Late Cretaceous origin of the rice tribe provides evidence for early diversification in Poaceae

Global analysis of Poales diversification - parallel evolution in space and time into open and closed habitats

Poales are one of the most species-rich, ecologically and economically important orders of plants and often characterise open habitats, enabled by unique suites of traits. We test six hypotheses regarding the evolution and assembly of Poales in open and closed habitats throughout the world, and examine whether diversification patterns demonstrate parallel evolution. We sampled 42% of Poales species and obtained taxonomic and biogeographic data from the World Checklist of Vascular Plants database, which was combined with open/closed habitat data scored by taxonomic experts. A dated supertree of Poales was constructed. We integrated spatial phylogenetics with regionalisation analyses, historical biogeography and ancestral state estimations. Diversification in Poales and assembly of open and closed habitats result from dynamic evolutionary processes that vary across lineages, time and space, most prominently in tropical and southern latitudes. Our results reveal parallel and recurrent patterns of habitat and trait transitions in the species-rich families Poaceae and Cyperaceae. Smaller families display unique and often divergent evolutionary trajectories. The Poales have achieved global dominance via parallel evolution in open habitats, with notable, spatially and phylogenetically restricted divergences into strictly closed habitats.

A New Fluorescence Detection Method for Tryptophan- and Tyrosine-Derived Allelopathic Compounds in Barley and Lupin

Barley (Hordeum vulgare) is one of the most widely cultivated crops for feedstock and beer production, whereas lupins (Lupinus spp.) are grown as fodder and their seeds are a source of protein. Both species produce the allelopathic alkaloids gramine and hordenine. These plant-specialized metabolites may be of economic interest for crop protection, depending on their tissue distribution. However, in high concentrations they pose a health risk to humans and animals that feed on them. This study was carried out to develop and validate a new method for monitoring these alkaloids and their related metabolites using fluorescence detection. Separation was performed on an HSS T3 column using slightly acidified water-acetonitrile eluents. Calibration plots expressed linearity over the range 0.09-100 pmol/µL for gramine. The accuracy and precision ranged from 97.8 to 123.4%, <7% RSD. The method was successfully applied in a study of the natural range of abundance of gramine, hordenine and their related metabolites, AMI, tryptophan and tyramine, in 22 barley accessions and 10 lupin species. This method provides accurate and highly sensitive chromatographic separation and detection of tryptophan- and tyrosine-derived allelochemicals and is an accessible alternative to LC-MS techniques for routine screening.

New Fossil Evidence Suggests That Angiosperms Flourished in the Middle Jurassic

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

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

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

Structure and functioning of wild and agricultural grazing ecosystems: A comparative review

For more than 10 million years, large, herd forming ruminants have thrived as parts of sustainable grazing ecosystems. Conversely, since their domestication 8,000–11,000 years ago, cattle, sheep, and goats have often exhibited dysfunctional relationships with the ecosystems they inhabit. A considerable literature, developed over decades, documents the negative impacts of animal agriculture and associated activities (e.g., feed production) on grassland ecosystems. Coincident with the accumulating data documenting the impacts of “conventional” animal agriculture, has been a growing interest in restoring functionality to agricultural grazing ecosystems. These “regenerative” protocols often seek to mimic the structure and functions of wild grazing ecosystems. The objectives of this paper were two-fold: First to review the literature describing the structure and some key functional attributes of wild and agricultural grazing ecosystems; and second, to examine these attributes in conventionally and regeneratively managed grazing ecosystems and, assuming the wild condition to be the standard for sustainable grazer-environment relationships, to ascertain whether similar relationships exist in conventionally or regeneratively managed agricultural grazing ecosystems. Not unexpectedly our review revealed the complexity of both wild and agricultural grazing ecosystems and the interconnectedness of biological, chemical, and physical factors and processes within these systems. Grazers may increase or decrease system functionality, depending upon environmental conditions (e.g., moisture levels). Our review revealed that biodiversity, nitrogen cycling, and carbon storage in regenerative grazing systems more closely resemble wild grazing ecosystems than do conventional grazing systems. We also found multiple points of disagreement in the literature, particularly with respect to aboveground primary production (ANPP). Finally, we acknowledge that, while much has been accomplished in understanding grazing ecosystems, much remains to be done. In particular, some of the variability in the results of studies, especially of meta-analyses, might be reduced if datasets included greater detail on grazing protocols, and a common definition of the term, “grazing intensity.”

Adaptive radiation in Orinus, an endemic alpine grass of the Qinghai-Tibet Plateau, based on comparative transcriptomic analysis

The species of Orinus (Poaceae) are important alpine plants with a variety of phenotypic traits and potential usages in molecular breeding toward drought-tolerant forage crops. However, the genetic basis of evolutionary adaption and diversification in the genus is still unclear. In the present study, we obtained transcriptomes for the two most divergent species, O. thoroldii and O. kokonoricus, using the Illumina platform and de novo assembly. In total, we generated 23,029 and 24,086 unigenes with N50 values of 1188 and 1203 for O. thoroldii and O. kokonoricus respectively, and identified 19,005 pairs of putative orthologs between the two species of Orinus. For these orthologs, estimations of non-synonymous/synonymous substitution rate ratios indicated that 568 pairs may be under strongly positive selection (Ka/Ks > 1), and Gene Ontogeny (GO) enrichment analysis revealed that significantly enriched pathways were in DNA repair and resistance to abiotic stress. Meanwhile, the divergence times of species between O. thoroldii and O. kokonoricus occurred 3.2 million years ago (Mya), and the recent evolutionary branch is an allotetraploid species, Cleistogenes songorica. We also detected a Ks peak of ∼0.60 for Orinus. Additionally, we identified 188 pairs of differentially expressed genes (DEGs) between the two species of Orinus, which were significantly enrich in stress resistance and lateral root development. Thus, we considered that the species diversification and evolutionary adaption of this genus was initiated by environmental selection, followed by phenotypic differentiation, finally leading to niche separation in the Qinghai-Tibet Plateau.

