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Abstract Background During evolution, plants and other organisms have developed a diversity of chemical defences, leading to the evolution of various groups of specialized metabolites selected for their endogenous biological function. A correlation between phylogeny and biosynthetic pathways could offer a predictive approach enabling more efficient selection of plants for the development of traditional medicine and lead discovery. However, this relationship has rarely been rigorously tested and the potential predictive power is consequently unknown. Results We produced a phylogenetic hypothesis for the medicinally important plant subfamily Amaryllidoideae (Amaryllidaceae) based on parsimony and Bayesian analysis of nuclear, plastid, and mitochondrial DNA sequences of over 100 species. We tested if alkaloid diversity and activity in bioassays related to the central nervous system are significantly correlated with phylogeny and found evidence for a significant phylogenetic signal in these traits, although the effect is not strong. Conclusions Several genera are non-monophyletic emphasizing the importance of using phylogeny for interpretation of character distribution. Alkaloid diversity and in vitro inhibition of acetylcholinesterase (AChE) and binding to the serotonin reuptake transporter (SERT) are significantly correlated with phylogeny. This has implications for the use of phylogenies to interpret chemical evolution and biosynthetic pathways, to select candidate taxa for lead discovery, and to make recommendations for policies regarding traditional use and conservation priorities.

Studies investigating the evolution of flowering plants have long focused on isolating mechanisms such as pollinator specificity. Some recent studies have proposed a role for introgressive hybridization between species, recognizing that isolating processes such as pollinator specialization may not be complete barriers to hybridization. Occasional hybridization may therefore lead to distinct yet reproductively connected lineages. We investigate the balance between introgression and reproductive isolation in a diverse clade using a densely sampled phylogenomic study of fig trees ( Ficus , Moraceae). Codiversification with specialized pollinating wasps (Agaonidae) is recognized as a major engine of fig diversity, leading to about 850 species. Nevertheless, some studies have focused on the importance of hybridization in Ficus , highlighting the consequences of pollinator sharing. Here, we employ dense taxon sampling (520 species) throughout Moraceae and 1,751 loci to investigate phylogenetic relationships and the prevalence of introgression among species throughout the history of Ficus . We present a well-resolved phylogenomic backbone for Ficus , providing a solid foundation for an updated classification. Our results paint a picture of phylogenetically stable evolution within lineages punctuated by occasional local introgression events likely mediated by local pollinator sharing, illustrated by clear cases of cytoplasmic introgression that have been nearly drowned out of the nuclear genome through subsequent lineage fidelity. The phylogenetic history of figs thus highlights that while hybridization is an important process in plant evolution, the mere ability of species to hybridize locally does not necessarily translate into ongoing introgression between distant lineages, particularly in the presence of obligate plant-pollinator relationships.

Arbuscular mycorrhizal fungi (AMF) have evolved associations with roots of 60% plant species, but the net benefit for plants vary broadly from mutualism to parasitism. Yet, we lack a general understanding of the evolutionary and ecological forces driving such variation. To this end, we conducted a comparative phylogenetic experiment with 24 species of Plantago, encompassing worldwide distribution, to address the effect of evolutionary history and environment on plant growth and chemical defenses in response to AMF colonization. We demonstrate that different species within one plant genus vary greatly in their ability to associate with AMF, and that AMF arbuscule colonization intensity decreases monotonically with increasing phylogenetic branch length, but not with concomitant changes in pedological and climatic conditions across species. Moreover, we demonstrate that species with the highest colonization levels are also those that change their defensive chemistry the least. We propose that the costs imposed by high AMF colonization in terms of reduced changes in secondary chemistry might drive the observed macroevolutionary decline in mycorrhization., Competing Interests: The authors declare no competing interests., (© 2023 The Author(s).)

The Andean fever tree ( Cinchona L.; Rubiaceae) is a source of bioactive quinine alkaloids used to treat malaria. C. pubescens Vahl is a valuable cash crop within its native range in northwestern South America, however, genomic resources are lacking. Here we provide the first highly contiguous and annotated nuclear and plastid genome assemblies using Oxford Nanopore PromethION-derived long-read and Illumina short-read data. Our nuclear genome assembly comprises 603 scaffolds with a total length of 904 Mbp (∼82 % of the full genome based on a genome size of 1.1 Gbp/1C). Using a combination of de novo and reference-based transcriptome assemblies we annotated 72,305 coding sequences comprising 83% of the BUSCO gene set and 4.6% fragmented sequences. Using additional plastid and nuclear datasets we place C. pubescens in the Gentianales order. This first genomic resource for C. pubescens opens new research avenues, including the analysis of alkaloid biosynthesis in the fever tree., Competing Interests: The authors declare that they have no competing interests., (© The Author(s) 2022.)

