Physalis and accelerates efficient utilization of this traditional herb.

Patterns of variation in fleshy diaspore size and abundance from Late Triassic-Oligocene

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

Unleashed Treasures of Solanaceae: Mechanistic Insights into Phytochemicals with Therapeutic Potential for Combatting Human Diseases

Plants that possess a diverse range of bioactive compounds are essential for maintaining human health and survival. The diversity of bioactive compounds with distinct therapeutic potential contributes to their role in health systems, in addition to their function as a source of nutrients. Studies on the genetic makeup and composition of bioactive compounds have revealed them to be rich in steroidal alkaloids, saponins, terpenes, flavonoids, and phenolics. The Solanaceae family, having a rich abundance of bioactive compounds with varying degrees of pharmacological activities, holds significant promise in the management of different diseases. Investigation into Solanum species has revealed them to exhibit a wide range of pharmacological properties, including antioxidant, hepatoprotective, cardioprotective, nephroprotective, anti-inflammatory, and anti-ulcerogenic effects. Phytochemical analysis of isolated compounds such as diosgenin, solamargine, solanine, apigenin, and lupeol has shown them to be cytotoxic in different cancer cell lines, including liver cancer (HepG2, Hep3B, SMMC-772), lung cancer (A549, H441, H520), human breast cancer (HBL-100), and prostate cancer (PC3). Since analysis of their phytochemical constituents has shown them to have a notable effect on several signaling pathways, a great deal of attention has been paid to identifying the biological targets and cellular mechanisms involved therein. Considering the promising aspects of bioactive constituents of different Solanum members, the main emphasis was on finding and reporting notable cultivars, their phytochemical contents, and their pharmacological properties. This review offers mechanistic insights into the bioactive ingredients intended to treat different ailments with the least harmful effects for potential applications in the advancement of medical research.

Understanding the relations between Solanaceae crops and their pollinators: a global meta-network

Crop-pollinator interactions are essential for world food security. Studying crop pollination from a network approach allows identification of target pollinators for conservation and management, and gaps in our knowledge. Solanaceae represents the third highest ranked family based on economic value, and its production is highly improved by animal pollination. This study aimed to integrate global data on solanaceous crop pollination and analyse the interaction patterns using a meta-network approach. Our questions were: (i) how are interactions structured and what are the structuring roles of species; and (ii) what are the main gaps in our knowledge? Data were obtained through a systematic review of the main scientific databases. The network structure was described using connectivity and modularity calculations, and the role of species using centrality metrics. The 251 pollinator species reported were in seven orders, mainly Hymenoptera (84.9%). The generalists Bombus and Apis species were the most common pollinators. The meta-network was modular, and all modules mostly included bees. Most species were peripherals, around 12% were connectors, and there were no module hubs. Apis mellifera was the only network hub (supergeneralist). The most important pollinators are the most managed pollinators worldwide; however, many native species play a role in structuring the meta-network. Main gaps include species of importance to pepper pollination, lack of species-specific identification, and the need for more robust experimental studies evaluating the pollination efficiency of native, manageable bees.

Fossil berries reveal global radiation of the nightshade family by the early Cenozoic

Fossil discoveries can transform our understanding of plant diversification over time and space. Recently described fossils in many plant families have pushed their known records farther back in time, pointing to alternative scenarios for their origin and spread. Here, we describe two new Eocene fossil berries of the nightshade family (Solanaceae) from the Esmeraldas Formation in Colombia and the Green River Formation in Colorado (USA). The placement of the fossils was assessed using clustering and parsimony analyses based on 10 discrete and five continuous characters, which were also scored in 291 extant taxa. The Colombian fossil grouped with members of the tomatillo subtribe, and the Coloradan fossil aligned with the chili pepper tribe. Along with two previously reported early Eocene fossils from the tomatillo genus, these findings indicate that Solanaceae were distributed at least from southern South America to northwestern North America by the early Eocene. Together with two other recently discovered Eocene berries, these fossils demonstrate that the diverse berry clade and, in turn, the entire nightshade family, is much older and was much more widespread in the past than previously thought.

The first Gondwanan Euphorbiaceae fossils reset the biogeographic history of the Macaranga-Mallotus clade

PREMISE

The spurge family Euphorbiaceae is prominent in tropical rainforests worldwide, particularly in Asia. There is little consensus on the biogeographic origins of the family or its principal lineages. No confirmed spurge macrofossils have come from Gondwana.

METHODS

We describe the first Gondwanan macrofossils of Euphorbiaceae, represented by two infructescences and associated peltate leaves from the early Eocene (52 Myr ago [Ma]) Laguna del Hunco site in Chubut, Argentina.

RESULTS

The infructescences are panicles bearing tiny, pedicellate, spineless capsular fruits with two locules, two axile lenticular seeds, and two unbranched, plumose stigmas. The fossils' character combination only occurs today in some species of the Macaranga-Mallotus clade (MMC; Euphorbiaceae), a widespread Old-World understory group often thought to have tropical Asian origins. The associated leaves are consistent with extant Macaranga.

CONCLUSIONS

The new fossils are the oldest known for the MMC, demonstrating its Gondwanan history and marking its divergence by at least 52 Ma. This discovery makes an Asian origin of the MMC unlikely because immense oceanic distances separated Asia and South America 52 Ma. The only other MMC reproductive fossils so far known are also from the southern hemisphere (early Miocene, southern New Zealand), far from the Asian tropics. The MMC, along with many other Gondwanan survivors, most likely entered Asia during the Neogene Sahul-Sunda collision. Our discovery adds to a substantial series of well-dated, well-preserved fossils from one undersampled region, Patagonia, that have changed our understanding of plant biogeographic history.

Phylogenomic discovery of deleterious mutations facilitates hybrid potato breeding

Hybrid potato breeding will transform the crop from a clonally propagated tetraploid to a seed-reproducing diploid. Historical accumulation of deleterious mutations in potato genomes has hindered the development of elite inbred lines and hybrids. Utilizing a whole-genome phylogeny of 92 Solanaceae and its sister clade species, we employ an evolutionary strategy to identify deleterious mutations. The deep phylogeny reveals the genome-wide landscape of highly constrained sites, comprising ∼2.4% of the genome. Based on a diploid potato diversity panel, we infer 367,499 deleterious variants, of which 50% occur at non-coding and 15% at synonymous sites. Counterintuitively, diploid lines with relatively high homozygous deleterious burden can be better starting material for inbred-line development, despite showing less vigorous growth. Inclusion of inferred deleterious mutations increases genomic-prediction accuracy for yield by 24.7%. Our study generates insights into the genome-wide incidence and properties of deleterious mutations and their far-reaching consequences for breeding.

Nuclear phylogeny and insights into whole-genome duplications and reproductive development of Solanaceae plants

Solanaceae, the nightshade family, have ∼2700 species, including the important crops potato and tomato, ornamentals, and medicinal plants. Several sequenced Solanaceae genomes show evidence for whole-genome duplication (WGD), providing an excellent opportunity to investigate WGD and its impacts. Here, we generated 93 transcriptomes/genomes and combined them with 87 public datasets, for a total of 180 Solanaceae species representing all four subfamilies and 14 of 15 tribes. Nearly 1700 nuclear genes from these transcriptomic/genomic datasets were used to reconstruct a highly resolved Solanaceae phylogenetic tree with six major clades. The Solanaceae tree supports four previously recognized subfamilies (Goetzeioideae, Cestroideae, Nicotianoideae, and Solanoideae) and the designation of three other subfamilies (Schizanthoideae, Schwenckioideae, and Petunioideae), with the placement of several previously unassigned genera. We placed a Solanaceae-specific whole-genome triplication (WGT1) at ∼81 million years ago (mya), before the divergence of Schizanthoideae from other Solanaceae subfamilies at ∼73 mya. In addition, we detected two gene duplication bursts (GDBs) supporting proposed WGD events and four other GDBs. An investigation of the evolutionary histories of homologs of carpel and fruit developmental genes in 14 gene (sub)families revealed that 21 gene clades have retained gene duplicates. These were likely generated by the Solanaceae WGT1 and may have promoted fleshy fruit development. This study presents a well-resolved Solanaceae phylogeny and a new perspective on retained gene duplicates and carpel/fruit development, providing an improved understanding of Solanaceae evolution.