The Original Form of C4-Photosynthetic Phosphoenolpyruvate Carboxylase Is Retained in Pooids but Lost in Rice

Poaceae is the most prominent monocot family that contains the primary cereal crops wheat, rice, and maize. These cereal species exhibit physiological diversity, such as different photosynthetic systems and environmental stress tolerance. Phosphoenolpyruvate carboxylase (PEPC) in Poaceae is encoded by a small multigene family and plays a central role in C4-photosynthesis and dicarboxylic acid metabolism. Here, to better understand the molecular basis of the cereal species diversity, we analyzed the PEPC gene family in wheat together with other grass species. We could designate seven plant-type and one bacterial-type grass PEPC groups, ppc1a, ppc1b, ppc2a, ppc2b, ppc3, ppc4, ppcC4, and ppc-b, respectively, among which ppc1b is an uncharacterized type of PEPC. Evolutionary inference revealed that these PEPCs were derived from five types of ancient PEPCs (ppc1, ppc2, ppc3, ppc4, and ppc-b) in three chromosomal blocks of the ancestral Poaceae genome. C4-photosynthetic PEPC (ppcC4 ) had evolved from ppc1b, which seemed to be arisen by a chromosomal duplication event. We observed that ppc1b was lost in many Oryza species but preserved in Pooideae after natural selection. In silico analysis of cereal RNA-Seq data highlighted the preferential expression of ppc1b in upper ground organs, selective up-regulation of ppc1b under osmotic stress conditions, and nitrogen response of ppc1b. Characterization of wheat ppc1b showed high levels of gene expression in young leaves, transcriptional responses under nitrogen and abiotic stress, and the presence of a Dof1 binding site, similar to ppcC4 in maize. Our results indicate the evolving status of Poaceae PEPCs and suggest the functional association of ppc1-derivatives with adaptation to environmental changes.

New Insights into the Genomic Structure of Avena L.: Comparison of the Divergence of A-Genome and One C-Genome Oat Species

We used next-generation sequencing analysis of the 3′-part of 18S rDNA, ITS1, and a 5′-part of the 5.8S rDNA region to understand genetic variation among seven diploid A-genome Avena species. We used 4−49 accessions per species that represented the As genome (A. atlantica, A. hirtula, and wiestii), Ac genome (A. canariensis), Ad genome (A. damascena), Al genome (A. longiglumis), and Ap genome (A. prostrata). We also took into our analysis one C-genome species, A. clauda, which previously was found to be related to A-genome species. The sequences of 169 accessions revealed 156 haplotypes of which seven haplotypes were shared by two to five species. We found 16 ribotypes that consisted of a unique sequence with a characteristic pattern of single nucleotide polymorphisms and deletions. The number of ribotypes per species varied from one in A. longiglumis to four in A. wiestii. Although most ribotypes were species-specific, we found two ribotypes shared by three species (one for A. damascena, A. hirtula, and A. wiestii, and the second for A. longiglumis, A. atlantica, and A. wiestii), and a third ribotype shared between A. atlantica and A. wiestii. A characteristic feature of the A. clauda ribotype, a diploid C-genome species, is that two different families of ribotypes have been found in this species. Some of these ribotypes are characteristic of Cc-genome species, whereas others are closely related to As-genome ribotypes. This means that A. clauda can be a hybrid between As- and C-genome oats.

A well-supported nuclear phylogeny of Poaceae and implications for the evolution of C4 photosynthesis

Poaceae (the grasses) includes rice, maize, wheat, and other crops, and is the most economically important angiosperm family. Poaceae is also one of the largest plant families, consisting of over 11 000 species with a global distribution that contributes to diverse ecosystems. Poaceae species are classified into 12 subfamilies, with generally strong phylogenetic support for their monophyly. However, many relationships within subfamilies, among tribes and/or subtribes, remain uncertain. To better resolve the Poaceae phylogeny, we generated 342 transcriptomic and seven genomic datasets; these were combined with other genomic and transcriptomic datasets to provide sequences for 357 Poaceae species in 231 genera, representing 45 tribes and all 12 subfamilies. Over 1200 low-copy nuclear genes were retrieved from these datasets, with several subsets obtained using additional criteria, and used for coalescent analyses to reconstruct a Poaceae phylogeny. Our results strongly support the monophyly of 11 subfamilies; however, the subfamily Puelioideae was separated into two non-sister clades, one for each of the two previously defined tribes, supporting a hypothesis that places each tribe in a separate subfamily. Molecular clock analyses estimated the crown age of Poaceae to be ∼101 million years old. Ancestral character reconstruction of C₃/C₄ photosynthesis supports the hypothesis of multiple independent origins of C₄ photosynthesis. These origins are further supported by phylogenetic analysis of the ppc gene family that encodes the phosphoenolpyruvate carboxylase, which suggests that members of three paralogous subclades (ppc-aL1a, ppc-aL1b, and ppc-B2) were recruited as functional C₄ppc genes. This study provides valuable resources and a robust phylogenetic framework for evolutionary analyses of the grass family.

Substandard starch grain4 may function in amyloplast development by influencing starch and lipid metabolism in rice endosperm

The amyloplast is a specialized plastid in rice endosperm cells where starch is synthesized and stored as starch granules (SGs). However, little is known about the molecular mechanism underlying amyloplast and SG development. In this study, a novel mutant (c134) demonstrating a floury endosperm with enlarged SGs and amyloplasts was identified. The floury endosperm was caused by rounder, loosely packed SG. Grain-quality profile and expression analysis showed reduced contents of total starch and amylose in the c134 mutant, as well as reduced expression of a number of genes involved in starch biosynthesis. Galactosyldiacylglycerol (GDG) content and fatty acid synthesis play important roles in plastid development, and in the c134 endosperm, an obvious decrease in GDG and various fatty acids was observed, with down-regulated expression of various genes involved in lipid biosynthesis. Furthermore, map-based cloning revealed an amino acid substitution (glycine to aspartic acid) in the substandard starch grain4 (SSG4) protein. The results of this study suggest that SSG4 influences the regulation of starch and lipid metabolism as well as amyloplast development, a finding that is useful for potential genetic improvement of rice grain quality in future starch and lipid breeding and biotechnology.

Phylogenetic, ecological and intraindividual variability patterns in grass phytolith shape

BACKGROUND AND AIMS

Grass silica short cell (GSSC) phytoliths appear to be the most reliable source of fossil evidence for tracking the evolutionary history and paleoecology of grasses. In recent years, modern techniques that quantitatively assess phytolith shape variation have widened opportunities for the classification of grass fossil phytoliths. However, phylogenetic, ecological and intraindividual variability patterns in phytolith shape remain largely unexplored.

METHODS

The full range of intraindividual phytolith shape variation [3650 two-dimensional (2-D) outlines] from 73 extant grass species, 48 genera, 18 tribes and eight subfamilies (particularly Pooideae) was analysed using geometric morphometric analysis based on semi-landmarks spanning phytolith outlines.

KEY RESULTS

The 2-D phytolith shape is mainly driven by deep-time diversification of grass subfamilies. There is distinct phytolith shape variation in early-diverging lineages of Pooideae (Meliceae, Stipeae). The amount of intraindividual variation in phytolith shape varies among species, resulting in a remarkable pattern across grass phylogeny.

CONCLUSIONS

The phylogenetic pattern in phytolith shape was successfully revealed by applying geometric morphometrics to 2-D phytolith shape outlines, strengthening the potential of phytoliths to track the evolutionary history and paleoecology of grasses. Geometric morphometrics of 2-D phytolith shape is an excellent tool for analysis requiring large numbers of phytolith outlines, making it useful for quantitative palaeoecological reconstruction.

