Fossil evidence and phylogeny: the age of major angiosperm clades based on mesofossil and macrofossil evidence from Cretaceous deposits

Adaptive generalization in pollination systems: Hawkmoths increase fitness to long-tubed flowers, but secondary pollinators remain important

Selection on floral traits by animal pollinators is important in the evolution of flowering plants, yet whether floral divergence requires specialized pollination remains uncertain. Longer floral tubes, a trait associated with long-tongued pollinators, can also exclude other pollinators from accessing rewards, a potential mechanism for specialization. Across most of its range, Castilleja sessiliflora displays much longer corollas than most Castilleja species, though tube length varies geographically and correlates partially with hawkmoth visitation. To assess whether long corolla tubes reflect adaptation to hawkmoth pollinators, we performed a day/night pollinator exclusion experiment in nine natural populations that varied in corolla length across the range of C. sessiliflora and short-tubed members of the parapatric C. purpurea complex. We compared the fitness contributions of nocturnal and diurnal visitors, revealing that long-tubed populations visited predominantly by hawkmoths experienced greater fruit set at night, in contrast with short-tubed populations or those visited mainly by diurnal pollinators. Next, leveraging a range-wide multiyear dataset of pollinator visitation to these species, we identify that hawkmoth visitation is associated with increased fitness in long-tubed populations overall, and that long tubes are associated with less diverse visitor assemblages. Thus, long corollas represent an adaptation to hawkmoth pollination at the exclusion of diverse pollinators. Nonetheless, while hawkmoths were scarce in the northern range, secondary diurnal pollinators contributed to fruit set across the range, providing reproductive assurance despite possible trait mismatch. This study illustrates adaptive generalization in pollination systems and that floral divergence may proceed along a continuum of generalized and specialized pollinator interactions.

Angiosperm phylogenetic diversity is lower in Africa than South America

Although originating from a common Gondwanan flora, the diversity and composition of the floras of Africa and South America have greatly diverged since continental breakup of Africa from South America now having much higher plant species richness. However, the phylogenetic diversity of the floras and what this tells us about their evolution remained unexplored. We show that for a given species richness and considering land surface area, topography, and present-day climate, angiosperm phylogenetic diversity in South America is higher than in Africa. This relationship holds regardless of whether all climatically matched areas or only matched areas in tropical climates are considered. Phylogenetic diversity is high relative to species richness in refugial areas in Africa and in northwestern South America, once the gateway for immigration from the north. While species richness is strongly influenced by massive plant radiations in South America, we detect a pervasive influence of historical processes on the phylogenetic diversity of both the South American and African floras.

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.

Flora of Ceará, Brazil: Rhamnaceae

Abstract We present the floristic-taxonomic and distribution survey of the family Rhamnaceae as part of the “Flora of Ceará: knowing to conserve” project. The survey was based on the analysis of morphological characters of specimens gathered during field expeditions and from herbaria collections, as well as the specialized literature. Rhamnaceae is represented by ten species in Ceará State belonging to five genera: Colubrina (2), Crumenaria (1), Gouania (3), Rhamnidium (1), and Sarcomphalus (3). The species were encountered in various phytophysiognomies, but especially occur in Seasonal Semideciduous Forests (Mata Seca) and the Coastal Zone Vegetation Complex (Lowland Semideciduous Forest). The species with the highest number of records was Sarcomphalus joazeiro, occurring in 62 municipalities. Seven species were encountered in 14 legally protected conservation areas in Ceará. Colubrina cordifolia, Rhamnidium molle, and Crumenaria decumbens occur exclusively in the Caatinga domain, with the first two being endemic to northeastern Brazil. Identification keys, morphological descriptions, comments on distributions, ecology, phenology, and uses of the species are provided, as well as maps and illustrations.

Barley Seeds miRNome Stability during Long-Term Storage and Aging

Seed aging is a complex biological process that has been attracting scientists’ attention for many years. High-throughput small RNA sequencing was applied to examine microRNAs contribution in barley seeds senescence. Unique samples of seeds that, despite having the same genetic makeup, differed in viability after over 45 years of storage in a dry state were investigated. In total, 61 known and 81 novel miRNA were identified in dry seeds. The highest level of expression was found in four conserved miRNA families, i.e., miR159, miR156, miR166, and miR168. However, the most astonishing result was the lack of significant differences in the level of almost all miRNAs in seed samples with significantly different viability. This result reveals that miRNAs in dry seeds are extremely stable. This is also the first identified RNA fraction that is not deteriorating along with the loss of seed viability. Moreover, the novel miRNA hvu-new41, with higher expression in seeds with the lowest viability as detected by RT-qPCR, has the potential to become an indicator of the decreasing viability of seeds during storage in a dry state.

Patterns of host tree use within a lineage of saproxlic snout-less weevils (Coleoptera: Curculionidae: Scolytinae: Scolytini)

The influence of plants in the diversification of herbivorous insects, specifically those that utilize moribund and dead hosts, is little explored. Host shifts are expected because the effectiveness of toxic secondary chemicals is lessened by decay of dead plants. Feeding on dead plants also releases herbivorous insect lineages from diversifying within a particular plant lineage. Thus, phylogenetic constraints on the herbivorous insect lineage imposed by the host plants are diminished and repeated patterns of species diversification in an association with unrelated host trees is hypothesized (i.e., taxon cycle). Scolytini, a diverse weevil tribe, specialize on many different dead and moribund plant taxa as a source of food. These species and their hosts offer an opportunity to examine the association between dead host plants and the extent of phylogenetic constraints. A phylogeny of the Scolytini was reconstructed with likelihood and Bayesian analyses of DNA sequence data from nuclear (28S, CAD, ArgK) and mitochondrial (COI) genes. Ancestral host usage and geography was reconstructed using likelihood criteria and conservation of host use was tested. Results supported a monophyletic Scolytini, Ceratolepis, Loganius, and a paraphyletic Scolytus, Camptocerus and Cnemonyx. Diversification of the Scolytini generally occurred well after their host taxa diversified and suggests a sequential evolution of host use. In this scenario the beetle imposes little selection pressure on the tree but the tree provides a platform for beetle evolution. Major changes in host tree use occurred during periods of global cooling associated with changes in beetle biogeography. Diversification of beetles occurred on common and widespread hosts and there was likely a single origination of conifer-feeding from angiosperm-feeding species during the early Pliocene and a radiation of beetle species from the Palearctic to the Nearctic. Overall, the observed patterns of Scolytini host use are conserved and are similar to those expected in a taxon pulse diversification. That is, after a host switch to an unrelated tree, the beetles diversify within the host plant lineage. The need to locate an ephemeral food resource, i.e., a dying tree, likely maintains host specificity once a host shift occurs. These findings suggest that characteristics of dead and moribund host plants (e.g. secondary chemicals) influence the diversification of these saproxlic weevils despite the reduction of selection pressures.

Late Campanian fossil of a legume fruit supports Mexico as a center of Fabaceae radiation

Fabaceae is one of the most diverse angiosperm families and is distributed across the globe in a variety of environments. The earliest evidence of the family, previous to this work, was from Paleogene sediments where it was found to be diverse in many fossil assemblages around the world. Here, we describe a fossil legume fruit from the Olmos Formation (upper Campanian) in northern Mexico. We designated the fossil fruit as Leguminocarpum olmensis Centeno-González, Martínez-Cabrera, Porras-Múzquiz et Estrada-Ruiz sp. nov., and related it with the Fabaceae family based on the presence of a dehiscent pod with two valves, an apex bearing stylar base, short stipe, and reticulated veins in the pericarp. We propose a new fossil species of Leguminocarpum for this fossil fruit. This fossil provides critical information on the long geologic history of Leguminosae around the world, significantly extending the record into the Cretaceous of Mexico.