Establishing Physalis as a Solanaceae model system enables genetic reevaluation of the inflated calyx syndrome

The highly diverse Solanaceae family contains several widely studied models and crop species. Fully exploring, appreciating, and exploiting this diversity requires additional model systems. Particularly promising are orphan fruit crops in the genus Physalis, which occupy a key evolutionary position in the Solanaceae and capture understudied variation in traits such as inflorescence complexity, fruit ripening and metabolites, disease and insect resistance, self-compatibility, and most notable, the striking inflated calyx syndrome (ICS), an evolutionary novelty found across angiosperms where sepals grow exceptionally large to encapsulate fruits in a protective husk. We recently developed transformation and genome editing in Physalis grisea (groundcherry). However, to systematically explore and unlock the potential of this and related Physalis as genetic systems, high-quality genome assemblies are needed. Here, we present chromosome-scale references for P. grisea and its close relative Physalis pruinosa and use these resources to study natural and engineered variations in floral traits. We first rapidly identified a natural structural variant in a bHLH gene that causes petal color variation. Further, and against expectations, we found that CRISPR-Cas9-targeted mutagenesis of 11 MADS-box genes, including purported essential regulators of ICS, had no effect on inflation. In a forward genetics screen, we identified huskless, which lacks ICS due to mutation of an AP2-like gene that causes sepals and petals to merge into a single whorl of mixed identity. These resources and findings elevate Physalis to a new Solanaceae model system and establish a paradigm in the search for factors driving ICS.

Resinoid from cape gooseberry fruit (Physalis peruviana L.) - volatile composition and application as an active ingredient in a cosmetic formulation

Cape gooseberry (Physalis peruviana L.), an exotic fruit gaining popularity in Bulgaria, has been recognized as a highly functional food, but has also the potential to be a resource for the fragrance and cosmetic industries. The main objective of this study was to assess the potential of the resinoid (a type of traditional aromatic products) obtained from locally-produced fruit (variety “Plovdiv”) for use in cosmetics, by revealing its volatile composition and characterizing the properties of an author-developed resinoid- enriched cosmetic cream. The resinoid (yield 58.78% DW) was a dark-orange viscous mass, with fruity, caramel notes and smoke accords odor. The GC-MS analysis identified 44 volatiles (98.69%), representing carbohydrates, alcohols, acids, along with minor miscellaneous compounds. A cosmetic cream (O/W emulsion) was developed, incorporating fruit resinoid (1.00%) as an active ingredient, compared to a control sample. Resinoid inclusion affected positively the sensory and physico-chemical properties of the cosmetic cream (color, odor, pH, stability). The studied emulsions had the rheological behavior of pseudoplastic non-Newtonian fluids, and resinoid presence reduced cream viscosity. It could be concluded that Cape gooseberry fruit resinoid had the potential to be a reasonable ingredient in cosmetic preparations; of course, further research is needed to assess its complex effects.

Multifunctional Contribution of the Inflated Fruiting Calyx: Implication for Cuticular Barrier Profiles of the Solanaceous Genera Physalis, Alkekengi, and Nicandra

Pivotal barrier properties of the hydrophobic plant cuticle covering aerial plant surfaces depend on its physicochemical composition. Among plant species and organs, compounds of this boundary layer between the plant interior and the environment vary considerably but cuticle-related studies comparing different organs from the same plant species are still scarce. Thus, this study focused on the cuticle profiles of Physalis peruviana, Physalis ixocarpa, Alkekengi officinarum, and Nicandra physalodes species. Inflated fruiting calyces enveloping fruits make Physalis, Alkekengi, and Nicandra highly recognizable genera among the Solanoideae subfamily. Although the inflation of fruiting calyces is well discussed in the literature still little is known about their post-floral functionalities. Cuticular composition, surface structure, and barrier function were examined and compared in fully expanded amphistomatous leaves, ripe astomatous fruits, and fully inflated hypostomatous fruiting calyces. Species- and organ-specific abundances of non-glandular and glandular trichomes revealed high structural diversity, covering not only abaxial and adaxial leaf surfaces but also fruiting calyx surfaces, whereas fruits were glabrous. Cuticular waxes, which limit non-stomatal transpiration, ranged from <1 μg cm^-2 on P. peruviana fruiting calyces and N. physalodes fruits to 22 μg cm^-2 on P. peruviana fruits. Very-long-chain aliphatic compounds, notably n-alkanes, iso-, and anteiso-branched alkanes, alkanols, alkanoic acids, and alkyl esters, dominated the cuticular wax coverages (≥86%). Diversity of cuticular wax patterns rose from leaves to fruiting calyces and peaked in fruits. The polymeric cutin matrix providing the structural framework for cuticular waxes was determined to range from 81 μg cm^-2 for N. physalodes to 571 μg cm^-2 for A. officinarum fruits. Cuticular transpiration barriers were highly efficient, with water permeabilities being ≤5 × 10^-5 m s^-1. Only the cuticular water permeability of N. physalodes fruits was 10 × 10^-5 m s^-1 leading to their early desiccation and fruits that easily split, whereas P. peruviana, P. ixocarpa, and A. officinarum bore fleshy fruits for extended periods after maturation. Regarding the functional significance, fruiting calyces establish a physicochemical shield that reduces water loss and enables fruit maturation within a protective microclimate, and promotes different seed dispersal strategies among plant species investigated.

Cunoniaceae infructescences from the early Eocene Laguna del Hunco flora, Patagonia, Argentina

PREMISE

Two distinct types of fossil infructescences from the early Eocene Laguna del Hunco flora, Chubut Province, Patagonia, Argentina, preserve features of the family Cunoniaceae. The goal of the study was to assess their affinities within Cunoniaceae and to interpret their evolutionary and biogeographical significance.

METHODS

Specimens were collected from the Tufolitas Laguna del Hunco, Huitrera Formation. They were prepared, photographed, and compared morphologically with similar extant and fossil fruits and infructescences using published literature and herbarium material.

RESULTS

The fruit and infructescence morphology place the fossil taxa within Cunoniaceae. They do not conform to any extant genus, supporting the erection of two new fossil genera. Racemofructus gen. nov. shares diagnostic features of the tribe Cunonieae, especially Weinmannia s.l., and exhibits two tribal morphological synapomorphies: a racemose inflorescence and a replum composed of a single column. Cunoniocarpa gen. nov. specimens are paniculate inflorescences with basipetally dehiscent, bicarpellate capsules that have persistent styles and calyces. Its replum morphology suggests an affinity to the tribe Caldcluvieae, particularly to the genus Ackama.