Phylotranscriptomics Resolves the Phylogeny of Pooideae and Uncovers Factors for Their Adaptive Evolution

Adaptation to cool climates has occurred several times in different angiosperm groups. Among them, Pooideae, the largest grass subfamily with ∼3,900 species including wheat and barley, have successfully occupied many temperate regions and play a prominent role in temperate ecosystems. To investigate possible factors contributing to Pooideae adaptive evolution to cooling climates, we performed phylogenetic reconstruction using five gene sets (with 1,234 nuclear genes and their subsets) from 157 transcriptomes/genomes representing all 15 tribes and 24 of 26 subtribes. Our phylogeny supports the monophyly of all tribes (except Diarrheneae) and all subtribes with at least two species, with strongly supported resolution of their relationships. Molecular dating suggests that Pooideae originated in the late Cretaceous, with subsequent divergences under cooling conditions first among many tribes from the early middle to late Eocene and again among genera in the middle Miocene and later periods. We identified a cluster of gene duplications (CGD5) shared by the core Pooideae (with 80% Pooideae species) near the Eocene–Oligocene transition, coinciding with the transition from closed to open habitat and an upshift of diversification rate. Molecular evolutionary analyses homologs of CBF for cold resistance uncovered tandem duplications during the core Pooideae history, dramatically increasing their copy number and possibly promoting adaptation to cold habitats. Moreover, duplication of AP1/FUL-like genes before the Pooideae origin might have facilitated the regulation of the vernalization pathway under cold environments. These and other results provide new insights into factors that likely have contributed to the successful adaptation of Pooideae members to temperate regions.

The rise of grasslands is linked to atmospheric CO2 decline in the late Palaeogene

Grasslands are predicted to experience a major biodiversity change by the year 2100. A better understanding of how grasslands have responded to past environmental changes will help predict the outcome of current and future environmental changes. Here, we explore the relationship between past atmospheric CO₂ and temperature fluctuations and the shifts in diversification rate of Poaceae (grasses) and Asteraceae (daisies), two exceptionally species-rich grassland families (~11,000 and ~23,000 species, respectively). To this end, we develop a Bayesian approach that simultaneously estimates diversification rates through time from time-calibrated phylogenies and correlations between environmental variables and diversification rates. Additionally, we present a statistical approach that incorporates the information of the distribution of missing species in the phylogeny. We find strong evidence supporting a simultaneous increase in diversification rates for grasses and daisies after the most significant reduction of atmospheric CO₂ in the Cenozoic (~34 Mya). The fluctuations of paleo-temperatures, however, appear not to have had a significant relationship with the diversification of these grassland families. Overall, our results shed new light on our understanding of the origin of grasslands in the context of past environmental changes.

A better understanding of how grasslands have responded to past environmental changes will help predict the outcomes of future changes. This study explores past climatic fluctuations and shifts in the diversification rate of grasses and daisies, finding strong evidence for a simultaneous increase in their diversification rates following a reduction of atmospheric CO₂ in the Cenozoic.

Defense mechanisms involving secondary metabolism in the grass family

Plants synthesize and accumulate a wide variety of compounds called secondary metabolites. Secondary metabolites serve as chemical barriers to protect plants from pathogens and herbivores. Antimicrobial secondary metabolites are accumulated to prevent pathogen infection. These metabolites are classified into phytoalexins (induced in response to pathogen attack) and phytoanticipins (present prior to pathogen infection). The antimicrobial compounds in the grass family (Poaceae) were studied from the viewpoint of evolution. The studies were performed at three hierarchies, families, genera, and species and include the following: 1) the distribution of benzoxazinoids (Bxs) in the grass family, 2) evolutionary replacement of phytoanticipins from Bxs to hydroxycinnamic acid amide dimers in the genus Hordeum, and 3) chemodiversity of flavonoid and diterpenoid phytoalexins in rice. These studies demonstrated dynamic changes in secondary metabolism during evolution, indicating the adaptation of plants to their environment by repeating scrap-and-build cycles.

Developmental and biophysical determinants of grass leaf size worldwide

One of the most notable ecological trends-described more than 2,300  years ago by Theophrastus-is the association of small leaves with dry and cold climates, which has recently been recognized for eudicotyledonous plants at a global scale^1-3. For eudicotyledons, this pattern has been attributed to the fact that small leaves have a thinner boundary layer that helps to avoid extreme leaf temperatures⁴ and their leaf development results in vein traits that improve water transport under cold or dry climates^5,6. However, the global distribution of leaf size and its adaptive basis have not been tested in the grasses, which represent a diverse lineage that is distinct in leaf morphology and that contributes 33% of terrestrial primary productivity (including the bulk of crop production)⁷. Here we demonstrate that grasses have shorter and narrower leaves under colder and drier climates worldwide. We show that small grass leaves have thermal advantages and vein development that contrast with those of eudicotyledons, but that also explain the abundance of small leaves in cold and dry climates. The worldwide distribution of leaf size in grasses exemplifies how biophysical and developmental processes result in convergence across major lineages in adaptation to climate globally, and highlights the importance of leaf size and venation architecture for grass performance in past, present and future ecosystems.

Silicon in the Soil-Plant Continuum: Intricate Feedback Mechanisms within Ecosystems

Plants' ability to take up silicon from the soil, accumulate it within their tissues and then reincorporate it into the soil through litter creates an intricate network of feedback mechanisms in ecosystems. Here, we provide a concise review of silicon's roles in soil chemistry and physics and in plant physiology and ecology, focusing on the processes that form these feedback mechanisms. Through this review and analysis, we demonstrate how this feedback network drives ecosystem processes and affects ecosystem functioning. Consequently, we show that Si uptake and accumulation by plants is involved in several ecosystem services like soil appropriation, biomass supply, and carbon sequestration. Considering the demand for food of an increasing global population and the challenges of climate change, a detailed understanding of the underlying processes of these ecosystem services is of prime importance. Silicon and its role in ecosystem functioning and services thus should be the main focus of future research.

A 313 plastome phylogenomic analysis of Pooideae: Exploring relationships among the largest subfamily of grasses

In this study, we analyzed 313 plastid genomes (plastomes) of Poaceae with a focus on expanding our current knowledge of relationships among the subfamily Pooideae, which represented over half the dataset (164 representatives). In total, 47 plastomes were sequenced and assembled for this study. This is the largest study of its kind to include plastome-level data, to not only increase sampling at both the taxonomic and molecular levels with the aim of resolving complex and reticulate relationships, but also to analyze the effects of alignment gaps in large-scale analyses, as well as explore divergences in the subfamily with an expanded set of 14 accepted grass fossils for more accurate calibrations and dating. Incorporating broad systematic assessments of Pooideae taxa conducted by authors within the last five years, we produced a robust phylogenomic reconstruction for the subfamily, which included all but two supergeneric taxa (Calothecinae and Duthieeae). We further explored how including alignment gaps in plastome analyses oftentimes can produce incorrect or misinterpretations of complex or reticulate relationships among taxa of Pooideae. This presented itself as consistently changing relationships at specific nodes for different stripping thresholds (percentage-based removal of gaps per alignment column). Our summary recommendation for large-scale genomic plastome datasets is to strip alignment columns of all gaps to increase pairwise identity and reduce errant signal from poly A/T bias. To do this we used the "mask alignment" tool in Geneious software. Finally, we determined an overall divergence age for Pooideae of roughly 84.8 Mya, which is in line with, but slightly older than most recent estimates.