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.

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.

Assessment of the elite accessions of bael [Aegle marmelos (L.) Corr.] in Sri Lanka based on morphometric, organoleptic, and elemental properties of the fruits and phylogenetic relationships

Aegle marmelos L. (Bael) is a native tree fruit species in the Indian subcontinent and Southeast Asia. Bael is a popular fruit because of its significant nutritional and medicinal properties. However, bael is an underutilized fruit species in Sri Lanka. Thus, Fruit Crop Research and Development Station of the Department of Agriculture of Sri Lanka has selected five elite bael accessions (Beheth Beli, Paragammana, Mawanella, Rambukkana, and Polonnaruwa-Supun). We assessed these five accessions for the variation of the fruit size, pulp, organoleptic preference, elemental properties, genetic diversity, and evolutionary history. The fruits at the golden-ripe stage were collected during the peak fruiting seasons in 2015, 2016, and 2017. The fruit size, pulp, shell thickness, and seed size were measured and subjected to the General Linear Model (GLM) and Principal Component (PC) Analyses. The fruit pulp was distributed among a group of 30 taste-panelists to rank for the parameters: external appearance, flesh color, aroma, texture, sweetness, and overall preference. The rank data were subjected to association and PC analyses. The elemental contents of the fruit pulp samples were measured using Inductively coupled plasma mass spectrometry and subjected to GLM and PC analyses. We observed a significant diversity in fruit size, organoleptic preference, and elemental contents among bael accessions. Rambukkana and Polonnaruwa-Supun yield the biggest and most preferred fruits. We used trnH-psbA, atpB-rbcL spacer, matk-trnT spacer, and trnL markers to construct phylogenies. Sri Lankan bael split from an Indian counterpart, approximately 8.52 MYA in the Pliocene epoch. However, broader germplasm of Indian bael must be assessed to see the presence of any independent evolution within Sri Lanka.

The fossil record of spiders revisited: implications for calibrating trees and evidence for a major faunal turnover since the Mesozoic

Studies in evolutionary biology and biogeography increasingly rely on the estimation of dated phylogenetic trees using molecular clocks. In turn, the calibration of such clocks is critically dependent on external evidence (i.e. fossils) anchoring the ages of particular nodes to known absolute ages. In recent years, a plethora of new fossil spiders, especially from the Mesozoic, have been described, while the number of studies presenting dated spider phylogenies based on fossil calibrations increased sharply. We critically evaluate 44 of these studies, which collectively employed 67 unique fossils in 180 calibrations. Approximately 54% of these calibrations are problematic, particularly regarding unsupported assignment of fossils to extant clades (44%) and crown (rather than stem) dating (9%). Most of these cases result from an assumed equivalence between taxonomic placement of fossils and their phylogenetic position. To overcome this limitation, we extensively review the literature on fossil spiders, with a special focus on putative synapomorphies and the phylogenetic placement of fossil species with regard to their importance for calibrating higher taxa (families and above) in the spider tree of life. We provide a curated list including 41 key fossils intended to be a basis for future estimations of dated spider phylogenies. In a second step, we use a revised set of 23 calibrations to estimate a new dated spider tree of life based on transcriptomic data. The revised placement of key fossils and the new calibrated tree are used to resolve a long-standing debate in spider evolution - we tested whether there has been a major turnover in the spider fauna between the Mesozoic and Cenozoic. At least 17 (out of 117) extant families have been recorded from the Cretaceous, implying that at least 41 spider lineages in the family level or above crossed the Cretaeous-Paleogene (K-Pg) boundary. The putative phylogenetic affinities of families known only from the Mesozoic suggest that at least seven Cretaceous families appear to have no close living relatives and might represent extinct lineages. There is no unambiguous fossil evidence of the retrolateral tibial apophysis clade (RTA-clade) in the Mesozoic, although molecular clock analyses estimated the major lineages within this clade to be at least ∼100 million years old. Our review of the fossil record supports a major turnover showing that the spider faunas in the Mesozoic and the Cenozoic are very distinct at high taxonomic levels, with the Mesozoic dominated by Palpimanoidea and Synspermiata, while the Cenozoic is dominated by Araneoidea and RTA-clade spiders.

The genome sequence of celery (Apium graveolens L.), an important leaf vegetable crop rich in apigenin in the Apiaceae family

Celery (Apium graveolens L.) is a vegetable crop in the Apiaceae family that is widely cultivated and consumed because it contains necessary nutrients and multiple biologically active ingredients, such as apigenin and terpenoids. Here, we report the genome sequence of celery based on the use of HiSeq 2000 sequencing technology to obtain 600.8 Gb of data, achieving ~189-fold genome coverage, from 68 sequencing libraries with different insert sizes ranging from 180 bp to 10 kb in length. The assembled genome has a total sequence length of 2.21 Gb and consists of 34,277 predicted genes. Repetitive DNA sequences represent 68.88% of the genome sequences, and LTR retrotransposons are the main components of the repetitive sequences. Evolutionary analysis showed that a recent whole-genome duplication event may have occurred in celery, which could have contributed to its large genome size. The genome sequence of celery allowed us to identify agronomically important genes involved in disease resistance, flavonoid biosynthesis, terpenoid metabolism, and other important cellular processes. The comparative analysis of apigenin biosynthesis genes among species might explain the high apigenin content of celery. The whole-genome sequences of celery have been deposited at CeleryDB (http://apiaceae.njau.edu.cn/celerydb). The availability of the celery genome data advances our knowledge of the genetic evolution of celery and will contribute to further biological research and breeding in celery as well as other Apiaceae plants.

Staminate flower of Prunus s. l. (Rosaceae) from Eocene Rovno amber (Ukraine)

The late Eocene ambers provide plethora of animal and plant fossils including well-preserved angiosperm flowers from the Baltic amber. The Rovno amber from NW Ukraine resembles in many aspects the Baltic amber; however, only fossilized animals and some bryophytes have yet been studied from the Rovno amber. We provide the first detailed description of an angiosperm flower from Rovno amber. The flower is staminate with conspicuous hypanthium, double pentamerous perianth and whorled androecium of 24 stamens much longer than the petals. Sepals are sparsely pubescent and petals are densely hirsute outside. The fossil shares important features with extant members of Prunus subgen. Padus s. l. (incl. Laurocerasus, Pygeum and Maddenia), especially with its evergreen paleotropical species. It is described here as a new species Prunus hirsutipetala D.D.Sokoloff, Remizowa et Nuraliev. Our study provides the first convincing record of fossil flowers of Rosaceae from Eocene of Europe and the earliest fossil flower of Prunus outside North America. Our record of a plant resembling extant tropical species supports palaeoentomological evidences for warm winters in northwestern Ukraine during the late Eocene, as well as suggesting a more significant role of tropical insects in Rovno amber than inferred from Baltic amber.