CONCLUSIONS

The new Patagonian fossils described herein constitute the oldest record of cunoniaceous capsules globally, supplementing a significant body of fossil evidence from pollen, wood, and reproductive structures from southern South America and Antarctica that suggests that the Cunoniaceae were diversified and widely distributed in the southern hemisphere by the early Eocene. Racemofructus and Cunoniocarpa are, respectively, the first fossil records from South America of reproductive structures with affinity to tribes Cunonieae and Caldcluvieae.

Evolution and development of inflorescences and floral symmetry in Solanaceae

PREMISE

The inflorescences of Solanaceae are unique and complex, which has led to long-standing disputes over floral symmetry mainly due to different interpretations of the cyme-like inflorescence structure. The main disagreements have been over how the phyllomes associated with the flower were arranged relative to the inflorescence axis especially during early flower initiation.

METHODS

Here we investigated the evolution of inflorescences in Solanaceae by analyzing inflorescence structure in the context of phylogeny using ancestral state reconstruction (ASR) to determine the evolutionary transitions between loosely arranged and tightly clustered inflorescences and between monochasial-like and dichasial-like cymes. We also reconstructed two- and three-dimensional models for 12 solanaceous species that represent both inflorescence and phylogenetic diversity in the family.

RESULTS

Our results indicate that the most recent common ancestor of Solanaceae had a loosely arranged and monochasial-like cyme, while tightly clustered inflorescences and dichasial-like cymes were derived. Compared to the known process of scorpioid cyme evolution, Solanaceae achieved their scorpioid cyme-like inflorescences through a previously undescribed way. Along the pedicel, the two flower-preceding prophylls are not in the typical transverse position of dicotyledonous plants; they frequently have axillary buds, and the main inflorescence axis continues in a sympodial fashion. As a result, the plane of symmetry of the flower is 36° from the median, and the inflorescence axis and the two flower-preceding prophylls are symmetrically located along that plane.

CONCLUSIONS

A better understanding of the morphological evolution of solanaceous inflorescence structure helped clarify the floral symmetry of Solanaceae.

Fire-prone Rhamnaceae with South African affinities in Cretaceous Myanmar amber

The rapid Cretaceous diversification of flowering plants remains Darwin's 'abominable mystery' despite numerous fossil flowers discovered in recent years. Wildfires were frequent in the Cretaceous and many such early flower fossils are represented by charcoalified fragments, lacking complete delicate structures and surface textures, making their similarity to living forms difficult to discern. Furthermore, scarcity of information about the ecology of early angiosperms makes it difficult to test hypotheses about the drivers of their diversification, including the role of fire in shaping flowering plant evolution. We report the discovery of two exquisitely preserved fossil flower species, one identical to the inflorescences of the extant crown-eudicot genus Phylica and the other recovered as a sister group to Phylica, both preserved as inclusions together with burned plant remains in Cretaceous amber from northern Myanmar (~99 million years ago). These specialized flower species, named Phylica piloburmensis sp. nov. and Eophylica priscastellata gen. et sp. nov., exhibit traits identical to those of modern taxa in fire-prone ecosystems such as the fynbos of South Africa, and provide evidence of fire adaptation in angiosperms.

The Physalis floridana genome provides insights into the biochemical and morphological evolution of Physalis fruits

The fruits of Physalis (Solanaceae) have a unique structure, a lantern-like fruiting calyx known as inflated calyx syndrome (ICS) or the Chinese lantern, and are rich in steroid-related compounds. However, the genetic variations underlying the origin of these characteristic traits and diversity in Physalis remain largely unknown. Here, we present a high-quality chromosome-level reference genome assembly of Physalis floridana (~1.40 Gb in size) with a contig N50 of ~4.87 Mb. Through evolutionary genomics and experimental approaches, we found that the loss of the SEP-like MADS-box gene MBP21 subclade is likely a key mutation that, together with the previously revealed mutation affecting floral MPF2 expression, might have contributed to the origination of ICS in Physaleae, suggesting that the origination of a morphological novelty may have resulted from an evolutionary scenario in which one mutation compensated for another deleterious mutation. Moreover, the significant expansion of squalene epoxidase genes is potentially associated with the natural variation of steroid-related compounds in Physalis fruits. The results reveal the importance of gene gains (duplication) and/or subsequent losses as genetic bases of the evolution of distinct fruit traits, and the data serve as a valuable resource for the evolutionary genetics and breeding of solanaceous crops.

Plastid phylogenomics and biogeography of the medicinal plant lineage Hyoscyameae (Solanaceae)

The cosmopolitan family Solanaceae, which originated and first diversified in South America, is economically important. The tribe Hyoscyameae is one of the three clades in Solanaceae that occurs outside of the New World; Hyoscyameae genera are distributed mainly in Europe and Asia, and have centers of species diversity in the Qinghai-Tibet Plateau and adjacent regions. Although many phylogenetic studies have focused on Solanaceae, the phylogenetic relationships within the tribe Hyoscyameae and its biogeographic history remain obscure. In this study, we reconstructed the phylogeny of Hyoscyameae based on whole chloroplast genome data, and estimated lineage divergence times according to the newly reported fruit fossil from the Eocene Patagonia, Physalis infinemundi, the earliest known fossil of Solanaceae. We reconstructed a robust phylogeny of Hyoscyameae that reveals the berry fruit-type Atropa is sister to the six capsule-bearing genera (Hyoscyameae sensu stricto), Atropanthe is sister to the clade (Scopolia, Physochlaina, Przewalskia), and together they are sister to the robustly supported Anisodus-Hyoscyamus clade. The stem age of Hyoscyameae was inferred to be in the Eocene (47.11 Ma, 95% HPD: 36.75-57.86 Ma), and the crown ages of Hyoscyameae sensu stricto were estimated as the early Miocene (22.52 Ma, 95% HPD: 15.19-30.53 Ma), which shows a close correlation with the rapid uplift of the Qinghai-Tibet Plateau at the Paleogene/Neogene boundary. Our results provide insights into the phylogenetic relationships and the history of the biogeographic diversification of the tribe Hyoscyameae, as well as plant diversification on the Qinghai-Tibet Plateau.

Uncertainty in Divergence Time Estimation

Understanding and representing uncertainty is crucial in academic research because it enables studies to build on the conclusions of previous studies, leading to robust advances in a particular field. Here, we evaluate the nature of uncertainty and the manner by which it is represented in divergence time estimation, a field that is fundamental to many aspects of macroevolutionary research, and where there is evidence that uncertainty has been seriously underestimated. We address this issue in the context of methods used in divergence time estimation, and with respect to the manner by which time-calibrated phylogenies are interpreted. With respect to methods, we discuss how the assumptions underlying different methods may not adequately reflect uncertainty about molecular evolution, the fossil record, or diversification rates. Therefore, divergence time estimates may not adequately reflect uncertainty and may be directly contradicted by subsequent findings. For the interpretation of time-calibrated phylogenies, we discuss how the use of time-calibrated phylogenies for reconstructing general evolutionary timescales leads to inferences about macroevolution that are highly sensitive to methodological limitations in how uncertainty is accounted for. By contrast, we discuss how the use of time-calibrated phylogenies to test specific hypotheses leads to inferences about macroevolution that are less sensitive to methodological limitations. Given that many biologists wish to use time-calibrated phylogenies to reconstruct general evolutionary timescales, we conclude that the development of methods of divergence time estimation that adequately account for uncertainty is necessary. [Divergence time estimation; macroevolution; uncertainty.].

