Extinction risk predictions for the world's flowering plants to support their conservation

More than 70% of all vascular plants lack conservation status assessments. We aimed to address this shortfall in knowledge of species extinction risk by using the World Checklist of Vascular Plants to generate the first comprehensive set of predictions for a large clade: angiosperms (flowering plants, c. 330 000 species). We used Bayesian Additive Regression Trees (BART) to predict the extinction risk of all angiosperms using predictors relating to range size, human footprint, climate, and evolutionary history and applied a novel approach to estimate uncertainty of individual species-level predictions. From our model predictions, we estimate 45.1% of angiosperm species are potentially threatened with a lower bound of 44.5% and upper bound of 45.7%. Our species-level predictions, with associated uncertainty estimates, do not replace full global, or regional Red List assessments, but can be used to prioritise predicted threatened species for full Red List assessment and fast-track predicted non-threatened species for Least Concern assessments. Our predictions and uncertainty estimates can also guide fieldwork, inform systematic conservation planning and support global plant conservation efforts and targets.

Re-evaluating the importance of threatened species in maintaining global phytoregions

Anthropogenic introductions are known to be changing the structure of global phytogeographical regions (phytoregions), but previous studies have been limited by incomplete or biased data sets that are likely to underestimate the importance of threatened species. In this work, we analyse a comprehensive data set of all known species and their occurrences (at botanical country resolution) to quantify the impact of potential future extinction scenarios. We used Infomap, a network-based community detection algorithm, to generate phytoregional delineations for six species-distribution scenarios (native, introduced and extinctions of species that are either documented as threatened or likely to be threatened, as well as combinations thereof). We compared the numbers and sizes of phytoregions to characterise the amount and spatial distribution of changes in global phytoregions under each scenario. Extinctions of species that are predicted to be threatened had a greater homogenising effect on phytoregions than introductions, and there was some evidence that introductions may even mitigate the homogenisation caused by extinctions, though this interaction is complex. This research provides the first evidence that the loss of threatened species would have significant ramifications for global phytoregions and demonstrates the need to consider extinction processes in studies of anthropogenic effects on biodiversity patterns.

rWCVP: a companion R package for the World Checklist of Vascular Plants

The World Checklist of Vascular Plants (WCVP) is an extremely valuable resource that is being used to address many fundamental and applied questions in plant science, conservation, ecology and evolution. However, databases of this size require data manipulation skills that pose a barrier to many potential users. Here, we present rWCVP, an open-source R package that aims to facilitate the use of the WCVP by providing clear, intuitive functions to execute many common tasks. These functions include taxonomic name reconciliation, geospatial integration, mapping and generation of multiple different summaries of the WCVP in both data and report format. We have included extensive documentation and tutorials, providing step-by-step guides that are accessible even to users with minimal programming experience. rWCVP is available on cran and GitHub.

Evidence-based guidelines for automated conservation assessments of plant species

Assessing species' extinction risk is vital to setting conservation priorities. However, assessment endeavors, such as those used to produce the IUCN Red List of Threatened Species, have significant gaps in taxonomic coverage. Automated assessment (AA) methods are gaining popularity to fill these gaps. Choices made in developing, using, and reporting results of AA methods could hinder their successful adoption or lead to poor allocation of conservation resources. We explored how choice of data cleaning type and level, taxonomic group, training sample, and automation method affect performance of threat status predictions for plant species. We used occurrences from the Global Biodiversity Information Facility (GBIF) to generate assessments for species in 3 taxonomic groups based on 6 different occurrence-based AA methods. We measured each method's performance and coverage following increasingly stringent occurrence cleaning. Automatically cleaned data from GBIF performed comparably to occurrence records cleaned manually by experts. However, all types of data cleaning limited the coverage of AAs. Overall, machine-learning-based methods performed well across taxa, even with minimal data cleaning. Results suggest a machine-learning-based method applied to minimally cleaned data offers the best compromise between performance and species coverage. However, optimal data cleaning, training sample, and automation methods depend on the study group, intended applications, and expertise.