Cornalean affinities, phylogenetic significance, and biogeographic implications of Operculifructus infructescences from the Late Cretaceous (Campanian) of Mexico

Premise of the Study Cretaceous Cornales provide a crucial record of the early history of asterids. Most lineages of the order are well represented in the fossil record, but South African families of Curtisiaceae and Grubbiaceae remain poorly understood. Seventy-three specimens of a fossil infructescence belonging to the genus Operculifructus Estrada-Ruiz & Cevallos-Ferriz emend. Hayes & Smith from the Late Cretaceous (Campanian) El Gallo Formation, Baja California, Mexico bear previously undescribed characters that suggest a relationship to Grubbiaceae. Methods Microstructures of the fossils were examined through light microscopy and x-ray microcomputed tomography (microCT) scanning. Modern Grubbia tomentosa (Thunb.) Harms fruits were scanned for comparison to the fossil material. Phylogenetic analyses using the 77 fruit characters of Atkinson () were performed to test relationships of the fossil to major lineages of the order. Several analyses applied topological constraints to the extant taxa, based on various genetically supported hypotheses of relationship within Cornales. Key Results Novel structures of Operculifructus newly observed here include (1) anatropous ovules, (2) drupaceous fruits, (3) an epigynous disc, (4) and a stylar canal in the center of the disc aligned with the micropylar protrusion of the seed. Phylogenetic analysis consistently resolves Operculifructus as sister to Grubbiaceae. Conclusions Operculifructus provides direct evidence for the occurrence of Grubbiaceae in the Late Cretaceous, much older than previous Eocene evidence. The phylogeny of Atkinson () indicates that the new phylogenetic position recovered for Operculifructus also establishes the presence of the most basal drupaceous cornalean fruits in North America by the Campanian. RESUMEN EN ESPAÑOL Hipótesis de la Investigación Cornales cretácicos representan un registro esencial en la historia de los astéridos. Casi todos los linajes del orden están bien representados en el registro fósil, pero las familias africanas sureñas Curtisiaceae y Grubbiaceae permanecen pobremente entendidas. Setenta y tres ejemplares de una infrutescencia fósil perteneciente al género Operculifructus Estrada-Ruiz & Cevallos-Ferriz emend. Hayes & Smith de la formación campaniana (Cretácico Tardío) El Gallo, Baja California, México, poseen caracteres no descritos previamente y sugieren una relación con Grubbiaceae. Metodología Microestructuras de los fósiles fueron examinadas con microscopio de luz y microtomografía computarizada (micro-CT) de rayos X. Frutos actuales de Grubbia tomentosa (Thunb.) Harms fueron escaneados para su comparación con el material fósil. Se realizaron análisis filogenéticos usando los 77 caracteres de frutos de Atkinson () para probar las relaciones de los fósiles con los linajes principales del orden. En algunos análisis se aplicaron restricciones topológicas a los taxa actuales basándose en varias hipótesis, soportadas genéticamente, de las relaciones dentro de Cornales. Resultados Centrales (Cruciales) Las estructuras novedosas de Operculifructus, recientemente observadas aquí, incluyen (1) óvulos anátropos; (2) frutos drupáceos; (3) disco epígino; y (4) un canal estilar en el centro del disco alineado con la protuberancia micropilar de la semilla. Los análisis filogenéticos consistentemente dan como resultado que Operculifructus es hermano de Grubbiaceae. Conclusiones Operculifructus proporciona evidencia directa de la presencia de Grubbiaceae en el Cretácico Tardío, mucho antes que la previa evidencia en el Eoceno. La filogenia de Atkinson () indica que la nueva posición filogenética recuperada para Operculifructus también resalta la presencia de frutos drupáceos cornaleanos más basales en Norteamérica durante el Campaniano.

Climatic Changes and Orogeneses in the Late Miocene of Eurasia: The Main Triggers of an Expansion at a Continental Scale?

Migrations from the Qinghai-Tibetan Plateau (QTP) to other temperate regions represent one of the main biogeographical patterns for the Northern Hemisphere. However, the ages and routes of these migrations are largely not known. We aimed to reconstruct a well-resolved and dated phylogeny of Hippophae L. (Elaeagnaceae) and test hypothesis of a westward migration of this plant out of the QTP across Eurasian mountains in the Miocene. We produced two data matrices of five chloroplast DNA (cpDNA) and five nuclear DNA markers for all distinct taxa of Hippophae. These matrices were used to reconstruct phylogenetic relationships in the genus. In dating analyses, we first estimated the stem node age of Elaeagnaceae using five fossil records evenly distributed across a tree of Rosales. We used this estimate and two fossil records to calibrate the cpDNA and nDNA phylogenies of Hippophae. The same phylogenies were used to reconstruct ancestral areas within the genus. The monophyly of Hippophae, all five species, and most of subspecies was strongly supported by both plastid and nuclear data sets. Diversification of Hippophae likely started in central Himalayas/southern Tibet in the early Miocene and all extant distinct species had probably originated by the middle Miocene. Diversification of Hippophae rhamnoides likely started in the late Miocene east of the QTP from where this species rapidly expanded to central and western Eurasia. Our findings highlight the impact of different stages in uplift of the QTP and Eurasian mountains and climatic changes in the Neogene on diversification and range shifts in the highland flora on the continent. The results provide support to the idea of an immigration route for some European highland plants from their ancestral areas on the QTP across central and western mountain ranges of Eurasia in the late Miocene.

The critical role of fossils in inferring deep-node phylogenetic relationships and macroevolutionary patterns in Cornales

PREMISE OF THE STUDY

The basal asterid order, Cornales, experienced a rapid radiation during the Cretaceous, which has made it difficult to elucidate the early evolution of the order using extant taxa only. Recent paleobotanical studies, however, have begun to shed light on the early diversification of Cornales. Herein, fossils are directly incorporated in phylogenetic and quantitative morphological analyses to reconstruct early cornalean evolution.

METHODS

A morphological matrix of 77 fruit characters and 58 taxa (24 extinct) was assembled. Parsimony analyses including and excluding fossils were conducted. A fossil inclusive tree was time-scaled to visualize the timing of the initial cornalean radiation. Disparity analyses were utilized to infer the morphological evolution of cornaleans with drupaceous fruits.

KEY RESULTS

Fossil inclusive and exclusive parsimony analyses resulted in well-resolved deep-node relationships within Cornales. Resolution in the fossil inclusive analysis is substantially higher, revealing a basal grade including Loasaceae, Hydrangeaceae, Hydrostachyaceae, Grubbiaceae, a Hironoia+Amersinia clade, and Curtisiaceae, respectively, that leads to a "core" group containing a clade comprising a Cretaceous grade leading to clade of Nyssaceae, Mastixiaceae, and Davidiaceae that is sister to a Cornaceae+Alangiaceae clade. The time-scaled tree indicates that the initial cornalean diversification occurred before 89.8 Ma. Disparity analyses suggest the morphological diversity of Cornales peaked during the Paleogene.

CONCLUSIONS

Phylogenetic analyses clearly demonstrate that novel character mosaics of Cretaceous cornaleans play a critical role in resolving deep-node relationships within Cornales. The post-Cretaceous increase of cornalean disparity is associated with a shift in morphospace occupation, which can be explained from ecological and developmental perspectives.

A late Cretaceous fagalean inflorescence preserved in amber from New Jersey

PREMISE OF THE STUDY

An inflorescence with three pistillate flowers in amber from the early Upper Cretaceous (Turonian, ~90-94 million years ago) of central New Jersey represents the oldest known flowers with features present in an early stem complex of the Fagales. The inflorescence has characteristics of Nothofagaceae, but also has strikingly distinct characters that suggest it is intermediate between Nothofagus and other Fagales. This intermediacy is consistent with its northern hemisphere distribution.

METHODS

We investigated this new fossil by comparing it with extant and fossil members of the Fagales using light microscopy and nano-computed tomography. In addition, for exploring its relationships, we mapped the morphological characters onto a widely accepted molecular-based tree of modern basal Fagales using standard methods of character optimization.