New physaloid fruit-fossil species from early Eocene South America

PREMISE

Solanaceae is a scientifically and economically important angiosperm family with a minimal fossil record and an intriguing early evolutionary history. Here, we report a newly discovered fossil lantern fruit with a suite of features characteristic of Physalideae within Solanaceae. The fossil comes from the early Eocene Laguna del Hunco site (ca. 52 Ma) in Chubut, Argentina, which previously yielded the only other physaloid fruit fossil, Physalis infinemundi.

METHODS

The fruit morphology and calyx venation pattern of the new fossil were compared with P. infinemundi and extant species of Solanaceae.

RESULTS

Physalis hunickenii sp. nov. is clearly distinct from P. infinemundi in its fruiting calyx with wider primary veins, longer and thinner lobes, and especially in its venation pattern with high density, transverse tertiary veins; these features support its placement in a new species. In comparison with extant physaloid genera, the calyx venation pattern and other diagnostic traits reinforce placement of the new fossil, like P. infinemundi, within the tribe Physalideae of Solanaceae.

CONCLUSIONS

Both species of fossil nightshades from Laguna del Hunco represent crown-group Solanaceae but are older than all prior age estimates of the family. Although at least 20 transoceanic dispersals have been proposed as the driver of range expansion of Solanaceae, the Patagonian fossils push back the diversification of the family to Gondwanan times. Thus, overland dispersal across Gondwana is now a likely scenario for at least some biogeographic patterns, in light of the ancient trans-Antarctic land connections between South America and Australia.

52 million years old Eucalyptus flower sheds more than pollen grains

PREMISE

Fossils provide fundamental evidence of the evolutionary processes that crafted today's biodiversity and consequently for understanding life on Earth. We report the finding of Myrtaceidites eucalyptoides pollen grains preserved within the anthers of a 52-million-year-old Eucalyptus flower collected at Laguna del Hunco locality of Argentinean Patagonia and discuss its implications in understanding the evolutionary history of the iconic Australian genus Eucalyptus.

METHODS

Pollen grains were extracted from the flower's anthers and were then observed under light microscopy and scanning electron microscopy. The phylogenetic position of the fossil was investigated by adding pollen data to a previously published total-evidence matrix and analyzing it using parsimony.

RESULTS

We erect the species Eucalyptus xoshemium for the fossil flower. Pollen extracted from E. xoshemium belongs to the species Myrtaceidites eucalyptoides, which, until now, was only known as dispersed pollen. The numerous pollen grains recovered from the single flower allowed estimation of M. eucalyptoides' variability. Results of the phylogenetic analysis reinforce the position of this fossil within crown group Eucalyptus.

CONCLUSIONS

The discovery of these pollen grains within a Patagonian Eucalyptus fossil flower confirms the hypothesis that Myrtaceidites eucalyptoides represents fossil pollen in the Eucalyptus lineage, extends the geographic and stratigraphic fossil pollen record, and supports an earlier age for crown-group eucalypts.

Evolution of a guarded decoy protease and its receptor in solanaceous plants

Rcr3 is a secreted protease of tomato that is targeted by fungal effector Avr2, a secreted protease inhibitor of the fungal pathogen Cladosporium fulvum. The Avr2-Rcr3 complex is recognized by receptor-like protein Cf-2, triggering hypersensitive cell death (HR) and disease resistance. Avr2 also targets Rcr3 paralog Pip1, which is not required for Avr2 recognition but contributes to basal resistance. Thus, Rcr3 acts as a guarded decoy in this interaction, trapping the fungus into a recognition event. Here we show that Rcr3 evolved > 50 million years ago (Mya), whereas Cf-2 evolved <6Mya by co-opting the pre-existing Rcr3 in the Solanum genus. Ancient Rcr3 homologs present in tomato, potato, eggplants, pepper, petunia and tobacco can be inhibited by Avr2 with the exception of tobacco Rcr3. Four variant residues in Rcr3 promote Avr2 inhibition, but the Rcr3 that co-evolved with Cf-2 lacks three of these residues, indicating that the Rcr3 co-receptor is suboptimal for Avr2 binding. Pepper Rcr3 triggers HR with Cf-2 and Avr2 when engineered for enhanced inhibition by Avr2. Nicotiana benthamiana (Nb) is a natural null mutant carrying Rcr3 and Pip1 alleles with deleterious frame-shift mutations. Resurrected NbRcr3 and NbPip1 alleles were active proteases and further NbRcr3 engineering facilitated Avr2 inhibition, uncoupled from HR signalling. The evolution of a receptor co-opting a conserved pathogen target contrasts with other indirect pathogen recognition mechanisms.

A review of nutritional properties and health benefits of Physalis species

The Physalis genus of the Solanaceae family is home to many edible food crops including tomatillo, goldenberry, and groundcherry. These Physalis members have garnered more attention as consumer interest in novel fruits and vegetables has increased because of increasing awareness of the health benefits of eating a diverse diet. As a result of this interest, several preliminary studies were conducted of these Physalis to evaluate their nutritional and chemical profiles associated with health benefits. Results showed these crops contain many essential minerals and vitamins, notably potassium and immune system supporting Vitamin C, also known for its antioxidant activity. Beyond nutritional properties, these crops also contain a class of steroidal lactones called withanolides, which have been recognized for their antitumor, and antinflammatory properties. In some studies, withanolide extract from Physalis species have exhibited cytotoxicity towards cancers cells. Overall, this review focuses on the nutritional and physiochemical properties of tomatillo, goldenberry, and groundcherry and how they relate to human health.

The delayed and geographically heterogeneous diversification of flowering plant families

The Early Cretaceous (145-100 million years ago (Ma)) witnessed the rise of flowering plants (angiosperms), which ultimately lead to profound changes in terrestrial plant communities. However, palaeobotanical evidence shows that the transition to widespread angiosperm-dominated biomes was delayed until the Palaeocene (66-56 Ma). Important aspects of the timing and geographical setting of angiosperm diversification during this period, and the groups involved, remain uncertain. Here we address these aspects by constructing and dating a new and complete family-level phylogeny, which we integrate with 16 million geographic occurrence records for angiosperms on a global scale. We show substantial time lags (mean, 37-56 Myr) between the origin of families (stem age) and the diversification leading to extant species (crown ages) across the entire angiosperm tree of life. In turn, our results show that families with the shortest lags are overrepresented in temperate and arid biomes compared with tropical biomes. Our results imply that the diversification and ecological expansion of extant angiosperms was geographically heterogeneous and occurred long after most of their phylogenetic diversity originated during the Cretaceous Terrestrial Revolution.

Eocene Araucaria Sect. Eutacta from Patagonia and floristic turnover during the initial isolation of South America

PREMISE

Eocene floras of Patagonia document biotic response to the final separation of Gondwana. The conifer genus Araucaria, distributed worldwide during the Mesozoic, has a disjunct extant distribution between South America and Australasia. Fossils assigned to Australasian Araucaria Sect. Eutacta usually are represented by isolated organs, making diagnosis difficult. Araucaria pichileufensis E.W. Berry, from the middle Eocene Río Pichileufú (RP) site in Argentine Patagonia, was originally placed in Sect. Eutacta and later reported from the early Eocene Laguna del Hunco (LH) locality. However, the relationship of A. pichileufensis to Sect. Eutacta and the conspecificity of the Araucaria material among these Patagonian floras have not been tested using modern methods.

METHODS

We review the type material of A. pichileufensis alongside large (n = 192) new fossil collections of Araucaria from LH and RP, including multi-organ preservation of leafy branches, ovuliferous complexes, and pollen cones. We use a total evidence phylogenetic analysis to analyze relationships of the fossils to Sect. Eutacta.