Madagascar’s extraordinary biodiversity: Evolution, distribution, and use

Madagascar’s biota is hyperdiverse and includes exceptional levels of endemicity. We review the current state of knowledge on Madagascar’s past and current terrestrial and freshwater biodiversity by compiling and presenting comprehensive data on species diversity, endemism, and rates of species description and human uses, in addition to presenting an updated and simplified map of vegetation types. We report a substantial increase of records and species new to science in recent years; however, the diversity and evolution of many groups remain practically unknown (e.g., fungi and most invertebrates). Digitization efforts are increasing the resolution of species richness patterns and we highlight the crucial role of field- and collections-based research for advancing biodiversity knowledge and identifying gaps in our understanding, particularly as species richness corresponds closely to collection effort. Phylogenetic diversity patterns mirror that of species richness and endemism in most of the analyzed groups. We highlight humid forests as centers of diversity and endemism because of their role as refugia and centers of recent and rapid radiations. However, the distinct endemism of other areas, such as the grassland-woodland mosaic of the Central Highlands and the spiny forest of the southwest, is also biologically important despite lower species richness. The documented uses of Malagasy biodiversity are manifold, with much potential for the uncovering of new useful traits for food, medicine, and climate mitigation. The data presented here showcase Madagascar as a unique “living laboratory” for our understanding of evolution and the complex interactions between people and nature. The gathering and analysis of biodiversity data must continue and accelerate if we are to fully understand and safeguard this unique subset of Earth’s biodiversity.

Madagascar’s extraordinary biodiversity: Threats and opportunities

Madagascar’s unique biota is heavily affected by human activity and is under intense threat. Here, we review the current state of knowledge on the conservation status of Madagascar’s terrestrial and freshwater biodiversity by presenting data and analyses on documented and predicted species-level conservation statuses, the most prevalent and relevant threats, ex situ collections and programs, and the coverage and comprehensiveness of protected areas. The existing terrestrial protected area network in Madagascar covers 10.4% of its land area and includes at least part of the range of the majority of described native species of vertebrates with known distributions (97.1% of freshwater fishes, amphibians, reptiles, birds, and mammals combined) and plants (67.7%). The overall figures are higher for threatened species (97.7% of threatened vertebrates and 79.6% of threatened plants occurring within at least one protected area). International Union for Conservation of Nature (IUCN) Red List assessments and Bayesian neural network analyses for plants identify overexploitation of biological resources and unsustainable agriculture as the most prominent threats to biodiversity. We highlight five opportunities for action at multiple levels to ensure that conservation and ecological restoration objectives, programs, and activities take account of complex underlying and interacting factors and produce tangible benefits for the biodiversity and people of Madagascar.

Harnessing Large-Scale Herbarium Image Datasets Through Representation Learning

The mobilization of large-scale datasets of specimen images and metadata through herbarium digitization provide a rich environment for the application and development of machine learning techniques. However, limited access to computational resources and uneven progress in digitization, especially for small herbaria, still present barriers to the wide adoption of these new technologies. Using deep learning to extract representations of herbarium specimens useful for a wide variety of applications, so-called "representation learning," could help remove these barriers. Despite its recent popularity for camera trap and natural world images, representation learning is not yet as popular for herbarium specimen images. We investigated the potential of representation learning with specimen images by building three neural networks using a publicly available dataset of over 2 million specimen images spanning multiple continents and institutions. We compared the extracted representations and tested their performance in application tasks relevant to research carried out with herbarium specimens. We found a triplet network, a type of neural network that learns distances between images, produced representations that transferred the best across all applications investigated. Our results demonstrate that it is possible to learn representations of specimen images useful in different applications, and we identify some further steps that we believe are necessary for representation learning to harness the rich information held in the worlds' herbaria.

Plants used traditionally as antimalarials in Latin America: Mining the tree of life for potential new medicines

ETHNOPHARMACOLOGICAL RELEVANCE

Malaria remains a serious and challenging disease. Traditional antimalarial medicines are largely based on plants, and ethnopharmacological research has inspired the development of antimalarial pharmaceuticals such as artemisinin. Antimalarial drug resistance is an increasing problem in Plasmodium species, and new therapeutic strategies to combat malaria are needed. Although the number of malaria cases has been decreasing in Latin America, malaria remains a significant threat in many regions. Local people in Latin America have been using numerous plant species to treat malaria, some of which have been scientifically studied, but many others have not.

AIM OF THE STUDY

Our principal objective is to harness ethnobotanical data on species used traditionally to treat malaria, combined with phylogenetic approaches, to understand how ethnobotany could help identify plant genera as potential sources of new medicines.

MATERIALS AND METHODS

Plants used to treat malaria in Latin America were compiled from published and grey literature, unpublished data, and herbarium specimens. Initial assessment of potentially important species/genera/families included compiling the number of species used within the genus, the number of use reports per genus and species, and the geographic distribution of their use. The analysis of taxonomic distribution of species reported as antimalarial in Latin America (excluding the Southern Cone) was conducted, to determine which genera and families with reputed antimalarial properties are over-represented, and phylogenetic analyses were performed to identify if there was evidence for antimalarial species being dispersed/clustered throughout the tree or at its tips. This approach enabled 'hot-nodes' in certain families to be identified, to predict new genera with potential antimalarial properties.