KEY RESULTS

The phylogenetic position of the fossil inflorescence can be unequivocally determined by the presence of unique features, singly and in combination, that are found only in "basal" members of Fagales. The fossil adds critical information on the features of the early stem Fagales, evolution of the cupule in Nothofagaceae and Fagaceae, and a reasonable biogeographic hypothesis for the differentiation of southern (e.g., Nothofagaceae) and northern hemisphere Fagales.

CONCLUSIONS

This new fossil provides insight into the early evolution of Fagales and suggests that early stem Fagales that had not yet differentiated into modern families were present in the Late Cretaceous of North America. Based on available evidence, the fossil is best interpreted as an early stem member of the Fagales, with features that suggest a transition from a more generalized Nothofagus-like fagalean ancestor with some unique presumably plesiomorphic features. The presence of an enlarged perianth and flexuous styles also suggests the possibility of insect pollination, which has been lost in all Fagales with the exception of some members of subfamily Castaneoideae in Fagaceae sensu stricto (which otherwise are very different from this fossil). The poorly developed, bract-like cupule valves of the fossil can be interpreted as primitive (i.e., incipient) or as reduced from more developed cupules that are found in most modern Fagaceae and Nothofagaceae.

Grimmiaceae in the Early Cretaceous: Tricarinella crassiphylla gen. et sp. nov. and the value of anatomically preserved bryophytes

Background and Aims

Widespread and diverse in modern ecosystems, mosses are rare in the fossil record, especially in pre-Cenozoic rocks. Furthermore, most pre-Cenozoic mosses are known from compression fossils, which lack detailed anatomical information. When preserved, anatomy significantly improves resolution in the systematic placement of fossils. Lower Cretaceous (Valanginian) deposits on Vancouver Island (British Columbia, Canada) contain a diverse anatomically preserved flora including numerous bryophytes, many of which have yet to be characterized. Among them is the grimmiaceous moss described here.

Methods

One fossil moss gametophyte preserved in a carbonate concretion was studied in serial sections prepared using the cellulose acetate peel technique.

Key Results

Tricarinella crassiphylla gen. et sp. nov. is a moss with tristichous phyllotaxis and strongly keeled leaves. The combination of an acrocarpous condition (inferred based on a series of morphological features), a central conducting strand, a homogeneous leaf costa and a lamina with bistratose portions and sinuous cells, and multicellular gemmae, supports placement of Tricarinella in family Grimmiaceae. Tricarinella is similar to Grimmia, a genus that exhibits broad morphological variability. However, tristichous phyllotaxis and especially the lamina, bistratose at the base but not in distal portions of the leaf, set Tricarinella apart as a distinct genus.

Conclusions

Tricarinella crassiphylla marks the oldest record for both family Grimmiaceae and sub-class Dicranidae, providing a hard minimum age (136 million years) for these groups. The fact that this fossil could be placed in an extant family, despite a diminutive size, emphasizes the considerable resolving power of anatomically preserved bryophyte fossils, even when recovered from allochthonous assemblages of marine sediments, such as the Apple Bay flora. Discovery of Tricarinella re-emphasizes the importance of paleobotanical studies as the only approach allowing access to a significant segment of biodiversity, the extinct biodiversity, which is unattainable by other means of investigation.

Phylogenomic analysis of Apoidea sheds new light on the sister group of bees

Background

Apoid wasps and bees (Apoidea) are an ecologically and morphologically diverse group of Hymenoptera, with some species of bees having evolved eusocial societies. Major problems for our understanding of the evolutionary history of Apoidea have been the difficulty to trace the phylogenetic origin and to reliably estimate the geological age of bees. To address these issues, we compiled a comprehensive phylogenomic dataset by simultaneously analyzing target DNA enrichment and transcriptomic sequence data, comprising 195 single-copy protein-coding genes and covering all major lineages of apoid wasps and bee families.

Results

Our compiled data matrix comprised 284,607 nucleotide sites that we phylogenetically analyzed by applying a combination of domain- and codon-based partitioning schemes. The inferred results confirm the polyphyletic status of the former family “Crabronidae”, which comprises nine major monophyletic lineages. We found the former subfamily Pemphredoninae to be polyphyletic, comprising three distantly related clades. One of them, Ammoplanina, constituted the sister group of bees in all our analyses. We estimate the origin of bees to be in the Early Cretaceous (ca. 128 million years ago), a time period during which angiosperms rapidly radiated. Finally, our phylogenetic analyses revealed that within the Apoidea, (eu)social societies evolved exclusively in a single clade that comprises pemphredonine and philanthine wasps as well as bees.

Conclusion

By combining transcriptomic sequences with those obtained via target DNA enrichment, we were able to include an unprecedented large number of apoid wasps in a phylogenetic study for tracing the phylogenetic origin of bees. Our results confirm the polyphyletic nature of the former wasp family Crabonidae, which we here suggest splitting into eight families. Of these, the family Ammoplanidae possibly represents the extant sister lineage of bees. Species of Ammoplanidae are known to hunt thrips, of which some aggregate on flowers and feed on pollen. The specific biology of Ammoplanidae as predators indicates how the transition from a predatory to pollen-collecting life style could have taken place in the evolution of bees. This insight plus the finding that (eu)social societies evolved exclusively in a single subordinated lineage of apoid wasps provides new perspectives for future comparative studies.

Electronic supplementary material

The online version of this article (10.1186/s12862-018-1155-8) contains supplementary material, which is available to authorized users.

Reinvestigating an enigmatic Late Cretaceous monocot: morphology, taxonomy, and biogeography of Viracarpon

Angiosperm-dominated floras of the Late Cretaceous are essential for understanding the evolutionary, ecological, and geographic radiation of flowering plants. The Late Cretaceous–early Paleogene Deccan Intertrappean Beds of India contain angiosperm-dominated plant fossil assemblages known from multiple localities in central India. Numerous monocots have been documented from these assemblages, providing a window into an important but poorly understood time in their diversification. One component of the Deccan monocot diversity is the genus Viracarpon, known from anatomically preserved infructescences. Viracarpon was first collected over a century ago and has been the subject of numerous studies. However, resolution of its three-dimensional (3D) morphology and anatomy, as well as its taxonomic affinities, has remained elusive. In this study we investigated the morphology and taxonomy of genus Viracarpon, combining traditional paleobotanical techniques and X-ray micro-computed tomography (μCT). Re-examination of type and figured specimens, 3D reconstructions of fruits, and characterization of structures in multiple planes of section using μCT data allowed us to resolve conflicting interpretations of fruit morphology and identify additional characters useful in refining potential taxonomic affinities. Among the four Viracarpon species previously recognized, we consider two to be valid (Viracarponhexaspermum and Viracarponelongatum), and the other two to be synonyms of these. Furthermore, we found that permineralized infructescences of Coahuilocarpon phytolaccoides from the late Campanian of Mexico correspond closely in morphology to V. hexaspermum. We argue that Viracarpon and Coahuilocarpon are congeneric and provide the new combination, Viracarpon phytolaccoides (Cevallos-Ferriz, Estrada-Ruiz & Perez-Hernandez) Matsunaga, S.Y. Smith, & Manchester comb. nov. The significant geographic disjunction between these two occurrences indicates that the genus Viracarpon was widespread and may be present in other Late Cretaceous assemblages. Viracarpon exhibits character combinations not present in any extant taxa and its affinities remain unresolved, possibly representing an extinct member of Alismatales. The character mosaic observed in Viracarpon and the broad distribution of the genus provide new data relevant to understanding early monocot evolution and suggest that the (thus far) largely invisible Late Cretaceous monocot diversification was characterized by enigmatic and/or stem taxa.