Premise: The Campanulaceae (Lobelioideae) is the Hawaiian plant family with the most endangered and extinct species. Although seeds of Hawaiian lobelioids are desiccation tolerant, the species are exceptional (i.e., they present challenges at various stages of the conventional ex situ conservation chain) due to their generally poor seed survival at the conventional seed-banking temperature (-18°C). Both morphological dormancy (MD) and morphophysiological dormancy (MPD) have been identified in the seeds of other Hawaiian lobelioids; however, the class of dormancy and germination requirements of the Critically Endangered genus Brighamia have not yet been determined., Methods: We measured the embryonic growth in 12-week-old seeds of B. rockii and tested their germination at three temperature regimes (15/5°C, 20/10°C, and 25/15°C) in light and at 25/15°C in darkness., Results: The embryos grew prior to radicle emergence, and the seeds germinated rapidly to high percentages in all tested conditions., Discussion: Whether fresh B. rockii seeds have MD or MPD still needs to be determined; nevertheless, 12-week-old seeds germinated well in light and darkness, and thus the seeds can be used for conservation purposes. Germination in the dark suggests that the species may not form a long-lived soil seed bank in its native habitat., (© 2022 The Authors. Applications in Plant Sciences published by Wiley Periodicals LLC on behalf of Botanical Society of America.)

The International Union for Conservation of Nature's Red List of Threatened Species (IUCN Red List) is the world's most comprehensive information source on the global conservation status of species. Governmental agencies and conservation organizations increasingly rely on IUCN Red List assessments to develop conservation policies and priorities. Funding agencies use the assessments as evaluation criteria, and researchers use meta-analysis of red-list data to address fundamental and applied conservation science questions. However, the circa 143,000 IUCN assessments represent a fraction of the world's biodiversity and are biased in regional and organismal coverage. These biases may affect conservation priorities, funding, and uses of these data to understand global patterns. Isolated oceanic islands are characterized by high endemicity, but the unique biodiversity of many islands is experiencing high extinction rates. The archipelago of Hawaii has one of the highest levels of endemism of any floristic region; 90% of its 1367 native vascular plant taxa are classified as endemic. We used the IUCN's assessment of the complete single-island endemic (SIE) vascular plant flora of Kauai, Hawaii, to assess the proportion and drivers of decline of threatened plants in an oceanic island setting. We compared the IUCN assessments with federal, state, and other local assessments of Kauai species or taxa of conservation concern. Finally, we conducted a preliminary assessment for all 1044 native vascular plants of Hawaii based on IUCN criterion B by estimating area of occupancy, extent of occurrence, and number of locations to determine whether the pattern found for the SIE vascular flora of Kauai is comparable to the native vascular flora of the Hawaiian Islands. We compared our results with patterns observed for assessments of other floras. According to IUCN, 256 SIE vascular plant taxa are threatened with extinction and 5% are already extinct. This is the highest extinction risk reported for any flora to date. The preliminary assessment of the native vascular flora of Hawaii showed that 72% (753 taxa) is threatened. The flora of Hawaii may be one of the world's most threatened; thus, increased and novel conservation measures in the state and on other remote oceanic islands are urgently needed., (© 2022 The Authors. Conservation Biology published by Wiley Periodicals LLC on behalf of Society for Conservation Biology.)

Retracing pathways of historical species introductions is fundamental to understanding the factors involved in the successful colonization and spread, centuries after a species' establishment in an introduced range. Numerous plants have been introduced to regions outside their native ranges both intentionally and accidentally by European voyagers and early colonists making transoceanic journeys; however, records are scarce to document this. We use genotyping-by-sequencing and genotype-likelihood methods on the selfing, global weed, Plantago major , collected from 50 populations worldwide to investigate how patterns of genomic diversity are distributed among populations of this global weed. Although genomic differentiation among populations is found to be low, we identify six unique genotype groups showing very little sign of admixture and low degree of outcrossing among them. We show that genotype groups are latitudinally restricted, and that more than one successful genotype colonized and spread into the introduced ranges. With the exception of New Zealand, only one genotype group is present in the Southern Hemisphere. Three of the most prevalent genotypes present in the native Eurasian range gave rise to introduced populations in the Americas, Africa, Australia, and New Zealand, which could lend support to the hypothesis that P. major was unknowlingly dispersed by early European colonists. Dispersal of multiple successful genotypes is a likely reason for success. Genomic signatures and phylogeographic methods can provide new perspectives on the drivers behind the historic introductions and the successful colonization of introduced species, contributing to our understanding of the role of genomic variation for successful establishment of introduced taxa., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Iwanycki Ahlstrand, Gopalakrishnan, Vieira, Bieker, Meudt, Dunbar-Co, Rothfels, Martinez-Swatson, Maldonado, Hassemer, Shipunov, Bowers, Gardner, Xu, Ghorbani, Amano, Grace, Pringle, Bishop, Manzanilla, Cotrim, Blaney, Zubov, Choi, Yesil, Bennett, Vimolmangkang, El-Seedi, Staub, Li, Boldbaatar, Hislop, Caddy, Muasya, Saslis-Lagoudakis, Gilbert, Zerega and Rønsted.)