Inter- and intraspecific variation in grass phytolith shape and size: a geometric morphometrics perspective

BACKGROUND AND AIMS

The relative contributions of inter- and intraspecific variation to phytolith shape and size have only been investigated in a limited number of studies. However, a detailed understanding of phytolith variation patterns among populations or even within a single plant specimen is of key importance for the correct taxonomic identification of grass taxa in fossil samples and for the reconstruction of vegetation and environmental conditions in the past. In this study, we used geometric morphometric analysis for the quantification of different sources of phytolith shape and size variation.

METHODS

We used landmark-based geometric morphometric methods for the analysis of phytolith shapes in two extant grass species (Brachypodium pinnatum and B. sylvaticum). For each species, 1200 phytoliths were analysed from 12 leaves originating from six plants growing in three populations. Phytolith shape and size data were subjected to multivariate Procrustes analysis of variance (ANOVA), multivariate regression, principal component analysis and linear discriminant analysis.

KEY RESULTS

Interspecific variation largely outweighed intraspecific variation with respect to phytolith shape. Individual phytolith shapes were classified with 83 % accuracy into their respective species. Conversely, variation in phytolith shapes within species but among populations, possibly related to environmental heterogeneity, was comparatively low.

CONCLUSIONS

Our results imply that phytolith shape relatively closely corresponds to the taxonomic identity of closely related grass species. Moreover, our methodological approach, applied here in phytolith analysis for the first time, enabled the quantification and separation of variation that is not related to species discrimination. Our findings strengthen the role of grass phytoliths in the reconstruction of past vegetation dynamics.

Rice Stomatal Mega-Papillae Restrict Water Loss and Pathogen Entry

Rice (Oryza sativa) is a water-intensive crop, and like other plants uses stomata to balance CO₂ uptake with water-loss. To identify agronomic traits related to rice stomatal complexes, an anatomical screen of 64 Thai and 100 global rice cultivars was undertaken. Epidermal outgrowths called papillae were identified on the stomatal subsidiary cells of all cultivars. These were also detected on eight other species of the Oryza genus but not on the stomata of any other plant species we surveyed. Our rice screen identified two cultivars that had "mega-papillae" that were so large or abundant that their stomatal pores were partially occluded; Kalubala Vee had extra-large papillae, and Dharia had approximately twice the normal number of papillae. These were most accentuated on the flag leaves, but mega-papillae were also detectable on earlier forming leaves. Energy dispersive X-Ray spectrometry revealed that silicon is the major component of stomatal papillae. We studied the potential function(s) of mega-papillae by assessing gas exchange and pathogen infection rates. Under saturating light conditions, mega-papillae bearing cultivars had reduced stomatal conductance and their stomata were slower to close and re-open, but photosynthetic assimilation was not significantly affected. Assessment of an F₃ hybrid population treated with Xanthomonas oryzae pv. oryzicola indicated that subsidiary cell mega-papillae may aid in preventing bacterial leaf streak infection. Our results highlight stomatal mega-papillae as a novel rice trait that influences gas exchange, stomatal dynamics, and defense against stomatal pathogens which we propose could benefit the performance of future rice crops.

A comprehensive calibrated phytolith based climatic index from the Himalaya and its application in palaeotemperature reconstruction

Past climate reconstructions from palaeoecological records require an understanding of relationships between modern vegetation and climate. Phytoliths are being used widely to reconstruct variations in C3/C4 grasses in the past vegetation and corresponding climate. However, little understanding is available on their relationships with the climate driver(s). Even though, the driver(s) regulating C3/C4 grass distributions vary regionally, while reconstructing the past distributions, a grass phytolith-based climatic index (Ic) has often been found to be used globally without assessing its regional consistency. In the Himalaya, the working potential of Ic has proven to be unsatisfactory when compared to other regions of the globe. To improve the efficacy of Ic, we have identified the redundant grass phytolith morphs and revised it by including four exclusive C3-grass indicator morphotypes (bilobate trapezoidal, bilobate scooped, saddle tall and saddle plateaued) to the existing Ic calculation. Thus, a new climatic index, revised Ic (rIc) is proposed in this article. We have compared the rIc with modern climate variables and a relationship with mean annual temperature (MAT) is established with statistical validation. To assess the working potential of the proposed calibration function in the past temperature reconstructions, we have estimated the late Holocene MAT variations in the Himalaya using rIc. We infer that in the mountainous regions like the Himalaya, even with irregular precipitation distribution, variability in C3/C4 grass distributions and their phytolith spectra seem to be a primary function of temperature. Further, we recommend that rIc can be satisfactorily used to reconstruct past temperature variations in the Himalaya and similar mountainous regions where soil water availability is not a limiting factor.

Continued Adaptation of C4 Photosynthesis After an Initial Burst of Changes in the Andropogoneae Grasses

C\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}$_{4}$\end{document} photosynthesis is a complex trait that sustains fast growth and high productivity in tropical and subtropical conditions and evolved repeatedly in flowering plants. One of the major C\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}$_{4}$\end{document} lineages is Andropogoneae, a group of \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}$\sim $\end{document}1200 grass species that includes some of the world’s most important crops and species dominating tropical and some temperate grasslands. Previous efforts to understand C\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}$_{4}$\end{document} evolution in the group have compared a few model C\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}$_{4}$\end{document} plants to distantly related C\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}$_{3}$\end{document} species so that changes directly responsible for the transition to C\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}$_{4}$\end{document} could not be distinguished from those that preceded or followed it. In this study, we analyze the genomes of 66 grass species, capturing the earliest diversification within Andropogoneae as well as their C\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}$_{3}$\end{document} relatives. Phylogenomics combined with molecular dating and analyses of protein evolution show that many changes linked to the evolution of C\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}$_{4}$\end{document} photosynthesis in Andropogoneae happened in the Early Miocene, between 21 and 18 Ma, after the split from its C\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}$_{3}$\end{document} sister lineage, and before the diversification of the group. This initial burst of changes was followed by an extended period of modifications to leaf anatomy and biochemistry during the diversification of Andropogoneae, so that a single C\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}$_{4}$\end{document} origin gave birth to a diversity of C\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}$_{4}$\end{document} phenotypes during 18 million years of speciation events and migration across geographic and ecological spaces. Our comprehensive approach and broad sampling of the diversity in the group reveals that one key transition can lead to a plethora of phenotypes following sustained adaptation of the ancestral state. [Adaptive evolution; complex traits; herbarium genomics; Jansenelleae; leaf anatomy; Poaceae; phylogenomics.]