Two early eudicot fossil flowers from the Kamikitaba assemblage (Coniacian, Late Cretaceous) in northeastern Japan

Two new fossil taxa referable to the basal eudicot grade are described from the Kamikitaba locality (ca. 89 MYBP, early Coniacian: Late Cretaceous) of the Futaba Group in Japan. These charcoalified mesofossils exhibit well-preserved three-dimensional structure and were analyzed using synchrotron-radiation X-ray microtomography to document their composition and internal structure. Cathiaria japonica sp. nov. is represented by infructescence segments that consist of an axis bearing three to four fruits. The capsular fruits are sessile and dehiscent and consist of a gynoecium subtended by a bract. No perianth parts are present. The gynoecium is monocarpellate containing two pendulous seeds. The carpel is ascidiate in the lower half and conduplicate in the upper part, and the style is deflected abaxially with a large, obliquely decurrent stigma. Pollen grains are tricolpate with a reticulate exine. The morphological features of Cathiaria are consistent with an assignment to the Buxaceae s. l. (including Didymelaceae). Archaestella verticillatus gen. et sp. nov. is represented by flowers that are small, actinomorphic, pedicellate, bisexual, semi-inferior, and multicarpellate. The floral receptacle is cup shaped with a perigynous perianth consisting of several tepals inserted around the rim. The gynoecium consists of a whorl of ten conduplicate, laterally connate but distally distinct carpels with a conspicuous dorsal bulge, including a central cavity. The styles are short, becoming recurved with a ventrally decurrent stigma. Seeds are ca. 10 per carpel, marginal, pendulous from the broad, oblique summit of the locule. Pollen grains are tricolpate with a reticulate exine pattern, suggesting a relationship to eudicots. The morphological features of Archaestella indicate a possible relationship to Trochodendraceae in the basal grade of eudicots. The fossil currently provides the earliest record of the family and documents the presence of Trochodendraceae in eastern Eurasia during the middle part of the Late Cretaceous.

The Exceptional Preservation of Plant Fossils: A Review of Taphonomic Pathways and Biases in the Fossil Record

The exceptional preservation of plant fossils falls into two categories: whole plant preservation and anatomical detail. Whole plant preservation is controlled primarily by transport and event preservation (e.g., ash falls), whereas anatomical preservation can occur through one of several taphonomic pathways: compression-impression, silicification, coal-ball formation, pyritization, and charcoalification. This review focuses on these taphonomic pathways, highlighting important factors and controls on the exceptional preservation of plants. Special emphasis is given to data garnered from experimental and actualistic approaches.

In silico analysis reveals widespread presence of three gene families, MAPK, MAPKK and MAPKKK, of the MAPK cascade from crop plants of Solanaceae in comparison to the distantly-related syntenic species from Rubiaceae, coffee

Mitogen-activated protein kinases (MAPKs) are an important family of genes which play roles in vital plant processes, and they also help in coping against various kinds of environmental stresses including abiotic as well as biotic factors. The advancement of genomics calls for the annotation, identification, and detailed processing of the essential gene families in plants in order to provide insights into the importance of their central roles as well as for providing the basis for making their growth vigorous even under stressed conditions and, ultimately, to benefit from them by foreseeing the potential threats to their growth. In the current study, MAPK, MAPKK, and MAPKKK families of the MAPK cascade were identified and reported from five different agriculturally and economically important crop species of the Solanaceae and Rubiaceae families based on conserved signature motifs aligned throughout the members of the families under this gene superfamily. Genes reported from the species after strict filtering were: 89, tomato; 108, potato; 63, eggplant; 79, pepper; 64, coffee. These MAPKs were found to be randomly distributed throughout the genome on the chromosomes of the respective species. Various characteristics of the identified genes were studied including gene structure, gene and coding sequence length, protein length, isoelectric point, molecular weight, and subcellular localization. Moreover, maximum likelihood test of phylogeny was conducted on the retrieved sequences for the three MAPK cascade families to determine their homologous relationships which were also analyzed quantitatively by heat plots.

Flowering after disaster: Early Danian buckthorn (Rhamnaceae) flowers and leaves from Patagonia

Southern-Hemisphere terrestrial communities from the early Paleocene are poorly known, but recent work on Danian plant fossils from the Salamanca Formation in Chubut Province, Argentina are providing critical data on earliest Paleocene floras. The fossils described here come from a site in the Salamanca Formation dating to ca. 1 million years or less after the end-Cretaceous extinction event; they are the first fossil flowers reported from the Danian of South America, and possible the entire Southern Hemisphere. They are compressions and impressions in flat-laminated light gray shale, and they belong to the family Rhamnaceae (buckthorns). Flowers of Notiantha grandensis gen. et sp. nov. are pentamerous, with distinctly keeled calyx lobes projecting from the hypanthium, clawed and cucullate emarginate petals, antepetalous stamens, and a pentagonal floral disk that fills the hypanthium. Their phylogenetic position was evaluated using a molecular scaffold approach combined with morphological data. Results indicate that the flowers are most like those of extant ziziphoid Rhamnaceae. The associated leaves, assigned to Suessenia grandensis gen. et sp. nov. are simple and ovate, with serrate margins and three acrodromous basal veins. They conform to the distinctive leaves of some extant Rhamnaceae in the ziziphoid and ampelozizyphoid clades. These fossils provide the first unequivocal megafossil evidence of Rhamnaceae in the Southern Hemisphere, demonstrating that Rhamnaceae expanded beyond the tropics by the earliest Paleocene. Given previous reports of rhamnaceous pollen in the late Paleogene and Neogene of Antarctica and southern Australia, this new occurrence increases the possibility of high-latitude dispersal of this family between South America and Australia via Antarctica during the Cenozoic.

A Complete Fossil-Calibrated Phylogeny of Seed Plant Families as a Tool for Comparative Analyses: Testing the 'Time for Speciation' Hypothesis

Explaining the uneven distribution of species richness across the branches of the tree of life has been a major challenge for evolutionary biologists. Advances in phylogenetic reconstruction, allowing the generation of large, well-sampled, phylogenetic trees have provided an opportunity to contrast competing hypotheses. Here, we present a new time-calibrated phylogeny of seed plant families using Bayesian methods and 26 fossil calibrations. While there are various published phylogenetic trees for plants which have a greater density of species sampling, we are still a long way from generating a complete phylogeny for all ~300,000+ plants. Our phylogeny samples all seed plant families and is a useful tool for comparative analyses. We use this new phylogenetic hypothesis to contrast two alternative explanations for differences in species richness among higher taxa: time for speciation versus ecological limits. We calculated net diversification rate for each clade in the phylogeny and assessed the relationship between clade age and species richness. We then fit models of speciation and extinction to individual branches in the tree to identify major rate-shifts. Our data suggest that the majority of lineages are diversifying very slowly while a few lineages, distributed throughout the tree, are diversifying rapidly. Diversification is unrelated to clade age, no matter the age range of the clades being examined, contrary to both the assumption of an unbounded lineage increase through time, and the paradigm of fixed ecological limits. These findings are consistent with the idea that ecology plays a role in diversification, but rather than imposing a fixed limit, it may have variable effects on per lineage diversification rates through time.