RESULTS

We describe Araucaria huncoensis sp. nov. from LH and improve the whole-plant concept for Araucaria pichileufensis from RP. The two species respectively resolve in the crown and stem of Sect. Eutacta.

CONCLUSIONS

Our results confirm the presence and indicate the survival of Sect. Eutacta in South America during early Antarctic separation. The exceptionally complete fossils significantly predate several molecular age estimates for crown Eutacta. The differentiation of two Araucaria species demonstrates conifer turnover during climate change and initial South American isolation from the early to middle Eocene.

The temporal dynamics of evolutionary diversification in Ipomoea

Molecular phylogenies are used as a basis for making inferences about macroevolutionary history. However, a robust phylogeny does not contain the information that is necessary to make many of these inferences. Complex methodologies that incorporate important assumptions about the nature of evolutionary history are therefore required. Here, we explore the implications of these assumptions for making inferences about the macroevolutionary history of Ipomoea - a large pantropical genus of flowering plants that contains the sweet potato (Ipomoea batatas), a crop of global economic importance. We focus on assumptions that underlie inferences of divergence times, and diversification parameters (speciation rates, extinction rates, and net diversification rates). These are among the most fundamental variables in macroevolutionary research. We use a series of novel approaches to explore the implications of these assumptions for inferring the age of Ipomoea, the ages of major clades within Ipomoea, whether there are significant differences in diversification parameters among clades within Ipomoea, and whether the storage root of I. batatas evolved in pre-human times. We show that inferring an age estimate for Ipomoea and major clades within Ipomoea is highly problematic. Inferred divergence times are sensitive to uncertain fossil calibrations and differing assumptions about among-branch-substitution-rate-variation. Despite this uncertainty, we are able to make robust inferences about patterns of variation in diversification parameters within Ipomoea, and that the storage root of I. batatas evolved in pre-human times. Taken together, this study presents novel and generalizable insights into the implications of methodological assumptions for making inferences about macroevolutionary history. Further, by presenting novel findings relating to the temporal dynamics of evolution in Ipomoea, as well as more specifically to I. batatas, this study makes a valuable contribution to our understanding of tropical plant evolution, and the evolutionary context in which economically important crops evolve.

A large-scale species level dated angiosperm phylogeny for evolutionary and ecological analyses

Phylogenies are a central and indispensable tool for evolutionary and ecological research. Even though most angiosperm families are well investigated from a phylogenetic point of view, there are far less possibilities to carry out large-scale meta-analyses at order level or higher. Here, we reconstructed a large-scale dated phylogeny including nearly 1/8th of all angiosperm species, based on two plastid barcoding genes, matK (incl. trnK) and rbcL. Novel sequences were generated for several species, while the rest of the data were mined from GenBank. The resulting tree was dated using 56 angiosperm fossils as calibration points. The resulting megaphylogeny is one of the largest dated phylogenetic tree of angiosperms yet, consisting of 36,101 sampled species, representing 8,399 genera, 426 families and all orders. This novel framework will be useful for investigating different broad scale research questions in ecological and evolutionary biology.

Insights from Empirical Analyses and Simulations on Using Multiple Fossil Calibrations with Relaxed Clocks to Estimate Divergence Times

Relaxed clock methods account for among-branch-rate-variation when estimating divergence times by inferring different rates for individual branches. In order to infer different rates for individual branches, important assumptions are required. This is because molecular sequence data do not provide direct information about rates but instead provide direct information about the total number of substitutions along any branch, which is a product of the rate and time for that branch. Often, the assumptions required for estimating rates for individual branches depend heavily on the implementation of multiple fossil calibrations in a single phylogeny. Here, we show that the basis of these assumptions is often critically undermined. First, we highlight that the temporal distribution of the fossil record often violates key assumptions of methods that use multiple fossil calibrations with relaxed clocks. With respect to “node calibration” methods, this conclusion is based on our inference that different fossil calibrations are unlikely to reflect the relative ages of different clades. With respect to the fossilized birth–death process, this conclusion is based on our inference that the fossil recovery rate is often highly heterogeneous. We then demonstrate that methods of divergence time estimation that use multiple fossil calibrations are highly sensitive to assumptions about the fossil record and among-branch-rate-variation. Given the problems associated with these assumptions, our results highlight that using multiple fossil calibrations with relaxed clocks often does little to improve the accuracy of divergence time estimates.

Eocene "Chusquea" fossil from Patagonia is a conifer, not a bamboo

Chusquea oxyphylla Freng. & Parodi, 1941, a fossilized leafy branch from the early Eocene (52 Ma), late-Gondwanan Laguna del Hunco biota of southern Argentina, is still cited as the oldest potential bamboo fossil and as evidence for a Gondwanan origin of bamboos. On recent examination, the holotype specimen was found to lack any typical bamboo characters such as nodes, sheaths, ligules, pseudopetioles, or parallel leaf venation. Instead, it has decurrent, clasping, univeined, heterofacially twisted leaves with thickened, central-longitudinal bands of presumed transfusion tissue. These and other features allow confident placement in the living Neotropical and West Pacific disjunct genus Retrophyllum (Podocarpaceae), which was recently described from the same fossil site based on abundant, well-preserved material. However, the 1941 fossil holds nomenclatural priority, requiring the new combination Retrophyllum oxyphyllum (Freng. & Parodi) Wilf, comb. nov. No reliable bamboo fossils remain from Gondwana, and the oldest South American bamboo fossils are Pliocene. Chusquea joins a growing list of living New World genera that are no longer included in Paleogene Patagonian floras, whose extant relatives are primarily concentrated in Australasia and Malesia via the ancient Gondwanan route through Antarctica.

Fossil fern rhizomes as a model system for exploring epiphyte community structure across geologic time: evidence from Patagonia

Background

In extant ecosystems, complex networks of ecological interactions between organisms can be readily studied. In contrast, understanding of such interactions in ecosystems of the geologic past is incomplete. Specifically, in past terrestrial ecosystems we know comparatively little about plant biotic interactions besides saprotrophy, herbivory, mycorrhizal associations, and oviposition. Due to taphonomic biases, epiphyte communities are particularly rare in the plant-fossil record, despite their prominence in modern ecosystems. Accordingly, little is known about how terrestrial epiphyte communities have changed across geologic time. Here, we describe a tiny in situ fossil epiphyte community that sheds light on plant-animal and plant-plant interactions more than 50 million years ago.

Methods

A single silicified Todea (Osmundaceae) rhizome from a new locality of the early Eocene (ca. 52 Ma) Tufolitas Laguna del Hunco (Patagonia, Argentina) was studied in serial thin sections using light microscopy. The community of organisms colonizing the tissues of the rhizome was characterized by identifying the organisms and mapping and quantifying their distribution. A 200 × 200 µm grid was superimposed onto the rhizome cross section, and the colonizers present at each node of the grid were tallied.

Results

Preserved in situ, this community offers a rare window onto aspects of ancient ecosystems usually lost to time and taphonomic processes. The community is surprisingly diverse and includes the first fossilized leafy liverworts in South America, also marking the only fossil record of leafy bryophyte epiphytes outside of amber deposits; as well as several types of fungal hyphae and spores; microsclerotia with possible affinities in several ascomycete families; and evidence for oribatid mites.