3D shape analysis of grass silica short cell phytoliths: a new method for fossil classification and analysis of shape evolution

Fossil grass silica short cell phytoliths (GSSCP) have been used to reconstruct the biogeography of Poaceae, untangle crop domestication history and detect past vegetation shifts. These inferences depend on accurately identifying the clade to which the fossils belong. Patterns of GSSCP shape and size variation across the family have not been established and current classification methods are subjective or based on a 2D view that ignores important 3D shape variation. Focusing on Poaceae subfamilies Anomochlooideae, Pharoideae, Pueliodieae, Bambusoideae and Oryzoideae, we observed in situ GSSCP to establish their orientation and imaged isolated GSSCP using confocal microscopy to produce 3D models. 3D geometric morphometrics was used to analyze GSSCP shape and size. Classification models were applied to GSSCP from Eocene sediments from Nebraska, USA, and Anatolia, Turkey. There were significant shape differences between nearly all recognized GSSCP morphotypes and between clades with shared morphotypes. Most of the Eocene GSSCP were classified as woody bamboos with some distinctive Nebraska GSSCP classified as herbaceous bamboos. 3D morphometrics hold great promise for GSSCP classification. It accounts for the complete GSSCP shape, automates size measurements and accommodates the complete range of morphotypes within a single analytical framework.

Phylogenomic proof of Recurrent Demipolyploidization and Evolutionary Stalling of the "Triploid Bridge" in Arundo (Poaceae)

Polyploidization is a frequent phenomenon in plants, which entails the increase from one generation to the next by multiples of the haploid number of chromosomes. While tetraploidization is arguably the most common and stable outcome of polyploidization, over evolutionary time triploids often constitute only a transient phase, or a "triploid bridge", between diploid and tetraploid levels. In this study, we reconstructed in a robust phylogenomic and statistical framework the evolutionary history of polyploidization in Arundo, a small genus from the Poaceae family with promising biomass, bioenergy and phytoremediation species. Through the obtainment of 10 novel leaf transcriptomes for Arundo and outgroup species, our results prove that recurrent demiduplication has likely been a major driver of evolution in this species-poor genus. Molecular dating further demonstrates that the species originating by demiduplication stalled in the "triploid bridge" for evolutionary times in the order of millions of years without undergoing tetratploidization. Nevertheless, we found signatures of molecular evolution highlighting some of the processes that accompanied the genus radiation. Our results clarify the complex nature of Arundo evolution and are valuable for future gene functional validation as well as reverse and comparative genomics efforts in the Arundo genus and other Arundinoideae.

Exploitation and utilization of tropical rainforests indicated in dental calculus of ancient Oceanic Lapita culture colonists

Remote Oceania, which largely consists of islands covered in tropical forests, was the last region on earth to be successfully colonized by humans, beginning 3,000 years ago. We examined human dental calculus from burials in an ancient Lapita culture cemetery to gain insight into the early settlement of this previously untouched tropical environment, specifically on the island of Efate in Vanuatu. Dental calculus is an ideal material to analyse questions of human and plant interactions due to the ingestion of plant-derived microparticles that become incorporated into the calculus as it forms throughout a person's life. Most of the microparticles identified here are from tree and shrub resources, including a ~2,900 calibrated (cal) BP example of banana in Remote Oceania, providing direct evidence for the importance of forests and arboriculture during the settlement of Remote Oceania.

Phylogenetic Shifts in Gene Body Methylation Correlate with Gene Expression and Reflect Trait Conservation

A subset of genes in plant genomes are labeled with DNA methylation specifically at CG residues. These genes, known as gene-body methylated (gbM), have a number of associated characteristics. They tend to have longer sequences, to be enriched for intermediate expression levels, and to be associated with slower rates of molecular evolution. Most importantly, gbM genes tend to maintain their level of DNA methylation between species, suggesting that this trait is under evolutionary constraint. Given the degree of conservation in gbM, we still know surprisingly little about its function in plant genomes or whether gbM is itself a target of selection. To address these questions, we surveyed DNA methylation across eight grass (Poaceae) species that span a gradient of genome sizes. We first established that genome size correlates with genome-wide DNA methylation levels, but less so for genic levels. We then leveraged genomic data to identify a set of 2,982 putative orthologs among the eight species and examined shifts of methylation status for each ortholog in a phylogenetic context. A total of 55% of orthologs exhibited a shift in gbM, but these shifts occurred predominantly on terminal branches, indicating that shifts in gbM are rarely conveyed over time. Finally, we found that the degree of conservation of gbM across species is associated with increased gene length, reduced rates of molecular evolution, and increased gene expression level, but reduced gene expression variation across species. Overall, these observations suggest a basis for evolutionary pressure to maintain gbM status over evolutionary time.

Estimated dietary intake of essential elements from four selected staple foods in Najran City, Saudi Arabia

The estimated dietary intake (EDI) of essential elements selenium (Se), zinc (Zn), manganese (Mn) and copper (Cu) has not been previously investigated for Najran city, Saudi Arabia. This type of information can be valuable for protecting public health. The aim of this study was to estimate the EDI of these elements. A food frequency questionnaire (FFQ) was completed by the study participants (n = 80) to obtain dietary intake of selected staple foods (rice, wheat, meat and chicken). The concentrations of Se, Zn, Mn and Cu in these staple foods were determined using inductively coupled plasma-mass spectrometry (ICP-MS). The ranges of concentrations (mg/kg, wet weight) were as follows: Se (0.07–0.24), Zn (3.91–20.89), Mn (0.63–14.69) and Cu (0.69–2.41). The calculated ranges of EDIs (mg/kg bw/day) for the essential elements were as follows: Se 9.55 × 10⁻⁵–5.75 × 10⁻⁴, Zn 1.33 × 10⁻²–5.83 × 10⁻², Mn 1.49 × 10⁻³–3.31 × 10⁻², Cu 1.65 × 10⁻³–5.42 × 10⁻³. The highest EDI for Cu and Mn came from wheat. In the case of Se and Zn, the foods that contributed the highest EDI were chicken and meat, respectively. The lowest EDIs were found for Se in wheat, Zn in rice and both Mn and Cu in chicken. The percentages (%) of provisional maximum tolerable daily intake (PMTDI) for Se, Zn, Mn and Cu were 13%, 11%, 14% and 3.4%, respectively when contributions from all the four classes of foods were combined. The percentage of the recommended daily allowance (RDA) derived from these foods were 80%, 20%, 17% and 5.6% for Se, Zn, Mn and Cu were, respectively. This raises the possibility of Cu deficiency in the Najran population. However, a total diet study and human biomonitoring study is needed in the future to fully assess if people in Najran city are at risk of deficiency or excessive exposure to trace elements.