Molecular phylogeny, divergence time estimates and historical biogeography within one of the world's largest monocot genera

A primary aim of historical biogeography is to identify the causal factors or processes that have shaped the composition and distribution of biotas over time. Another is to infer the evolution of geographic ranges of species and clades in a phylogenetic context. To this end, historical biogeography addresses important questions such as: Where were ancestors distributed? Where did lineages originate? Which processes cause geographic ranges to evolve through time? Allium subgenus Anguinum comprises approximately twelve taxa with a disjunct distribution in the high mountains from south-western Europe to eastern Asia and in northeastern North America. Although both the systematic position and the geographical limits of Anguinum have been identified, to date no molecular systematic study has been performed utilizing a comprehensive sampling of these species. With an emphasis on the Anguinum eastern Asian geographical group, the goals of the present study were: (i) to infer species-level phylogenetic relationships within Anguinum, (ii) to assess molecular divergence and estimated the times of the major splits in Anguinum and (iii) to trace the biogeographic history of the subgenus. Four DNA sequences (ITS, matK, trnH-psbA, rps16) were used to reconstruct the phylogeny of Allium subgen. Anguinum RbcL sequences were used to estimate divergences time for Allium, and sequences of ITS were used to estimate the divergence times for Anguinum and its main lineages and to provide implications for the evolutionary history of the subgenus. Phylogenetic analyses for all Allium corroborate that Anguinum is monophyletic and indicate that Anguinum is composed of two sister groups: one with a Eurasian-American distribution, and the other restricted to eastern Asia. In the eastern Asian geographical group, incongruence between gene trees and morphology-based taxonomies was recovered as was incongruence between data from plastid and nuclear sequences. This incongruence is likely due to the combined effects of a recent radiation, incomplete lineage sorting, and hybridization/introgression. Divergence time estimates suggest that the crown group of Anguinum originated during the late Miocene (ca. 7.16 Mya) and then diverged and dispersed. Biogeographic analyses using statistical dispersal-vicariance analysis (S-DIVA) and a likelihood method support an eastern Asia origin of Anguinum It is inferred that in the late Pliocene/Early Pleistocene, with cooling climates and the uplift of the Himalayas and Hengduan Mountains, the ancestor of the eastern Asian alliance clade underwent a very recent radiation.

Dispersal largely explains the Gondwanan distribution of the ancient tropical clusioid plant clade

PREMISE OF THE STUDY

The clusioid clade (Malpighiales) has an ancient fossil record (∼90 Ma) and extant representatives exhibit a pantropical distribution represented on all former Gondwanan landmasses (Africa, Australia, India, Madagascar, and South America) except Antarctica. Several biogeographers have hypothesized that the clusioid distribution is an example of Gondwanan vicariance. Our aim is to test the hypothesis that the modern distribution of the clusioid clade is largely explained by Gondwanan fragmentation.

METHODS

Using a four gene, 207-taxon data set we simultaneously estimated the phylogeny and divergence times of the clusioid clade using a Bayesian Markov chain Monte Carlo approach. Ancestral Area Reconstructions (AARs) were then conducted on a distribution of 1000 trees and summarized on a reduced phylogeny.

KEY RESULTS

Divergence time estimates and AARs revealed only two or four cladogenic events that are potentially consistent with Gondwanan vicariance, depending on the placement of the ancient fossil Paleoclusia. In contrast, dispersal occurred on > 25% of the branches, indicating the current distribution of the clade likely reflects extensive recent dispersal during the Cenozoic (< 65 Ma), most of which occurred after the beginning of the Eocene (∼56 Ma).

CONCLUSIONS

These results support growing evidence that suggests many traditionally recognized angiosperm clades (families and genera) are too young for their distributions to have been influenced strictly by Gondwanan fragmentation. Instead, it appears that corridors of dispersal may be the best explanation for numerous angiosperm clades with Gondwanan distributions.

Putting scales into evolutionary time: the divergence of major scale insect lineages (Hemiptera) predates the radiation of modern angiosperm hosts

The radiation of flowering plants in the mid-Cretaceous transformed landscapes and is widely believed to have fuelled the radiations of major groups of phytophagous insects. An excellent group to test this assertion is the scale insects (Coccomorpha: Hemiptera), with some 8,000 described Recent species and probably the most diverse fossil record of any phytophagous insect group preserved in amber. We used here a total-evidence approach (by tip-dating) employing 174 morphological characters of 73 Recent and 43 fossil taxa (48 families) and DNA sequences of three gene regions, to obtain divergence time estimates and compare the chronology of the most diverse lineage of scale insects, the neococcoid families, with the timing of the main angiosperm radiation. An estimated origin of the Coccomorpha occurred at the beginning of the Triassic, about 245 Ma [228–273], and of the neococcoids 60 million years later [210–165 Ma]. A total-evidence approach allows the integration of extinct scale insects into a phylogenetic framework, resulting in slightly younger median estimates than analyses using Recent taxa, calibrated with fossil ages only. From these estimates, we hypothesise that most major lineages of coccoids shifted from gymnosperms onto angiosperms when the latter became diverse and abundant in the mid- to Late Cretaceous.

The evolution of dwarf shrubs in alpine environments: a case study of Alchemilla in Africa

BACKGROUND AND AIMS

Alpine and arctic environments worldwide, including high mountains, are dominated by short-stature woody plants (dwarf shrubs). This conspicuous life form asserts considerable influence on local environmental conditions above the treeline, creating its own microhabitat. This study reconstructs the evolution of dwarf shrubs in Alchemilla in the African tropical alpine environment, where they represent one of the largest clades and are among the most common and abundant plants.

METHODS

Different phylogenetic inference methods were used with plastid and nuclear DNA sequence markers, molecular dating (BEAST and RelTime), analyses of diversification rate shifts (MEDUSA and BAMM) and ancestral character and area reconstructions (Mesquite).

KEY RESULTS

It is inferred that African Alchemilla species originated following long-distance dispersal to tropical East Africa, but that the evolution of dwarf shrubs occurred in Ethiopia and in tropical East Africa independently. Establishing a timeframe is challenging given inconsistencies in age estimates, but it seems likely that they originated in the Pleistocene, or at the earliest in the late Miocene. The adaptation to alpine-like environments in the form of dwarf shrubs has apparently not led to enhanced diversification rates. Ancestral reconstructions indicate reversals in Alchemilla from plants with a woody base to entirely herbaceous forms, a transition that is rarely reported in angiosperms.

CONCLUSIONS

Alchemilla is a clear example of in situ tropical alpine speciation. The dwarf shrub life form typical of African Alchemilla has evolved twice independently, further indicating its selective advantage in these harsh environments. However, it has not influenced diversification, which, although recent, was not rapid.

A highly specific microRNA-mediated mechanism silences LTR retrotransposons of strawberry

Small RNAs are involved in a plethora of functions in plant genomes. In general, transcriptional gene silencing is mediated by 24-nucleotide siRNAs and is required for maintaining transposable elements in a silenced state. However, microRNAs are not commonly associated with transposon silencing. In this study, we performed small RNA transcriptome and degradome analyses of the Rosaceae model plant Fragaria vesca (the woodland strawberry) at the genome-wide level, and identified miRNA families and their targets. We report a highly specific mechanism of LTR retrotransposon silencing mediated by an abundant, ubiquitously expressed miRNA (fve-miR1511) generated from a single locus. This miRNA specifically targets LTR retroelements, silencing them post-transcriptionally by perfectly pairing to the highly conserved primer binding site for methionyl initiator tRNA that is essential for reverse transcription. We investigated the possible origins of this miRNA, and present evidence that the pre-miR1511 hairpin structure probably derived from a locus coding for tRNA(iM) (et) through a single microinversion event. Our study shows that this miRNA targets retrotransposons specifically and constitutively, and contributes to features such as genome stability, size and architecture in a far more direct way than previously thought.

Paraphyly changes understanding of timing and tempo of diversification in subtribe Hakeinae (Proteaceae), a giant Australian plant radiation

PREMISE OF THE STUDY

Subtribe Hakeinae (526 spp.) represents a large Australian plant radiation central to our understanding of that flora's evolution and ecology. It contains Grevillea-the third largest plant genus in Australia and a group inferred to have among the highest diversification rates in the angiosperms. However, we lack a robust phylogenetic framework for understanding subtribe Hakeinae and recognize that Grevillea lacks an unambiguous synapomorphy supporting its monophyly.