Discussion

The community associated with the Patagonian rhizome enriches our understanding of terrestrial epiphyte communities in the distant past and adds to a growing body of literature on osmundaceous rhizomes as important hosts for component communities in ancient ecosystems, just as they are today. Because osmundaceous rhizomes represent an ecological niche that has remained virtually unchanged over time and space and are abundant in the fossil record, they provide a paleoecological model system that could be used to explore epiphyte community structure through time.

Conventional and qPCR reveals the presence of 'Candidatus Liberibacter solanacearum' haplotypes A, and B in Physalis philadelphica plant, seed, and Βactericera cockerelli psyllids, with the assignment of a new haplotype H in Convolvulaceae

The husk tomato (Physalis philadelphica Lam.) is an important Solanaceae native to Mesoamerica that is grown for its green fruit used as an important ingredient in domestic and international cuisine. Nevertheless, husk tomato plants with symptoms resembling those caused by 'Candidatus Liberibacter solanacearum' (CLso) have been observed during the last decade in plantations located in the State of Mexico, Michoacan and Sinaloa in Mexico. These areas are located near other solanaceous crops where Bactericera cockerelli the well-known psyllid transmitter of CLso is frequently present. Thus, the goal of this study was to determine if CLso haplotypes are present in husk tomato varieties in commercial fields in Mexico. From 2015 to 2016, plants and fruit showing evident symptoms of CLso infection, as well as psyllids were collected in these states and assayed by PCR for CLso using primer sets OA2/OI2c and LpFrag 1-25F/427R. Phylogenetic reconstruction was performed with Bayesian analysis and maximum likelihood methods using amplicon sequences obtained in this work along with those deposited in the GenBank database corresponding to the CLso detected in Solanaceae, Apiaceae, and Convolvulaceae host families. In addition, all the sequences were subjected to haplotype determination through an analysis of DNA polymorphisms using the DnaSP software. Furthermore, quantitative PCR (qPCR) was performed using CLso-specific primers and probes. Phylogenetic reconstruction and qPCR confirmed the presence of CLso in plants, seeds and insect-vectors, and CLso sequences from plants and seeds completely matched haplotype B, whereas CLso haplotypes A and B were detected in B. cockerelli psyllids. Polymorphism analysis identified a novel Convolvulaceae-associated CLso haplotype, which was named haplotype H. The results of this study will enable the dissemination of infected seeds to new husk tomato production areas to be avoided.

Eocene Fagaceae from Patagonia and Gondwanan legacy in Asian rainforests

The beech-oak family Fagaceae dominates forests from the northern temperate zone to tropical Asia and Malesia, where it reaches its southern limit. We report early Eocene infructescences of Castanopsis, a diverse and abundant fagaceous genus of Southeast Asia, and co-occurring leaves from the 52-million-year-old Laguna del Hunco flora of southern Argentina. The fossil assemblage notably includes many plant taxa that associate with Castanopsis today. The discovery reveals novel Gondwanan history in Fagaceae and the characteristic tree communities of Southeast Asian lower-montane rainforests. The living diaspora associations persisted through Cenozoic climate change and plate movements as the constituent lineages tracked post-Gondwanan mesic biomes over thousands of kilometers, underscoring their current vulnerability to rapid climate change and habitat loss.

Origin and divergence of Afro-Indian Picrodendraceae: linking pollen morphology, dispersal modes, fossil records, molecular dating and paleogeography

The pantropical Picrodendraceae produce mostly spheroidal to slightly oblate, echinate pollen grains equipped with narrow circular to elliptic pori that can be hard to identify to family level in both extant and fossil material using light microscopy only. Fossil pollen of the family have been described from the Paleogene of America, Antarctica, Australia, New Zealand, and Europe, but until now none have been reported from Afro-India. Extant pollen described here include representatives from all recent Picrodendraceae genera naturally occurring in Africa and/or Madagascar and south India and selected closely related tropical American taxa. Our analyses, using combined light microscopy and scanning electron microscopy, show that pollen of the Afro-Indian genera encompass three morphological types: Type 1, comprising only Hyaenanche; Type 2, including Aristogeitonia, Mischodon, Oldfieldia and Voatamalo; Type 3, comprising the remaining two genera, Androstachys and Stachyandra. Based on the pollen morphology presented here it is evident that some previous light microscopic accounts of spherical and echinate fossil pollen affiliated with Arecaceae, Asteraceae, Malvaceae, and Myristicaceae from the African continent could belong to Picrodendraceae. The pollen morphology of Picrodendraceae, fossil pollen records, a dated intra-familial phylogeny, seed dispersal modes, and the regional Late Cretaceous to early Cenozoic paleogeography, together suggest the family originated in the Americas and dispersed from southern America across Antarctica and into Australasia. A second dispersal route is believed to have occurred from the Americas into continental Africa via the North Atlantic Land Bridge and Europe.

Integrating historical biogeography and environmental niche evolution to understand the geographic distribution of Datureae

PREMISE

The distributions of plant clades are shaped by abiotic and biotic factors as well as historical aspects such as center of origin. Dispersals between distant areas may lead to niche evolution when lineages are established in new environments. Alternatively, dispersing lineages may exhibit niche conservatism, moving between areas with similar environmental conditions. Here we test these contrasting hypotheses in the Datureae clade (Solanaceae).

METHODS

We used maximum likelihood methods to estimate the ancestral range of Datureae along with the history of biogeographic events. We then characterized the niche of each taxon using climatic and soil variables and tested for shifts in environmental niche optima. Finally, we examined how these shifts relate to the niche breadth of taxa and clades within Datureae and the degree of overlap between them.

RESULTS

Datureae originated in the Andes and subsequently expanded its range to North America and non-Andean regions of South America. The ancestral niche, and that of most Datura and Trompettia species, is dry, while Brugmansia species likely shifted toward a more mesic environment. Nonetheless, most Datureae present moderate to high overlap in niche breadth today.

CONCLUSIONS

The expansion of Datureae into North America was associated with niche conservatism, with dispersal into similarly dry areas as occupied by the ancestral lineage. Subsequent niche evolution, including the apparent shift to a mesic niche in Brugmansia, diversified the range of habitats occupied by species in the tribe Datureae but also led to significant niche overlap among the three genera.

Expression of a tobacco nicotine biosynthesis gene depends on the JRE4 transcription factor in heterogenous tomato

The jasmonate-responsive transcription factor ERF189 in tobacco (Nicotiana tabacum) and its ortholog JRE4 in tomato (Solanum lycopersicum) regulate a series of biosynthetic genes involved in the nicotine and steroidal glycoalkaloid pathways. In tobacco, QUINOLINATE PHOSPHORIBOSYL TRANSFERASE 2 (NtQPT2) is regulated by ERF189; however, we found that the tomato QPT gene is not regulated by JRE4. Here, we explored whether and how NtQPT2 is regulated in a heterogenous tomato host. We used a NtQPT2 promoter-driven reporter gene to examine the cell type-specific and jasmonate-induced expression of this gene in transgenic tomato hairy roots. The downregulation of the reporter in the jre4 loss-of-function tomato mutant and its transactivation by JRE4 in transient expression experiments suggested that JRE4, like its ortholog ERF189 in tobacco, activates the NtQPT2 promoter in tomato. We discuss the evolution of QPT2 in the Nicotiana lineage, which mainly occurred through mutational changes in the promoter that altered the control of the functionally conserved transcription factors.