Plant molecular identification studies have, until recently, been limited to the use of highly conserved markers from plastid and other organellar genomes, compromising resolution in highly diverse plant clades. Due to their higher evolutionary rates and reduced paralogy, low-copy nuclear genes overcome this limitation but are difficult to sequence with conventional methods and require high-quality input DNA. Aloe vera and its relatives in the Alooideae clade (Asphodelaceae, subfamily Asphodeloideae) are of economic interest for food and health products and have horticultural value. However, pressing conservation issues are increasing the need for a molecular identification tool to regulate the trade. With > 600 species and an origin of ± 15 million years ago, this predominantly African succulent plant clade is a diverse and taxonomically complex group for which low-copy nuclear genes would be desirable for accurate species discrimination. Unfortunately, with an average genome size of 16.76 pg, obtaining high coverage sequencing data for these genes would be prohibitively costly and computationally demanding. We used newly generated transcriptome data to design a customised RNA-bait panel targeting 189 low-copy nuclear genes in Alooideae. We demonstrate its efficacy in obtaining high-coverage sequence data for the target loci on Illumina sequencing platforms, including degraded DNA samples from museum specimens, with considerably improved phylogenetic resolution. This customised target capture sequencing protocol has the potential to confidently indicate phylogenetic relationships of Aloe vera and related species, as well as aid molecular identification applications., (© 2021. The Author(s).)

High-throughput sequencing, when combined with taxonomic expertise, is a powerful tool to refine and advance taxonomic classification, including at the species level. In the present work, a new species, Plantago campestris , is described out of the P. commersoniana species complex, based on phylogenomic and morphological evidence. The main morphological characters that distinguish the new species from P. commersoniana are the glabrous posterior sepals and the slightly broader leaves. The new species is known from only three localities, all in natural high-elevation grasslands in Paraná and Santa Catarina states, southern Brazil. According to the IUCN criteria new species should be assessed as Endangered (EN). We present field photographs of P. campestris and related species, and we provide an identification key to the species previously included within the circumscription of P. commersoniana ., Competing Interests: The authors declare there are no competing interests., (©2021 Hassemer et al.)

Although most point sources of persistent organic pollutants (POPs), including polycyclic aromatic hydrocarbons (PAHs), are at lower latitudes, the Arctic region is contaminated. In particular, PAHs now dominate the POP body burden of the region's marine biota at the lower trophic levels. Greenlandic Inuits have the most elevated levels of POPs in their blood compared to any other population, due to their consumption of seal meat and other marine mammals. PAHs, the by-products of the incomplete combustion of petroleum products, are known carcinogens and have been shown to affect the immune system, reproduction, endocrine functions, and the nervous system. With industrial activities and climate change set to increase local PAH emissions, it is paramount to document changes in atmospheric PAH deposition to further investigate PAH exposure in the region and attribute contaminations to their sources. As a measure of atmospheric pollution, we sampled bryophyte herbarium specimens of three common and widespread species collected in Greenland between the 1920s and 1970s after which time new collections were not available. They were analyzed for 19 PAHs using GC-MS (gas chromatography mass spectrometry). The presence of more low-molecular-weight PAHs than high-molecular-weight PAHs is evidence that the PAH contamination in Greenland is due to long-range transport rather than originating from local sources. The results show peaks in PAH atmospheric deposition in the first part of the 19th century followed by a trend of decrease, which mirror global trends in atmospheric pollution known from those periods. PAHs associated with wood and fossil-fuel combustion decrease in the 1970s coinciding with the disappearance of charcoal pits and foundries in Europe and North America, and a shift away from domestic heating with wood during the 19 th century. The results highlight the value of bryophytes as bioindicators to measure PAH atmospheric pollution as well as the unrealized potential of herbaria as historical records of environmental change., (Copyright © 2020 Martinez-Swatson, Mihály, Lange, Ernst, Dela Cruz, Price, Mikkelsen, Christensen, Lundholm and Rønsted.)