METHODS

We used four plastid and one nuclear DNA region from a taxonomically even sampling of a third of the species to infer a time-calibrated phylogeny of Hakeinae and absolute diversification rates of major clades. We developed the R package addTaxa to add unsampled taxa to the tree for diversification rate inference.

KEY RESULTS

Grevillea is paraphyletic with respect to Hakea and Finschia. Under most parameter combinations, Hakea contains the major clade with the highest diversification rate in Hakeinae, rather than Grevillea. The crown age of the Grevillea+Hakea+Finschia crown group is about double that of prior estimates.

CONCLUSIONS

We demonstrate that the paraphyly of Grevillea considerably enlarges the number of Australian descendants from its most recent common ancestor but has also misled investigators who considered a single operational taxonomic unit as adequate to represent the genus for inferences of diversification rate and timing. Our time-calibrated phylogeny can form the basis of future evolutionary, comparative ecology, and biogeography studies involving this large Australian plant radiation, as well as nomenclatural changes.

Biogeography of the Malagasy Celastraceae: Multiple independent origins followed by widespread dispersal of genera from Madagascar

Of the 97 currently recognized genera of Celastraceae, 19 are native to Madagascar, including six endemics. In this study we conducted the most thorough phylogenetic analysis of Celastraceae yet completed with respect to both character and taxon sampling, and include representatives of five new endemic genera. Fifty-one new accessions, together with 328 previously used accessions of Celastrales, were sampled for morphological characters, two rDNA gene regions, and two plastid gene regions. The endemic Malagasy genera are resolved in two separate lineages-Xenodrys by itself and all other endemic genera in a clade that also includes four lineages inferred to have dispersed from Madagascar: Brexia madagascariensis (Mascarene Islands, coastal Africa), Elaeodendron (West Indies, Africa to New Caledonia), and Pleurostylia (Africa to New Caledonia). Of the 12 extant Malagasy Celastraceae lineages identified, eight are clearly of African origin. The origins of the remaining four lineages are less clear, but reasonable possibilities include America, Eurasia, Africa, southern India, Malesia, and Australia. Based on 95% credible age intervals from fossil-calibrated molecular dating, all 12 extant Malagasy Celastraceae lineages appear to have arisen following dispersal after the separation of Madagascar from other landmasses within the last 70 million years.

Chemical Composition and Vasorelaxant and Antispasmodic Effects of Essential Oil from Rosa indica L. Petals

Rosa indica L. belongs to the family Rosaceae and is locally known as gulaab. It has different traditional uses in cardiovascular and gastrointestinal disorders but there is no scientific data available in this regard. Therefore, the basic aim of this study was to explore the chemical composition and gastrointestinal and cardiovascular effects of the essential oil obtained from R. indica. The chemical composition of the essential oil was investigated using gas chromatography-mass spectrometry (GC-MS) technique. The cardiovascular and gastrointestinal effects were investigated using electrophysiological measurements. The GC-MS analysis of the essential oil showed various chemical components including acetic acid, mercaptohexyl ester, butanoic acid, 2-methyl-5-oxo-1-cyclopentene-1-yl ester, artemiseole, methyl santonilate, isosteviol, caryophyllene oxide, pentyl phenyl acetate, dihydromyrcene, 1,5-octadecadien, octadecanoic acid, ethyl ester, palmitic acid (2-phenyl-1,3-dioxolan-4-yl methyl ester), santolina epoxide, and 9-farnesene. The electrophysiological measurements revealed that essential oil was more potent against K(+) (80 mM) than phenylephrine precontractions using isolated rabbit aorta preparations. In isolated rabbit jejunum preparations, it showed more potency against high K(+) induced contractions than spontaneous contractions. Considering these evidences, it can be concluded that R. indica essential oil may work as a complementary and alternative medicine in gastrointestinal and cardiovascular diseases.

Assessing the Fossil Record of Asterids in the Context of Our Current Phylogenetic Framework

The fossil record provides good evidence for the minimum ages of important events in the diversification and geographic spread of Asteridae, with earliest examples extending back to the Turonian stage of the Late Cretaceous (~89 Ma). Some of the fossil identifications accepted in previous considerations of asterid phylogeny do not stand up to careful scrutiny. Nevertheless, among major clades of asterids, there is good evidence for a range of useful anchor points. Here we provide a synopsis of fossil occurrences that we consider as reliable representatives of modern Asterid families and genera. In addition, we provide new examples documented by fossil dispersed pollen investigated by both light and scanning electron microscopy studies including representatives of Loranthaceae, Amaranthaceae, Cornaceae (incl. Nyssa L., Mastixia Blume, Diplopanax Hand.-Mazz.), Sapotaceae, Ebenaceae, Ericaceae, Icacinaceae, Oleaceae, Asteraceae, Araliaceae, Adoxaceae and Caprifoliaceae from Paleogene sites in Greenland, western North America, and central Europe, and of Lamiaceae and Asteraceae from the middle to late Miocene northeastern China. We emphasize that dispersed pollen, taken along with megafossil and mesofossil data, continue to fill gaps in our knowledge of the paleobotanical record.

A revised time tree of the asterids: establishing a temporal framework for evolutionary studies of the coffee family (rubiaceae)

Divergence time analyses in the coffee family (Rubiaceae) have all relied on the same Gentianales crown group age estimate, reported by an earlier analysis of the asterids, for defining the upper age bound of the root node in their analyses. However, not only did the asterid analysis suffer from several analytical shortcomings, but the estimate itself has been used in highly inconsistent ways in these Rubiaceae analyses. Based on the original data, we here reanalyze the divergence times of the asterids using relaxed-clock models and 14 fossil-based minimum age constraints. We also expand the data set to include an additional 67 taxa from Rubiaceae sampled across all three subfamilies recognized in the family. Three analyses are conducted: a separate analysis of the asterids, which completely mirrors the original asterid analysis in terms of taxon sample and data; a separate analysis of the Gentianales, where the result from the first analysis is used for defining a secondary root calibration point; and a combined analysis where all taxa are analyzed simultaneously. Results are presented in the form of a time-calibrated phylogeny, and age estimates for asterid groups, Gentianales, and major groups of Rubiaceae are compared and discussed in relation to previously published estimates. Our updated age estimates for major groups of Rubiaceae provide a significant step forward towards the long term goal of establishing a robust temporal framework for the divergence of this biologically diverse and fascinating group of plants.

Integrated genome sequence and linkage map of physic nut (Jatropha curcas L.), a biodiesel plant

The family Euphorbiaceae includes some of the most efficient biomass accumulators. Whole genome sequencing and the development of genetic maps of these species are important components in molecular breeding and genetic improvement. Here we report the draft genome of physic nut (Jatropha curcas L.), a biodiesel plant. The assembled genome has a total length of 320.5 Mbp and contains 27,172 putative protein-coding genes. We established a linkage map containing 1208 markers and anchored the genome assembly (81.7%) to this map to produce 11 pseudochromosomes. After gene family clustering, 15,268 families were identified, of which 13,887 existed in the castor bean genome. Analysis of the genome highlighted specific expansion and contraction of a number of gene families during the evolution of this species, including the ribosome-inactivating proteins and oil biosynthesis pathway enzymes. The genomic sequence and linkage map provide a valuable resource not only for fundamental and applied research on physic nut but also for evolutionary and comparative genomics analysis, particularly in the Euphorbiaceae.