Recent range expansion in Australian hummock grasses (Triodia) inferred using genotyping-by-sequencing

The Australian arid zone (AAZ) has undergone aridification and the formation of vast sandy deserts since the mid-Miocene. Studies on AAZ organisms, particularly animals, have shown patterns of mesic ancestry, persistence in rocky refugia and range expansions in arid lineages. There has been limited molecular investigation of plants in the AAZ, particularly of taxa that arrived in Australia after the onset of aridification. Here we investigate populations of the widespread AAZ grass Triodia basedowii to determine whether there is evidence for a recent range expansion, and if so, its source and direction. We also undertake a dating analysis for the species complex to which T. basedowii belongs, in order to place its diversification in relation to changes in AAZ climate and landscapes. We analyse a genomic single nucleotide polymorphism data set from 17 populations of T. basedowii in a recently developed approach for detecting the signal and likely origin of a range expansion. We also use alignments from existing and newly sequenced plastomes from across Poaceae for analysis in BEAST to construct fossil-calibrated phylogenies. Across a range of sampling parameters and outgroups, we detected a consistent signal of westward expansion for T. basedowii, originating in central or eastern Australia. Divergence time estimation indicates that Triodia began to diversify in the late Miocene (crown 7.0-8.8 million years (Ma)), and the T. basedowii complex began to radiate during the Pleistocene (crown 1.4-2.0 Ma). This evidence for range expansion in an arid-adapted plant is consistent with similar patterns in AAZ animals and likely reflects a general response to the opening of new habitat during aridification. Radiation of the T. basedowii complex through the Pleistocene has been associated with preferences for different substrates, providing an explanation why only one lineage is widespread across sandy deserts.

Leaf shape and size track habitat transitions across forest-grassland boundaries in the grass family (Poaceae)

Grass leaf shape is a strong indicator of their habitat with linear leaves predominating in open areas and ovate leaves distinguishing forest-associated grasses. This pattern among extant species suggests that ancestral shifts between forest and open habitats may have coincided with changes in leaf shape or size. We tested relationships between habitat, climate, photosynthetic pathway, and leaf shape and size in a phylogenetic framework to evaluate drivers of leaf shape and size variation over the evolutionary history of the family. We also estimated the ancestral habitat of Poaceae and tested whether forest margins served as transitional zones for shifts between forests and grasslands. We found that grass leaf shape is converging toward different shape optima in the forest understory, forest margins, and open habitats. Leaf size also varies with habitat. Grasses have smaller leaves in open and drier areas, and in areas with high solar irradiance. Direct transitions between linear and ovate leaves are rare as are direct shifts between forest and open habitats. The most likely ancestral habitat of the family was the forest understory and forest margins along with an intermediate leaf shape served as important transitional habitat and morphology, respectively, for subsequent shifts across forest-grassland biome boundaries.

Evolution of phytolith deposition in modern bryophytes, and implications for the fossil record and influence on silica cycle in early land plant evolution

Anecdotal evidence indicating substantial silica accumulation in tissues of bryophytes suggests that silica (phytolith) deposition evolved early on in embryophytes. To test this hypothesis, we conducted the first survey of phytolith content representing the major liverwort, moss and hornwort clades. We also assessed the diagnostic value of bryophyte phytoliths. Silica extracted from bryophyte material through wet-ashing was described, focusing on abundance, classifying taxa as nonproducers, light producers and higher producers; and phytolith morphotypes. Ancestral state reconstruction of these characters was performed for mosses and liverworts using published phylogenies. Phytoliths are present in multiple subclades within liverworts, mosses and hornworts, but these phyla were not ancestrally high silica-producers. Higher deposition occurs in liverworts and mosses with specialized water-conducting cells. We hypothesize that active, high silica accumulation was not ancestral for embryophytes, but became possible in clades with increased water conductance. Phytoliths of diagnostic structures (e.g. pegged rhizoids) could help track bryophyte clades or water conductance evolution in the fossil record.

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.

Opposite macroevolutionary responses to environmental changes in grasses and insects during the Neogene grassland expansion

The rise of Neogene C4 grasslands is one of the most drastic changes recently experienced by the biosphere. A central - and widely debated - hypothesis posits that Neogene grasslands acted as a major adaptive zone for herbivore lineages. We test this hypothesis with a novel model system, the Sesamiina stemborer moths and their associated host-grasses. Using a comparative phylogenetic framework integrating paleoenvironmental proxies we recover a negative correlation between the evolutionary trajectories of insects and plants. Our results show that paleoenvironmental changes generated opposing macroevolutionary dynamics in this insect-plant system and call into question the role of grasslands as a universal adaptive cradle. This study illustrates the importance of implementing environmental proxies in diversification analyses to disentangle the relative impacts of biotic and abiotic drivers of macroevolutionary dynamics.

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.

In silico identification and characterization of a diverse subset of conserved microRNAs in bioenergy crop Arundo donax L

MicroRNAs (miRNAs) are small non-coding RNA molecules involved in the post-transcriptional regulation of gene expression in plants. Arundo donax L. is a perennial C₃ grass considered one of the most promising bioenergy crops. Despite its relevance, many fundamental aspects of its biology still remain to be elucidated. In the present study we carried out the first in silico mining and tissue-specific characterization of microRNAs and their putative targets in A. donax. We identified a total of 141 miRNAs belonging to 14 families along with the corresponding primary miRNAs, precursor miRNAs and a total of 462 high-confidence predicted targets and novel target sites were validated by 5′-race. Gene Ontology functional annotation showed that miRNA targets are constituted mainly by transcription factors, but three of the newly validated targets are enzymes involved in novel functions like RNA editing, acyl lipid metabolism and post-Golgi trafficking. Folding variability of pre-miRNA loops and phylogenetic analyses indicate variable selective pressure acting on the different miRNA families. The set of miRNAs identified in this study will pave the road to further miRNA research in Arundo donax and contribute towards a better understanding of miRNA-mediated gene regulatory processes in other bioenergy crops.

Whole-Genome Duplication and Plant Macroevolution

Whole-genome duplication (WGD) is characteristic of almost all fundamental lineages of land plants. Unfortunately, the timings of WGD events are loosely constrained and hypotheses of evolutionary consequence are poorly formulated, making them difficult to test. Using examples from across the plant kingdom, we show that estimates of timing can be improved through the application of molecular clock methodology to multigene datasets. Further, we show that phenotypic change can be quantified in morphospaces and that relative phenotypic disparity can be compared in the light of WGD. Together, these approaches facilitate tests of hypotheses on the role of WGD in plant evolution, underscoring the potential of plants as a model system for investigating the role WGD in macroevolution.