Background and Aims: There are a number of disparate models predicting variation in plant chemical defences between species, and within a single species over space and time. These can give conflicting predictions. Here we review a number of these theories, before assessing their power to predict the spatial-temporal variation of thapsigargins between and within populations of the deadly carrot (Thapsia garganica). By utilizing multiple models simultaneously (optimum defence theory, growth rate hypothesis, growth-differentiation balance hypothesis, intra-specific framework and resource exchange model of plant defence), we will highlight gaps in their predictions and evaluate the performance of each., Methods: Thapsigargins are potent anti-herbivore compounds that occur in limited richness across the different plant tissues of T. garganica, and therefore represent an ideal system for exploring these models. Thapsia garganica plants were collected from six locations on the island of Ibiza, Spain, and the thapsigargins quantified within reproductive, vegetative and below-ground tissues. The effects of sampling time, location, mammalian herbivory, soil nutrition and changing root-associated fungal communities on the concentrations of thapsigargins within these in situ observations were analysed, and the results were compared with our model predictions., Key Results: The models performed well in predicting the general defence strategy of T. garganica and the above-ground distribution of thapsigargins, but failed to predict the considerable proportion of defences found below ground. Models predicting variation over environmental gradients gave conflicting and less specific predictions, with intraspecific variation remaining less understood., Conclusion: Here we found that multiple models predicting the general defence strategy of plant species could likely be integrated into a single model, while also finding a clear need to better incorporate below-ground defences into models of plant chemical defences. We found that constitutive and induced thapsigargins differed in their regulation, and suggest that models predicting intraspecific defences should consider them separately. Finally, we suggest that in situ studies be supplemented with experiments in controlled environments to identify specific environmental parameters that regulate variation in defences within species., (© The Author(s) 2019. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

Ethnopharmacological Relevance: Species of the genus Cinchona (Rubiaceae) have been used in traditional medicine, and as a source for quinine since its discovery as an effective medicine against malaria in the 17th century. Despite being the sole cure of malaria for almost 350 years, little is known about the chemical diversity between and within species of the antimalarial alkaloids found in the bark. Extensive historical Cinchona bark collections housed at the Royal Botanic Gardens, Kew, UK, and in other museums may shed new light on the alkaloid chemistry of the Cinchona genus and the history of the quest for the most effective Cinchona barks., Aim of the Study: We used High-Pressure Liquid Chromatography (HPLC) coupled with fluorescence detection (FLD) to reanalyze a set of Cinchona barks originally annotated for the four major quinine alkaloids by John Eliot Howard and others more than 150 years ago., Materials and Methods: We performed an archival search on the Cinchona bark collections in the Economic Botany Collection housed in Kew, focusing on those with historical alkaloid content information. Then, we performed HPLC analysis of the bark samples to separate and quantify the four major quinine alkaloids and the total alkaloid content using fluorescence detection. Correlations between historic and current annotations were calculated using Spearman's rank correlation coefficient, before paired comparisons were performed using Wilcox rank sum tests. The effects of source were explored using generalized linear modelling (GLM), before the significance of each parameter in predicting alkaloid concentrations were assessed using chi-square tests as likelihood ratio testing (LRT) models., Results: The total alkaloid content estimation obtained by our HPLC analysis was comparatively similar to the historical chemical annotations made by Howard. Additionally, the quantity of two of the major alkaloids, quinine and cinchonine, and the total content of the four alkaloids obtained were significantly similar between the historical and current day analysis using linear regression., Conclusions: This study demonstrates that the historical chemical analysis by Howard and current day HPLC alkaloid content estimations are comparable. Current day HPLC analysis thus provide a realistic estimate of the alkaloid contents in the historical bark samples at the time of sampling more than 150 years ago. Museum collections provide a powerful but underused source of material for understanding early use and collecting history as well as for comparative analyses with current day samples., (Copyright © 2019 Elsevier B.V. All rights reserved.)

Plantago is a cosmopolitan genus including over 250 species, concentrated in temperate and high-elevation tropical regions. The taxonomy of Plantago is very difficult, mainly because of its reduced morphology, which features relatively few characters for species classification. Consequently, the infrageneric classification of the genus remains controversial and inadequate. In this study we applied high-throughput plastid genome skimming to provide powerful phylogenetic resolution to clarify the relationships within subg. Plantago, which is the largest, most broadly distributed and poorest understood subgenus of Plantago. Ninety-four samples covering ~56% of all species and representing all sections of subg. Plantago as well as an outgroup were successfully sequenced. The resulting phylogenetic topology was used, complemented by field and herbarium studies, to revise the sectional classification of subg. Plantago and present a complete listing of the accepted species in the subgenus. Our phylogenetic results were also tested for their usefulness in clarifying the taxonomic placement of some taxonomically complicated species in the subgenus. We conclude that a combination of morphological studies and state-of-the art high-throughput DNA data provide a useful toolbox for resolving outstanding taxonomic puzzles exemplified by the genus Plantago., (Copyright © 2019 Elsevier Inc. All rights reserved.)