Comparative transcriptome analysis of eggplant (Solanum melongena L.) and turkey berry (Solanum torvum Sw.): phylogenomics and disease resistance analysis

BACKGROUND

Eggplant (Solanum melongena L.) and turkey berry (S. torvum Sw.), a wild ally of eggplant with promising multi-disease resistance traits, are of great economic, medicinal and genetic importance, but genomic resources for these species are lacking. In the present study, we sequenced the transcriptomes of eggplant and turkey berry to accelerate research on these two non-model species.

RESULTS

We built comprehensive, high-quality de novo transcriptome assemblies of the two Leptostemonum clade Solanum species from short-read RNA-Sequencing data. We obtained 34,174 unigenes for eggplant and 38,185 unigenes for turkey berry. Functional annotations based on sequence similarity to known plant datasets revealed a distribution of functional categories for both species very similar to that of tomato. Comparison of eggplant, turkey berry and another 11 plant proteomes resulted in 276 high-confidence single-copy orthologous groups, reasonable phylogenetic tree inferences and reliable divergence time estimations. From these data, it appears that eggplant and its wild Leptostemonum clade relative turkey berry split from each other in the late Miocene, ~6.66 million years ago, and that Leptostemonum split from the Potatoe clade in the middle Miocene, ~15.75 million years ago. Furthermore, 621 and 815 plant resistance genes were identified in eggplant and turkey berry respectively, indicating the variation of disease resistance genes between them.

CONCLUSIONS

This study provides a comprehensive transcriptome resource for two Leptostemonum clade Solanum species and insight into their evolutionary history and biological characteristics. These resources establish a foundation for further investigations of eggplant biology and for agricultural improvement of this important vegetable. More generally, we show that RNA-Seq is a fast, reliable and cost-effective method for assessing genome evolution in non-model species.

Draft genome sequence of the mulberry tree Morus notabilis

Human utilization of the mulberry–silkworm interaction started at least 5,000 years ago and greatly influenced world history through the Silk Road. Complementing the silkworm genome sequence, here we describe the genome of a mulberry species Morus notabilis. In the 330-Mb genome assembly, we identify 128 Mb of repetitive sequences and 29,338 genes, 60.8% of which are supported by transcriptome sequencing. Mulberry gene sequences appear to evolve ~3 times faster than other Rosales, perhaps facilitating the species’ spread worldwide. The mulberry tree is among a few eudicots but several Rosales that have not preserved genome duplications in more than 100 million years; however, a neopolyploid series found in the mulberry tree and several others suggest that new duplications may confer benefits. Five predicted mulberry miRNAs are found in the haemolymph and silk glands of the silkworm, suggesting interactions at molecular levels in the plant–herbivore relationship. The identification and analyses of mulberry genes involved in diversifying selection, resistance and protease inhibitor expressed in the laticifers will accelerate the improvement of mulberry plants.

Mulberry trees are the primary food source for silkworms, which are reared for the production of silk. In this study, He et al. present the draft genome sequence of Morus notabilis and find that it evolved significantly faster than other plants in the Rosales order.

Root diameter variations explained by anatomy and phylogeny of 50 tropical and temperate tree species

Root diameter, a critical indicator of root physiological function, varies greatly among tree species, but the underlying mechanism of this high variability is unclear. Here, we sampled 50 tree species across tropical and temperate zones in China, and measured root morphological and anatomical traits along the first five branch orders in each species. Our objectives were (i) to reveal the relationships between root diameter, cortical thickness and stele diameter among tree species in tropical and temperate forests, and (ii) to investigate the relationship of both root morphological and anatomical traits with divergence time during species radiation. The results showed that root diameter was strongly affected by cortical thickness but less by stele diameter in both tropical and temperate species. Changes in cortical thickness explained over 90% of variation in root diameter for the first order, and ∼74-87% for the second and third orders. Thicker roots displayed greater cortical thickness and more cortical cell layers than thinner roots. Phylogenetic analysis demonstrated that root diameter, cortical thickness and number of cortical cell layers significantly correlated with divergence time at the family level, showing similar variation trends in geological time. The results also suggested that trees tend to decrease their root cortical thickness rather than stele diameter during species radiation. The close linkage of variations in root morphology and anatomy to phylogeny as demonstrated by the data from the 50 tree species should provide some insights into the mechanism of root diameter variability among tree species.

New methods reveal oldest known fossil epiphyllous moss: Bryiidites utahensis gen. et sp. nov. (Bryidae)

PREMISE OF THE STUDY

Epiphyllous bryophytes are a highly characteristic feature of many humid tropical forest ecosystems. In contrast to the extensive fossil record for the leaves of their host plants, the record is virtually nonexistent for the epiphylls themselves, despite a fossil record for mosses that begins in the Middle Carboniferous Period, 330 million years ago.

METHODS

Epifluorescence optical microscopy, scanning electron microscopy, and atomic force microscopy were employed to investigate an intimate association between a newly discovered epiphyllous moss and a Lauraceae plant host from the middle Cretaceous.

KEY RESULTS

We describe the oldest fossil specimen of an epiphyllous moss, Bryiidites utahensis gen. et sp. nov., identified from an individual specimen only 450 µm long, situated on an approximately one millimeter square fossil leaf fragment. The moss epiphyll is exquisitely preserved as germinating spores and short-celled protonemata with transverse and oblique cross-walls closely matching those of extant epiphyllous mosses on the surface of the plant-leaf hosts.

CONCLUSIONS

The extension of the epiphyll record back to the middle Cretaceous provides fossil evidence for the appearance of epiphyllous mosses during the diversification of flowering plants, at least 95 million years ago. It also provides substantive evidence for a tropical maritime climate in central North America during the middle Cretaceous.

Comprehensive analysis of expressed sequence tags from cultivated and wild radish (Raphanus spp.)

BACKGROUND

Radish (Raphanus sativus L., 2n = 2× = 18) is an economically important vegetable crop worldwide. A large collection of radish expressed sequence tags (ESTs) has been generated but remains largely uncharacterized.

RESULTS

In this study, approximately 315,000 ESTs derived from 22 Raphanus cDNA libraries from 18 different genotypes were analyzed, for the purpose of gene and marker discovery and to evaluate large-scale genome duplication and phylogenetic relationships among Raphanus spp. The ESTs were assembled into 85,083 unigenes, of which 90%, 65%, 89% and 89% had homologous sequences in the GenBank nr, SwissProt, TrEMBL and Arabidopsis protein databases, respectively. A total of 66,194 (78%) could be assigned at least one gene ontology (GO) term. Comparative analysis identified 5,595 gene families unique to radish that were significantly enriched with genes related to small molecule metabolism, as well as 12,899 specific to the Brassicaceae that were enriched with genes related to seed oil body biogenesis and responses to phytohormones. The analysis further indicated that the divergence of radish and Brassica rapa occurred approximately 8.9-14.9 million years ago (MYA), following a whole-genome duplication event (12.8-21.4 MYA) in their common ancestor. An additional whole-genome duplication event in radish occurred at 5.1-8.4 MYA, after its divergence from B. rapa. A total of 13,570 simple sequence repeats (SSRs) and 28,758 high-quality single nucleotide polymorphisms (SNPs) were also identified. Using a subset of SNPs, the phylogenetic relationships of eight different accessions of Raphanus was inferred.

CONCLUSION

Comprehensive analysis of radish ESTs provided new insights into radish genome evolution and the phylogenetic relationships of different radish accessions. Moreover, the radish EST sequences and the associated SSR and SNP markers described in this study represent a valuable resource for radish functional genomics studies and breeding.