Investigation of mitochondrial-derived plastome sequences in the Paspalum lineage (Panicoideae; Poaceae)

BACKGROUND

The grass family (Poaceae), ca. 12,075 species, is a focal point of many recent studies that aim to use complete plastomes to reveal and strengthen relationships within the family. The use of Next Generation Sequencing technology has revealed intricate details in many Poaceae plastomes; specifically the trnI - trnL intergenic spacer region. This study investigates this region and the putative mitochondrial inserts within it in complete plastomes of Paspalum and other Poaceae.

RESULTS

Nine newly sequenced plastomes, seven of which contain an insert within the trnI - trnL intergenic spacer, were combined into plastome phylogenomic and divergence date analyses with 52 other species. A robust Paspalum topology was recovered, originating at 10.6 Ma, with the insert arising at 8.7 Ma. The alignment of the insert across Paspalum reveals 21 subregions with pairwise homology in 19. In an analysis of emergent self-organizing maps of tetranucleotide frequencies, the Paspalum insert grouped with mitochondrial DNA.

CONCLUSIONS

A hypothetical ancestral insert, 17,685 bp in size, was found in the trnI - trnL intergenic spacer for the Paspalum lineage. A different insert, 2808 bp, was found in the same region for Paraneurachne muelleri. Seven different intrastrand deletion events were found within the Paspalum lineage, suggesting selective pressures to remove large portions of noncoding DNA. Finally, a tetranucleotide frequency analysis was used to determine that the origin of the insert in the Paspalum lineage is mitochondrial DNA.

Building the monocot tree of death: Progress and challenges emerging from the macrofossil-rich Zingiberales

PREMISE OF THE STUDY

Inclusion of fossils in phylogenetic analyses is necessary in order to construct a comprehensive "tree of death" and elucidate evolutionary history of taxa; however, such incorporation of fossils in phylogenetic reconstruction is dependent on the availability and interpretation of extensive morphological data. Here, the Zingiberales, whose familial relationships have been difficult to resolve with high support, are used as a case study to illustrate the importance of including fossil taxa in systematic studies.

METHODS

Eight fossil taxa and 43 extant Zingiberales were coded for 39 morphological seed characters, and these data were concatenated with previously published molecular sequence data for analysis in the program MrBayes.

KEY RESULTS

Ensete oregonense is confirmed to be part of Musaceae, and the other seven fossils group with Zingiberaceae. There is strong support for Spirematospermum friedrichii, Spirematospermum sp. 'Goth', S. wetzleri, and Striatornata sanantoniensis in crown Zingiberaceae while "Musa" cardiosperma, Spirematospermum chandlerae, and Tricostatocarpon silvapinedae are best considered stem Zingiberaceae. Inclusion of fossils explains how different topologies from morphological and molecular data sets is due to shared plesiomorphic characters shared by Musaceae, Zingiberaceae, and Costaceae, and most of the fossils.

CONCLUSIONS

Inclusion of eight fossil taxa expands the Zingiberales tree and helps explain the difficulty in resolving relationships. Inclusion of fossils was possible in part due to a large morphological data set built using nondestructive microcomputed tomography data. Collaboration between paleo- and neobotanists and technology such as microcomputed tomography will help to build the tree of death and ultimately improve our understanding of the evolutionary history of monocots.

Taxonomic Demarcation of Setaria pumila (Poir.) Roem. & Schult., S. verticillata (L.) P. Beauv., and S. viridis (L.) P. Beauv. (Cenchrinae, Paniceae, Panicoideae, Poaceae) From Phytolith Signatures

Background and Aims: The role and significance of phytoliths in taxonomic diagnosis of grass species has been well documented with a focus on the types found in foliar epidermis and the synflorescence. The present paper is an attempt to broaden the scope of phytoliths in species diagnosis of grasses by developing phytolith signatures of some species of the foxtail genus Setaria P. Beauv. through in situ location and physico-chemical analysis of various phytolith morphotypes in different parts of the plant body. Methods: Clearing solution and dry ashing extraction methods were employed for in situ location and isolation of phytolith morphotypes respectively. Ultrastructural details were worked out by Scanning Electron Microscopy (SEM) and Transmission Electron Microscopy. Morphometric and frequency data of phytolith morphotypes were also recorded. Biochemical architecture of various phytolith types was worked out through SEM-EDX, XRD, and FTIR analysis. Data were analyzed through Principal Component Analysis and Cluster Analysis. Key Results:In situ location of phytoliths revealed species specific epidermal patterns. The presence of cystoliths (calcium oxalate crystals) in the costal regions of adaxial leaf surface of S. verticillata (L.) P. Beauv. is the first report for the genus Setaria. Our results revealed marked variations in epidermal ornamentation and undulation patterns with a novel "Λ" (Lamda) type of undulated ornamentation reported in S. verticillata. Dry ashing method revealed species specific clusters of phytolith morphotypes. Conclusions: The study revealed that phytoliths can play a significant role in resolution of taxonomic identity of three species of Setaria. Each species was marked out by a unique assemblage of phytolith morphotypes from various parts of the plant body. Apart from in situ location and epidermal patterning, diagnostic shapes, frequency distribution, size dimensions, and biochemical architecture emerged as complementary traits that help in developing robust phytolith signatures for plant species.

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.

Molecular phylogeny of Panicum s. str. (Poaceae, Panicoideae, Paniceae) and insights into its biogeography and evolution

Panicum sensu stricto is a genus of grasses (Poaceae) with nearly, according to this study, 163 species distributed worldwide. This genus is included in the subtribe Panicinae together with Louisiella, the latter with 2 species. Panicum and subtribe Panicinae are characterized by including annual or perennial taxa with open and lax panicles, and spikelets with the lower glume reduced; all taxa also share a basic chromosome number of x = 9 and a Kranz leaf blade anatomy typical of the NAD-me subtype photosynthetic pathway. Nevertheless, the phylogenetic placements of many Panicum species, and the circumscription of the genus, remained untested. Therefore, phylogenetic analyses were conducted using sequence data from the ndhF plastid region, in an extensive worldwide sampling of Panicum and related genera, in order to infer evolutionary relationships and to provide a phylogenetic framework to review the classification of the genus. Diversification times, historical biogeography and evolutionary patterns of the life history (annual vs. perennial) in the subtribe and Panicum were also studied. Results obtained provide strong support for a monophyletic Panicum including 71 species and 7 sections, of which sections Arthragrostis and Yakirra are new in the genus; 7 new combinations are made here. Furthermore, 32 species traditionally assigned to Panicum were excluded from the genus, and discussed in other subtribes of Paniceae. Our study suggested that early diversification in subtribe Panicinae and Panicum occurred through the Early-Mid Miocene in the Neotropics, while the subsequent diversification of its sections mainly occurred in the Late Miocene-Pleistocene, involving multiple dispersals to all continents. Our analyses also showed that transition rates and changes between annual and perennial life history in Panicum were quite frequent, suggesting considerable lability of this trait. Changes of the life history, together with C4 photosynthesis, and the multiple dispersal events since the Mid Miocene, seem to have facilitated a widespread distribution of the genus. All these findings contribute to a better understanding of the systematics and evolution of Panicum.