Plants have evolved a multitude of adaptations to survive extreme conditions. Succulent plants have the capacity to tolerate periodically dry environments, due to their ability to retain water in a specialized tissue, termed hydrenchyma. Cell wall polysaccharides are important components of water storage in hydrenchyma cells. However, the role of the cell wall and its polysaccharide composition in relation to drought resistance of succulent plants are unknown. We investigate the drought response of leaf-succulent Aloe (Asphodelaceae) species using a combination of histological microscopy, quantification of water content, and comprehensive microarray polymer profiling. We observed a previously unreported mode of polysaccharide and cell wall structural dynamics triggered by water shortage. Microscopical analysis of the hydrenchyma cell walls revealed highly regular folding patterns indicative of predetermined cell wall mechanics in the remobilization of stored water and the possible role of homogalacturonan in this process. The in situ distribution of mannans in distinct intracellular compartments during drought, for storage, and apparent upregulation of pectins, imparting flexibility to the cell wall, facilitate elaborate cell wall folding during drought stress. We conclude that cell wall polysaccharide composition plays an important role in water storage and drought response in Aloe., (© 2019 The Authors Plant, Cell & Environment Published by John Wiley & Sons Ltd.)

Coevolutionary theory suggests that an arms race between plants and herbivores yields increased plant specialized metabolite diversity and the geographic mosaic theory of coevolution predicts that coevolutionary interactions vary across geographic scales. Consequently, plant specialized metabolite diversity is expected to be highest in coevolutionary hotspots, geographic regions, which exhibit strong reciprocal selection on the interacting species. Despite being well-established theoretical frameworks, technical limitations have precluded rigorous hypothesis testing. Here we aim at understanding how geographic separation over evolutionary time may have impacted chemical differentiation in the cosmopolitan plant genus Euphorbia . We use a combination of state-of-the-art computational mass spectral metabolomics tools together with cell-based high-throughput immunomodulatory testing. Our results show significant differences in specialized metabolite diversity across geographically separated phylogenetic clades. Chemical structural diversity of the highly toxic Euphorbia diterpenoids is significantly reduced in species native to the Americas, compared to Afro-Eurasia. The localization of these compounds to young stems and roots suggest a possible ecological relevance in herbivory defense. This is further supported by reduced immunomodulatory activity in the American subclade as well as herbivore distribution patterns. We conclude that computational mass spectrometric metabolomics coupled with relevant ecological data provide a strong tool for exploring plant specialized metabolite diversity in a chemo-evolutionary framework.

Aloe vera gel is a globally popular natural product used for the treatment of skin conditions. Its useful properties are attributed to the presence of bioactive polysaccharides. Nearly 25% of the 600 species in the genus Aloe are used locally in traditional medicine, indicating that the bioactive components in Aloe vera may be common across the genus Aloe . The complexity of the polysaccharides has hindered development of relevant assays for authentication of Aloe products. Carbohydrate detecting microarrays have recently been suggested as a method for profiling Aloe polysaccharide composition. The aim of this study was to use carbohydrate detecting microarrays to investigate the seasonal variation in the polysaccharide composition of two medicinal and two non-medicinal Aloe species over the course of a year. Microscopy was used to explore where in the cells the bioactive polysaccharides are present and predict their functional role in the cell wall structure. The carbohydrate detecting microarrays analyses showed distinctive differences in the polysaccharide composition between the different species and carbohydrate detecting microarrays therefore has potential as a complementary screening method directly targeting the presence and composition of relevant polysaccharides. The results also show changes in the polysaccharide composition over the year within the investigated species, which may be of importance for commercial growing in optimizing harvest times to obtain higher yield of relevant polysaccharides.

Herbarium samples are increasingly being recognized for their potential in answering a wide range of research questions. However, the suitability of herbarium samples for chemical analysis is largely unexplored as they are thought to be too degraded. The aim of this study was to explore terpenoid profiles across time and geographic space for four medicinal species of Salvia across the Mediterranean to assess the suitability of using herbarium specimens in chemical analyses. Herbarium samples of Salvia aethiopis, S. multicaulis, S. officinalis , and S. sclarea collected over 150 years across the Mediterranean were compared to modern samples using both targeted and untargeted gas chromatography-mass spectrometry analysis of terpene profiles. There was no effect of collection year on chemical composition, although the total concentration of the 20 assessed standards and two individual standards significantly decreased over time. Instead, chemical profiles were defined by species, with strong species effects identified on both the targeted and untargeted chemical composition. Geographic variation was a factor in regulating the untargeted chemical compositions, suggesting some underlying environmental effects. However, there was no effect of sample altitude on either the targeted or untargeted chemical compositions. Chemical composition of four Salvia species are predominantly defined by species, and there was a substantially smaller effect of year of sampling. Given these results herbarium collections may well represent a considerably underused resource for chemical analyses that can benefit biodiversity and other studies.