Repeated evolution of a morphological novelty: a phylogenetic analysis of the inflated fruiting calyx in the Physalideae tribe (Solanaceae)

PREMISE OF THE STUDY

The evolution of novel fruit morphologies has been integral to the success of angiosperms. The inflated fruiting calyx, in which the balloon-like calyx swells to completely surround the fruit, has evolved repeatedly across angiosperms and is postulated to aid in protection and dispersal. We investigated the evolution of this trait in the tomatillos and their allies (Physalideae, Solanaceae).

METHODS

The Physalideae phylogeny was estimated using four regions (ITS, LEAFY, trnL-F, waxy) with maximum likelihood (ML) and Bayesian inference. Under the best-fitting ML model of trait evolution, we estimated ancestral states along with the numbers of gains and losses of fruiting calyx accrescence and inflation with Bayesian stochastic mapping. Also, phylogenetic signal in calyx morphology was examined with two metrics (parsimony score and Fritz and Purvis's D).

KEY RESULTS

Based on our well-resolved and densely sampled phylogeny, we infer that calyx evolution has proceeded in a stepwise and directional fashion, from non-accrescent to accrescent to inflated. In total, we inferred 24 gains of accrescence, 24 subsequent transitions to a fully inflated calyx, and only two reversals. Despite this lability, fruiting calyx accrescence and inflation showed strong phylogenetic signal.

CONCLUSIONS

Our phylogeny greatly improves the resolution of Physalideae and highlights the need for taxonomic work. The comparative analyses reveal that the inflated fruiting calyx has evolved many times and that the trajectory toward this phenotype is generally stepwise and irreversible. These results provide a strong foundation for studying the genetic and developmental mechanisms responsible for the repeated origins of this charismatic fruit trait.

Chinese lantern in Physalis is an advantageous morphological novelty and improves plant fitness

The origin of morphological novelties is an important but neglected issue of evolutionary biology. The fruit of the genus Physalis, a berry, is encapsulated by a novel morphological feature of the post-floral, accrescent calyx that is referred to as a Chinese lantern. The evolutionary developmental genetics of the Chinese lantern have been investigated in the last decade; however, the selective values of the morphological novelty remain elusive. Here, we measured the photosynthetic parameters of the fruiting calyces, monitored microclimatic variation within the Chinese lanterns during fruit development, performed floral-calyx-removal experiments, and recorded the fitness-related traits in Physalis floridana. Ultimately, we show that the green-fruiting calyx of Physalis has photosynthetic capabilities, thus serving as an energy source for fruit development. Moreover, the developing Chinese lantern provides a microclimate that benefits the development and maturation of berry and seed, and it improves plant fitness in terms of fruit/seed weight and number, and fruit maturation under low-temperature environments. Furthermore, the lantern structure facilitates the dispersal of fruits and seeds by water and wind. Our results suggest that the Chinese lantern morphology of Physalis is an evolutionary adaptive trait and improves plant fitness, thus providing new insight into the origin of morphological novelties.

An unexpected noncarpellate epigynous flower from the Jurassic of China

The origin of angiosperms has been a long-standing botanical debate. The great diversity of angiosperms in the Early Cretaceous makes the Jurassic a promising period in which to anticipate the origins of the angiosperms. Here, based on observations of 264 specimens of 198 individual flowers preserved on 34 slabs in various states and orientations, from the South Xiangshan Formation (Early Jurassic) of China, we describe a fossil flower, Nanjinganthus dendrostyla gen. et sp. nov.. The large number of specimens and various preservations allow for an evidence-based reconstruction of the flower. From the evidence of the combination of an invaginated receptacle and ovarian roof, we infer that the seeds of Nanjinganthus were completely enclosed. Evidence of an actinomorphic flower with a dendroid style, cup-form receptacle, and angiospermy, is consistent with Nanjinganthus being a bona fide angiosperm from the Jurassic, an inference that we hope will re-invigorate research into angiosperm origins.

From oranges to apples, flowering plants produce most of the fruits and vegetables that we can see on display in a supermarket. While we may take little notice of the poppy fields and plum blossoms around us, how flowers came to be has been an intensely debated mystery.

The current understanding, which is mainly based on previously available fossils, is that flowers appeared about 125 million years ago in the Cretaceous, an era during which many insects such as bees also emerged. But not everybody agrees that this is the case. Genetic analyses, for example, suggest that flowering plants are much more ancient. Another intriguing element is that flowers seemed to have arisen during the Cretaceous ‘out of nowhere’.

Fossils are essential to help settle the debate but it takes diligence and luck to find something as fragile as a flower preserved in rocks for millions of years. In addition, digging out what could look like a bloom is not enough. It is only if the ovules (the cells that will become seeds when fertilized) of the plant are completely enclosed inside the ovary before pollination that researchers can definitely say that they have found a ‘true’ flower.

Now, Fu et al. describe over 200 specimens of a new fossil flower that presents this characteristic, as well as other distinctive features such as petals and sepals – the leaf-like parts that protect a flower bud. Called Nanjinganthus, the plant dates back to more than 174 million years ago, making it the oldest known record of a ‘true’ flower by almost 50 million years. Contrary to mainstream belief, this would place the apparition of flowering plants to the Early Jurassic, the period that saw dinosaurs dominating the planet. This discovery may reshape our current understanding of the evolution of flowers.

The Core Eudicot Boom Registered in Myanmar Amber

A perfect flower in a mid-Cretaceous (early Cenomanian) Myanmar amber is described as Lijinganthus revoluta gen. et sp. nov. The fossil flower is actinomorphic and pentamerous, including calyx, corolla, stamens, and gynoecium. The sepals are tiny, while the petals are large and revolute. The stamens are dorsifixed, filamentous, and each has a longitudinally dehiscing bisporangiate anther. The gynoecium is in the centre of the flower, composed of three fused carpels with a stout style. Lijinganthus revoluta gen. et sp. nov. demonstrates a great resemblance to the flowers of Pentapetalae (Eudicots), adding new information to the enigmatic early evolutionary history of Pentapetalae and Eudicots.

Paleocene Ipomoea (Convolvulaceae) from India with implications for an East Gondwana origin of Convolvulaceae

The morning glory family, Convolvulaceae, is globally important in medicine and food crops. The family has worldwide distribution in a variety of habitats; however, its fossil record is very poorly documented. The current fossil record suggests an origin in North America, which is in contrast to molecular data that indicate an East Gondwana origin. We report Ipomoea leaves from the late Paleocene (Thanetian; 58.7-55.8 million years ago) of India, which was a part of East Gondwana during this time. This is the earliest fossil record for both the family Convolvulaceae and the order Solanales. This suggests that the sister families Convolvulaceae and Solanaceae diverged before the Eocene in Gondwana-derived continents. The evidence presented here supports the conclusion from molecular phylogenetic analysis of an East Gondwana origin of Convolvulaceae.

Reconciling Conflicting Phylogenies in the Origin of Sweet Potato and Dispersal to Polynesia

The sweet potato is one of the world's most widely consumed crops, yet its evolutionary history is poorly understood. In this paper, we present a comprehensive phylogenetic study of all species closely related to the sweet potato and address several questions pertaining to the sweet potato that remained unanswered. Our research combined genome skimming and target DNA capture to sequence whole chloroplasts and 605 single-copy nuclear regions from 199 specimens representing the sweet potato and all of its crop wild relatives (CWRs). We present strongly supported nuclear and chloroplast phylogenies demonstrating that the sweet potato had an autopolyploid origin and that Ipomoea trifida is its closest relative, confirming that no other extant species were involved in its origin. Phylogenetic analysis of nuclear and chloroplast genomes shows conflicting topologies regarding the monophyly of the sweet potato. The process of chloroplast capture explains these conflicting patterns, showing that I. trifida had a dual role in the origin of the sweet potato, first as its progenitor and second as the species with which the sweet potato introgressed so one of its lineages could capture an I. trifida chloroplast. In addition, we provide evidence that the sweet potato was present in Polynesia in pre-human times. This, together with several other examples of long-distance dispersal in Ipomoea, negates the need to invoke ancient human-mediated transport as an explanation for its presence in Polynesia. These results have important implications for understanding the origin and evolution of a major global food crop and question the existence of pre-Columbian contacts between Polynesia and the American continent.