Dominant integration locus drives continuous diversification of plant immune receptors with exogenous domain fusions

BACKGROUND

The plant immune system is innate and encoded in the germline. Using it efficiently, plants are capable of recognizing a diverse range of rapidly evolving pathogens. A recently described phenomenon shows that plant immune receptors are able to recognize pathogen effectors through the acquisition of exogenous protein domains from other plant genes.

RESULTS

We show that plant immune receptors with integrated domains are distributed unevenly across their phylogeny in grasses. Using phylogenetic analysis, we uncover a major integration clade, whose members underwent repeated independent integration events producing diverse fusions. This clade is ancestral in grasses with members often found on syntenic chromosomes. Analyses of these fusion events reveals that homologous receptors can be fused to diverse domains. Furthermore, we discover a 43 amino acid long motif associated with this dominant integration clade which is located immediately upstream of the fusion site. Sequence analysis reveals that DNA transposition and/or ectopic recombination are the most likely mechanisms of formation for nucleotide binding leucine rich repeat proteins with integrated domains.

CONCLUSIONS

The identification of this subclass of plant immune receptors that is naturally adapted to new domain integration will inform biotechnological approaches for generating synthetic receptors with novel pathogen "baits."

Mitochondrial Retroprocessing Promoted Functional Transfers of rpl5 to the Nucleus in Grasses

Functional gene transfers from the mitochondrion to the nucleus are ongoing in angiosperms and have occurred repeatedly for all 15 ribosomal protein genes, but it is not clear why some of these genes are transferred more often than others nor what the balance is between DNA- and RNA-mediated transfers. Although direct insertion of mitochondrial DNA into the nucleus occurs frequently in angiosperms, case studies of functional mitochondrial gene transfer have implicated an RNA-mediated mechanism that eliminates introns and RNA editing sites, which would otherwise impede proper expression of mitochondrial genes in the nucleus. To elucidate the mechanisms that facilitate functional gene transfers and the evolutionary dynamics of the coexisting nuclear and mitochondrial gene copies that are established during these transfers, we have analyzed rpl5 genes from 90 grasses (Poaceae) and related monocots. Multiple lines of evidence indicate that rpl5 has been functionally transferred to the nucleus at least three separate times in the grass family and that at least seven species have intact and transcribed (but not necessarily functional) copies in both the mitochondrion and nucleus. In two grasses, likely functional nuclear copies of rpl5 have been subject to recent gene conversion events via secondarily transferred mitochondrial copies in what we believe are the first described cases of mitochondrial-to-nuclear gene conversion. We show that rpl5 underwent a retroprocessing event within the mitochondrial genome early in the evolution of the grass family, which we argue predisposed the gene towards successful, DNA-mediated functional transfer by generating a "pre-edited" sequence.

Resolving phylogenetic relationships of Delphacini and Tropidocephalini (Hemiptera: Delphacidae: Delphacinae) as inferred from four genetic loci

This paper explores the phylogeny of the delphacid subfamily Delphacinae based on nuclear ribosomal and mitochondrial DNA sequences of four genetic loci (16S rDNA, 28S rDNA, Cytochrome oxidase I and Cytochrome b). Maximum likelihood and Bayesian analyses yield robust phylogenetic trees. The topologies support the monophyly of Delphacinae and its basal split into three tribes, and provisionally support subdividing Delphacini into three clades, including a more broadly defined Numatina. The tribe Tropidocephalini is divided into two clades. In addition, Paranectopia is transferred from Tropidocephalini to Delphacini and Harmalia syn. nov. is regarded as a junior synonym of Opiconsiva. The genera Bambusiphaga, Megadelphax and Muirodelphax are found to be paraphyletic. The estimated time to the most recent common ancestor of Delphacinae is roughly at 90 million years ago in Late Cretaceous.

Evolutionary Insights Based on SNP Haplotypes of Red Pericarp, Grain Size and Starch Synthase Genes in Wild and Cultivated Rice

The origin and domestication of rice has been a subject of considerable debate in the post-genomic era. Rice varieties have been categorized based on isozyme and DNA markers into two broad cultivar groups, Indica and Japonica. Among other well-known cultivar groups Aus varieties are closer to Indica and Aromatic varieties including Basmati are closer to Japonica, while deep-water rice varieties share kinship to both Indica and Japonica cultivar groups. Here, we analyzed haplotype networks and phylogenetic relationships in a diverse set of genotypes including Indian Oryza nivara/Oryza rufipogon wild rice accessions and representative varieties of four rice cultivar groups based on pericarp color (Rc), grain size (GS3) and eight different starch synthase genes (GBSSI, SSSI, SSIIa, SSIIb, SSIIIa, SSIIIb, SSIVa, and SSIVb). Aus cultivars appear to have the most ancient origin as they shared the maximum number of haplotypes with the wild rice populations, while Indica, Japonica and Aromatic cultivar groups showed varying phylogenetic origins of these genes. Starch synthase genes showed higher variability in cultivated rice than wild rice populations, suggesting diversified selection during and after domestication. O. nivara/O. rufipogon wild rice accessions belonging to different sub-populations shared common haplotypes for all the 10 genes analyzed. Our results support polyphyletic origin of cultivated rice with a complex pattern of migration of domestication alleles from wild to different rice cultivar groups. The findings provide novel insights into evolutionary and domestication history of rice and will help utilization of wild rice germplasm for genetic improvement of rice cultivars.

Sequencing of Australian wild rice genomes reveals ancestral relationships with domesticated rice

The related A genome species of the Oryza genus are the effective gene pool for rice. Here, we report draft genomes for two Australian wild A genome taxa: O. rufipogon-like population, referred to as Taxon A, and O. meridionalis-like population, referred to as Taxon B. These two taxa were sequenced and assembled by integration of short- and long-read next-generation sequencing (NGS) data to create a genomic platform for a wider rice gene pool. Here, we report that, despite the distinct chloroplast genome, the nuclear genome of the Australian Taxon A has a sequence that is much closer to that of domesticated rice (O. sativa) than to the other Australian wild populations. Analysis of 4643 genes in the A genome clade showed that the Australian annual, O. meridionalis, and related perennial taxa have the most divergent (around 3 million years) genome sequences relative to domesticated rice. A test for admixture showed possible introgression into the Australian Taxon A (diverged around 1.6 million years ago) especially from the wild indica/O. nivara clade in Asia. These results demonstrate that northern Australia may be the centre of diversity of the A genome Oryza and suggest the possibility that this might also be the centre of origin of this group and represent an important resource for rice improvement.