Background: As the popularity of Aloe vera extracts continues to rise, a desire to fully understand the individual polymer components of the leaf mesophyll, their relation to one another, and the effects they have on the human body are increasing. Polysaccharides present in the leaf mesophyll have been identified as the components responsible for the biological activities of A. vera, and they have been widely studied in the past decades. However, the commonly used methods do not provide the desired platform to conduct large comparative studies of polysaccharide compositions, as most of them require a complete or near-complete fractionation of the polymers. Objective: The objective for this study was to assess whether carbohydrate microarrays could be used for the high-throughput analysis of cell wall polysaccharides in aloe leaf mesophyll. Methods: The method we chose is known as comprehensive microarray polymer profiling (CoMPP) and combines the high-throughput capacity of microarray technology with the specificity of molecular probes. Results: Preliminary findings showed that CoMPP can successfully be used for high-throughput screening of aloe leaf mesophyll tissue. Seventeen species of Aloe and closely related genera were analyzed, and a clear difference in the polysaccharide compositions of the mesophyll tissues was seen. Conclusions: These preliminary data suggest that the polysaccharides vary between species and that true species of Aloe may differ from segregate genera.

Ethnopharmacological Relevance: The discovery of the antimalarial agent artemisinin is considered one of the most significant success stories of ethnopharmacological research in recent times. The isolation of artemisinin was inspired by the use of Artemisia annua in traditional Chinese medicine (TCM) and was awarded a Nobel Prize in 2015. Antimalarial activity has since been demonstrated for a range of other Artemisia species, suggesting that the genus could provide alternative sources of antimalarial treatments. Given the stunning diversity of the genus (c. 500 species), a prioritisation of taxa to be investigated for their likely antimalarial properties is required., Materials and Methods: Here we use a phylogenetic approach to explore the potential for identifying species more likely to possess antimalarial properties. Ethnobotanical data from literature reports is recorded for 117 species. Subsequent phylogenetically informed analysis was used to identify lineages in which there is an overrepresentation of species used to treat malarial symptoms, and which could therefore be high priority for further investigation of antimalarial activity., Results: We show that these lineages indeed include several species with documented antimalarial activity. To further inform our approach, we use LC-MS/MS analysis to explore artemisinin content in fifteen species from both highlighted and not highlighted lineages. We detected artemisinin in nine species, in eight of them for the first time, doubling the number of Artemisia taxa known to content this molecule., Conclusions: Our findings indicate that artemisinin may be widespread across the genus, providing an accessible local resource outside the distribution area of Artemisia annua., (Copyright © 2018 The Authors. Published by Elsevier B.V. All rights reserved.)

Plants produce a multitude of metabolites that contribute to their fitness and survival and play a role in local adaptation to environmental conditions. The effects of environmental variation are particularly well studied within the genus Plantago ; however, previous studies have largely focused on targeting specific metabolites. Studies exploring metabolome-wide changes are lacking, and the effects of natural environmental variation and herbivory on the metabolomes of plants growing in situ remain unknown. An untargeted metabolomic approach using ultra-high-performance liquid chromatography-mass spectrometry, coupled with variation partitioning, general linear mixed modeling, and network analysis was used to detect differences in metabolic phenotypes of Plantago major in fifteen natural populations across Denmark. Geographic region, distance, habitat type, phenological stage, soil parameters, light levels, and leaf area were investigated for their relative contributions to explaining differences in foliar metabolomes. Herbivory effects were further investigated by comparing metabolomes from damaged and undamaged leaves from each plant. Geographic region explained the greatest number of significant metabolic differences. Soil pH had the second largest effect, followed by habitat and leaf area, while phenological stage had no effect. No evidence of the induction of metabolic features was found between leaves damaged by herbivores compared to undamaged leaves on the same plant. Differences in metabolic phenotypes explained by geographic factors are attributed to genotypic variation and/or unmeasured environmental factors that differ at the regional level in Denmark. A small number of specialized features in the metabolome may be involved in facilitating the success of a widespread species such as Plantago major into such wide range of environmental conditions, although overall resilience in the metabolome was found in response to environmental parameters tested. Untargeted metabolomic approaches have great potential to improve our understanding of how specialized plant metabolites respond to environmental change and assist in adaptation to local conditions.

Ficus (Moraceae) is well diversified in the Neotropics with two lineages inhabiting the wet forests of this region. The hemiepiphytes of section Americanae are the most diversified with c. 120 species, whereas section Pharmacosycea includes about 20 species mostly with a terrestrial habit. To reconstruct the biogeographical history and diversification of Ficus in the Americas, we produced a dated Bayesian phylogenetic hypothesis of Neotropical Ficus including two thirds of the species sequenced for five nuclear regions (At103, ETS, G3pdh, ITS/5.8S and Tpi). Ancestral range was estimated using all models available in Biogeobears and Binary State Speciation and Extinction analysis was used to evaluate the role of the initial habit and propagule size in diversification. The phylogenetic analyses resolved both Neotropical sections as monophyletic but the internal relationships between species in section Americanae remain unclear. Ficus started their diversification in the Neotropics between the Oligocene and Miocene. The genus experienced two bursts of diversification: in the middle Miocene and the Pliocene. Colonization events from the Amazon to adjacent areas coincide with the end of the Pebas system (10 Mya) and the connection of landmasses. Divergence of endemic species in the Atlantic forest is inferred to have happened after its isolation and the opening and consolidation of the Cerrado. Our results suggest a complex diversification in the Atlantic forest differing between postulated refuges and more instable areas in the South distribution of the forest. Finally the selection for initial hemiepiphytic habit and small to medium propagule size influenced the diversification and current distribution of the species at Neotropical forests marked by the historical instability and long-distance dispersal., (Copyright © 2018 Elsevier Inc. All rights reserved.)