Deciphering the Origin, Evolution, and Physiological Function of the Subtelomeric Aryl-Alcohol Dehydrogenase Gene Family in the Yeast Saccharomyces cerevisiae

Homology searches indicate that Saccharomyces cerevisiae strain BY4741 contains seven redundant genes that encode putative aryl-alcohol dehydrogenases (AAD). Yeast AAD genes are located in subtelomeric regions of different chromosomes, and their functional role(s) remain enigmatic. Here, we show that two of these genes, AAD4 and AAD14, encode functional enzymes that reduce aliphatic and aryl-aldehydes concomitant with the oxidation of cofactor NADPH, and that Aad4p and Aad14p exhibit different substrate preference patterns. Other yeast AAD genes are undergoing pseudogenization. The 5′ sequence of AAD15 has been deleted from the genome. Repair of an AAD3 missense mutation at the catalytically essential Tyr⁷³ residue did not result in a functional enzyme. However, ancestral-state reconstruction by fusing Aad6 with Aad16 and by N-terminal repair of Aad10 restores NADPH-dependent aryl-alcohol dehydrogenase activities. Phylogenetic analysis indicates that AAD genes are narrowly distributed in wood-saprophyte fungi and in yeast that occupy lignocellulosic niches. Because yeast AAD genes exhibit activity on veratraldehyde, cinnamaldehyde, and vanillin, they could serve to detoxify aryl-aldehydes released during lignin degradation. However, none of these compounds induce yeast AAD gene expression, and Aad activities do not relieve aryl-aldehyde growth inhibition. Our data suggest an ancestral role for AAD genes in lignin degradation that is degenerating as a result of yeast's domestication and use in brewing, baking, and other industrial applications.

IMPORTANCE Functional characterization of hypothetical genes remains one of the chief tasks of the postgenomic era. Although the first Saccharomyces cerevisiae genome sequence was published over 20 years ago, 22% of its estimated 6,603 open reading frames (ORFs) remain unverified. One outstanding example of this category of genes is the enigmatic seven-member AAD family. Here, we demonstrate that proteins encoded by two members of this family exhibit aliphatic and aryl-aldehyde reductase activity, and further that such activity can be recovered from pseudogenized AAD genes via ancestral-state reconstruction. The phylogeny of yeast AAD genes suggests that these proteins may have played an important ancestral role in detoxifying aromatic aldehydes in ligninolytic fungi. However, in yeast adapted to niches rich in sugars, AAD genes become subject to mutational erosion. Our findings shed new light on the selective pressures and molecular mechanisms by which genes undergo pseudogenization.

Evolutionary history of two pollen self-incompatibility factors reveals alternate routes to self-compatibility within Solanum

PREMISE OF THE STUDY

Self-incompatibility (SI) prevents self-fertilization and reduces inbreeding. While SI is common in plants, transitions to self-compatibility (SC) occur frequently. Little is known about the genetic changes and evolutionary steps underlying these shifts.

METHODS

In the Solanaceae, SI is gametophytic, with specificity determined by S-RNases in the pistil and S-locus F-box proteins (SLFs) in pollen. We examined the role of two pollen factors, Cullin1 (CUL1) and SLF-23, in SI → SC transitions in wild tomato species from the Arcanum species group (Solanum arcanum, S. neorickii, and S. chmielewskii). Pollen compatibility was assessed on tester lines that reject pollen lacking functional SLF-23 or CUL1. Complementation tests, gene sequencing, and phylogenetic analyses were used to characterize both functional and nonfunctional alleles.

KEY RESULTS

We found evidence for multiple independent SI → SC transitions. In S. arcanum and S. chmielewskii, SC is caused by loss of pistil S-RNase activity, while in S. neorickii SC is associated with expression of a functional SLF-23 that recognizes the S₉ type S-RNase expressed in its pistils. Interestingly, we found identical deletion mutations in CUL1 exon 7 of S. chmielewskii as previously seen in S. habrochaites.

CONCLUSIONS

Mating system transitions in the Arcanum group have occurred via both pistil loss-of-function and pollen gain-of-function SC mutations. Mutations common to S. chmielewskii and S. habrochaites must have arisen in a common ancestor, possibly to the entire tomato clade, then became fixed in different lineages after loss of pistil-side SI function.

Phylogenetic relationships of Deprea: New insights into the evolutionary history of physaloid groups

Deprea is the genus with the second highest species richness in tribe Physalideae (Solanaceae) and comprises 50 species that are mainly distributed in the Andes of South America. The taxonomy of Deprea has been unstable after controversial hypotheses about its position and circumscription. Additionally, biogeographical inferences are only based on observations of the restricted area of distribution of some species and no ancestral area estimation have been performed. Here, we present a phylogenetic analysis and an ancestral area reconstruction of Deprea in order to establish its circumscription, resolve its position within Physalideae, and reconstruct its biogeographical history. Phylogenetic analyses were conducted using Maximum Likelihood and Bayesian approaches. Forty-three Deprea species and 26 related taxa were sampled for three DNA markers (psbA-trnH, ITS, and waxy). A Bayesian binary MCMC model was applied in order to infer ancestral areas. Deprea is resolved as a strongly supported monophyletic group according to its current circumscription and is placed within subtribe Withaninae of Physalideae. The phylogenetic relationships enabled us to solve taxonomic problems including the rejection and acceptance of previous synonyms. The most probable ancestral area for Deprea is the Northern Andes of South America and the Amotape-Huancabamba zone. Our phylogeny provides increased resolution and support for the current position and circumscription of Deprea. Better resolution of interspecific relationships was also obtained, although some affinities remain unclear. The phylogenetic and ancestral area reconstructions provide a framework for addressing taxonomic problems and investigating new evolutionary questions.

Population Genomics in Wild Tomatoes-The Interplay of Divergence and Admixture

Hybridization between closely related plant species is widespread, but the outcomes of hybridization are not fully understood. This study investigates phylogenetic relationships and the history of hybridization in the wild tomato clade (Solanum sect. Lycopersicon). We sequenced RNA from individuals of 38 different populations and, by combining this with published data, build a comprehensive genomic data set for the entire clade. The data indicate that many taxa are not monophyletic and many individuals are admixed due to repeated hybridization. The most polymorphic species, Solanum peruvianum, has two genetic and geographical subpopulations, while its sister species, Solanum chilense, has distinct coastal populations and reduced heterozygosity indicating a recent expansion south following speciation from S. peruvianum circa 1.25 Ma. Discontinuous populations west of 72° are currently described as S. chilense, but are genetically intermediate between S. chilense and S. peruvianum. Based upon molecular, morphological, and crossing data, we test the hypothesis that these discontinuous "S. chilense" populations are an example of recombinational speciation. Recombinational speciation is rarely reported, and we discuss the difficulties in identifying it and differentiating between alternative demographic scenarios. This discovery presents a new opportunity to understand the genomic outcomes of hybridization in plants.