Introduction: Authentication of herbal products to ensure efficacy and safety require efficient separation and quantification of constituents. Standard assays for Cinchona bark used for the treatment of malaria and production of quinine, either use only spectrophotometry to detect two pairs of diastereoisomers of quinine and cinchonine type alkaloids (European Pharmacopoeia, Ph.Eur.) or liquid chromatography primarily optimised for detection of the four major alkaloids. However, numerous minor alkaloids occur in Cinchona and related species and efficient separation including gradient elution is necessary in order to obtain the full pattern of constituents in bark samples., Objective: To develop an optimised HPLC method for separation and quantitative analysis of the four major alkaloids in Cinchona bark using UV detection., Methodology: Dimethyl sulphoxide (DMSO) extracts of 50 mg of pulverised barks were prepared using ultrasonication. The chromatographic separation was performed on an XB-C18 column packed with 2.6 μm particles. Gradient elution using an ammonium formate buffer and methanol as organic modifier over 26 min was based on non-chiral separation of the diastereoisomers and the high solvent selectivity of methanol. Post column UV detection was performed at 250 nm and 330 nm. Fluorescence detection was performed using 330 nm for excitation and 420 nm for emission., Results: The optimised HPLC method facilitates efficient separation and quantification of the four major alkaloids in 26 min with a limit of quantification of 5 μg/g from 50 mg bark sample., Conclusion: The optimised HPLC method offers a simple and efficient quantification of the four major alkaloids. Copyright © 2017 John Wiley & Sons, Ltd., (Copyright © 2017 John Wiley & Sons, Ltd.)

Every plant species on Earth interacts in some way or another with microorganisms and it is well known that certain forms of symbiosis between different organisms can drive evolution. Within some clades of Rubiaceae (coffee family), a specific plant-bacteria interaction exists in which non-pathological endophytes are present in the leaves of their hosts. It is hypothesized that the bacterial endophytes, either alone or by interacting with the host, provide chemical protection against herbivory or pathogens by producing toxic or otherwise advantageous secondary metabolites. If the bacteria indeed have a direct beneficial influence on their hosts, it is reasonable to assume that the endophytes may increase the fitness of their hosts and therefore it is probable that their presence also has an influence on the long-term evolution of the particular plant lineages. In this study, the possible origin in time of non-nodulated bacterial leaf symbiosis in the Vanguerieae tribe of Rubiaceae is elucidated and dissimilarities in evolutionary dynamics between species with endophytes versus species without are investigated. Bacterial leaf symbiosis is shown to have most probably originated in the Late Miocene, a period when the savannah habitat is believed to have expanded on the African continent and herbivore pressure increased. The presence of bacterial leaf endophytes appears to be restricted to Old World lineages so far. Plant lineages with leaf endophytes show a significantly higher speciation rate than plant lineages without endophytes, while there is only a small difference in extinction rate. The transition rate shows that evolving towards having endophytes is twice as fast as evolving towards not having endophytes, suggesting that leaf symbiosis must be beneficial for the host plants. We conclude that the presence of bacterial leaf endophytes may also be an important driver for speciation of host plants., (Copyright © 2017 Elsevier Inc. All rights reserved.)

Standard Sanger chloroplast markers provide limited information to resolve species level relationships within plants, in particular within large genera. Figs (Ficus L., Moraceae) compose one of the 50 largest genera of angiosperms with ∼750 species occurring in the tropics and subtropics worldwide. Figs, in addition to being a keystone food resource in rainforests, are well-known for the mutualistic interactions with their pollinating wasps. It is regarded as a model system for understanding co-evolution dating back more than 75million years. However, despite significant taxon sampling, combinations of low copy nuclear, nuclear ribosomal and chloroplast regions have not been able to confidently resolve relationships among major groups of figs. Using a high throughput sequencing approach we attempted to resolve the major lineages of Ficus based on plastome data. In this study, we show that the use of a de novo assembled plastome from within the genus provides less ambiguity and higher coverage across the 59 Ficus and 6 outgroup plastome assemblies compared to using the nearest available reference plastome outside the genus resulting in improved resolution and higher support of the phylogenetic relationships within Ficus inferred from plastome data. Chloroplast genome data confidently resolved relationships among major groups of figs and largely support current understanding based on nuclear sequence data including passively pollinated Neotropical section Pharmacosycea as sister lineage to all other Ficus. However, conflicts between the new plastome topology and previous nuclear studies are observed for both individual species as well as relationships among some sections at deeper levels. Conflicts could be caused by lack of resolution in the nuclear data or may indicate potential cyto-nuclear discordance as previously observed in an African lineage of Ficus., (Copyright © 2017 Elsevier Inc. All rights reserved.)

Considerable inter- and intraspecific variation with respect to the quantity and composition of plant natural products exists. The processes that drive this variation remain largely unknown. Understanding which factors determine chemical diversity has the potential to shed light on plant defenses against herbivores and diseases and accelerate drug discovery. For centuries, Cinchona alkaloids were the primary treatment of malaria. Using Cinchona calisaya as a model, we generated genetic profiles of leaf samples from four plastid (trnL-F, matK, rps16, and ndhF) and one nuclear (ITS) DNA regions from twenty-two C. calisaya stands sampled in the Yungas region of Bolivia. Climatic and soil parameters were characterized and bark samples were analyzed for content of the four major alkaloids using HPLC-UV to explore the utility of evolutionary history (phylogeny) in determining variation within species of these compounds under natural conditions. A significant phylogenetic signal was found for the content of two out of four major Cinchona alkaloids (quinine and cinchonidine) and their total content. Climatic parameters, primarily driven by changing altitude, predicted 20.2% of the overall alkaloid variation, and geographical separation accounted for a further 9.7%. A clade of high alkaloid producing trees was identified that spanned a narrow range of altitudes, from 1,100 to 1,350 m. However, climate expressed by altitude was not a significant driver when accounting for phylogeny, suggesting that the chemical diversity is primarily driven by phylogeny. Comparisons of the relative effects of both environmental and genetic variability in determining plant chemical diversity have scarcely been performed at the genotypic level. In this study we demonstrate there is an essential need to do so if the extensive genotypic variation in plant biochemistry is to be fully understood.

The well-being of the global human population rests on provisioning services delivered by 12% of the Earth's ∼400,000 plant species 1 . Plant utilization by humans is influenced by species traits 2-4 , but it is not well understood which traits underpin different human needs 5 . Here, we focus on palms (Arecaceae), one of the most economically important plant groups globally 6 , and demonstrate that provisioning services related to basic needs, such as food and medicine, show a strong link to fundamental functional and geographic traits. We integrate data from 2,201 interviews on plant utilization from three biomes in South America-spanning 68 communities, 43 ethnic groups and 2,221 plant uses-with a dataset of 4 traits (leaf length, stem volume, fruit volume, geographic range size) and a species-level phylogeny 7 . For all 208 palm species occurring in our study area, we test for relations between their traits and perceived value. We find that people preferentially use large, widespread species rather than small, narrow-ranged species, and that different traits are linked to different uses. Further, plant size and geographic range size are stronger predictors of ecosystem service realization for palm services related to basic human needs than less-basic needs (for example, ritual). These findings suggest that reliance on plant size and availability may have prevented our optimal realization of wild-plant services, since ecologically rare yet functionally important (for example, chemically) clades may have been overlooked. Beyond expanding our understanding of how local people use biodiversity in mega-diverse regions, our trait- and phylogeny-based approach helps to understand the processes that underpin ecosystem service realization, a necessary step to meet societal needs in a changing world with a growing human population 5,8 .

Bolivia is one of the most biologically diverse countries on the planet. Between the Andes and the Amazon drainage basin spans the Yungas, a vast forested region shown to be extremely species rich in macro-organisms. However, it remains unclear whether this high diversity is also reflected in microbial diversity. Here we assess the genetic, taxonomic and functional diversity of root-associated fungi surrounding Cinchona calisaya trees, a typical element of the intermediate altitudes of the Bolivian Yungas. We determine the relative effects of edaphic properties, climate, and geography in regulating fungal community assembly. We show that α-diversity for these fungal communities was similar to temperate and arid ecosystems, averaging 90.1 operational taxonomic units (OTUs) per sample, with reads predominantly assigned to the Ascomycota phylum and with a saprotrophic lifestyle. ß-diversity was calculated as the distance-decay rate, and in contrast to α-diversity, was exceptionally high with a rate of -0.407. Soil properties (pH and P) principally regulated fungal community assembly in an analogous manner to temperate environments, with pH and phosphorus explaining 7.8 and 7.2% of community variation respectively. Surprisingly, altitude does not influence community formation, and there is limited evidence that climate (precipitation and temperature) play a role. Our results suggest that sampling should be performed over a wide geographical and environmental range in order to capture the full root-associated fungal diversity in subtropical regions. This study sheds further light on the diversity and distribution of the world's "hidden biodiversity."