RESULTS

Over 1000 plant species have been used to treat malaria in Latin America, of which over 600 species were cited only once. The genera with the highest number of antimalarial species were Aspidosperma, Solanum, Piper, Croton and Aristolochia. In terms of geographic distribution, the most widely used genera were Aspidosperma, Momordica, Cinchona, Senna and Stachytarpheta. Significant phylogenetic signal was detected in the distribution of native species used for malaria, analysed in a genus-level phylogenetic framework. The eudicot and magnoliidae lineages were over-represented, while monocots were not.

CONCLUSION

Analysis of ethnobotanical use reports in a phylogenetic framework reveals the existence of hot nodes for malaria across the Latin American flora. We demonstrate how species and genera currently lacking such reports could be pinpointed as of potential interest based on their evolutionary history. Extending this approach to other regions of the world and other diseases could accelerate the discovery of novel medicines and enhance healthcare in areas where new therapeutic strategies are needed.

Botanical Monography in the Anthropocene

Unprecedented changes in the Earth's biota are prompting urgent efforts to describe and conserve plant diversity. For centuries, botanical monographs - comprehensive systematic treatments of a family or genus - have been the gold standard for disseminating scientific information to accelerate research. The lack of a monograph compounds the risk that undiscovered species become extinct before they can be studied and conserved. Progress towards estimating the Tree of Life and digital information resources now bring even the most ambitious monographs within reach. Here, we recommend best practices to complete monographs urgently, especially for tropical plant groups under imminent threat or with expected socioeconomic benefits. We also highlight the renewed relevance and potential impact of monographies for the understanding, sustainable use, and conservation of biodiversity.

Harnessing the potential of integrated systematics for conservation of taxonomically complex, megadiverse plant groups

The value of natural history collections for conservation science research is increasingly recognized, despite their well-documented limitations in terms of taxonomic, geographic, and temporal coverage. Specimen-based analyses are particularly important for tropical plant groups for which field observations are scarce and potentially unreliable due to high levels of diversity-amplifying identification challenges. Specimen databases curated by specialists are rich sources of authoritatively identified, georeferenced occurrence data, and such data are urgently needed for large genera. We compared entries in a monographic database for the large Neotropical genus Myrcia in 2007 and 2017. We classified and quantified differences in specimen records over this decade and determined the potential impact of these changes on conservation assessments. We distinguished misidentifications from changes due to taxonomic remodeling and considered the effects of adding specimens and georeferences. We calculated the potential impact of each change on estimates of extent of occurrence (EOO), the most frequently used metric in extinction-risk assessments of tropical plants. We examined whether particular specimen changes were associated with species for which changes in EOO over the decade were large enough to change their conservation category. Corrections to specimens previously misidentified or lacking georeferences were overrepresented in such species, whereas changes associated with taxonomic remodeling (lumping and splitting) were underrepresented. Among species present in both years, transitions to less threatened status outnumbered those to more threatened (8% vs 3%, respectively). Species previously deemed data deficient transitioned to threatened status more often than to not threatened (10% vs 7%, respectively). Conservation scientists risk reaching unreliable conclusions if they use specimen databases that are not actively curated to reflect changing knowledge.

The use and misuse of herbarium specimens in evaluating plant extinction risks

Herbarium specimens provide verifiable and citable evidence of the occurrence of particular plants at particular points in space and time, and are vital resources for assessing extinction risk in the tropics, where plant diversity and threats to plants are greatest. We reviewed approaches to assessing extinction risk in response to the Convention on Biological Diversity's Global Strategy for Plant Conservation Target 2: an assessment of the conservation status of all known plant species by 2020. We tested five alternative approaches, using herbarium-derived data for trees, shrubs and herbs in five different plant groups from temperate and tropical regions. All species were previously fully assessed for the IUCN Red List. We found significant variation in the accuracy with which different approaches classified species as threatened or not threatened. Accuracy was highest for the machine learning model (90%) but the least data-intensive approach also performed well (82%). Despite concerns about spatial, temporal and taxonomic biases and uncertainties in herbarium data, when specimens represent the best available evidence for particular species, their use as a basis for extinction risk assessment is appropriate, necessary and urgent. Resourcing herbaria to maintain, increase and disseminate their specimen data is essential to guide and focus conservation action.This article is part of the theme issue 'Biological collections for understanding biodiversity in the Anthropocene'.

Tuning reaction products by constrained optimisation

An effective means of defining optimisation criteria for self-optimising criteria is described, applicable to situations where a compromise is sought between several competing objectives.

Volume of the Sexually Dimorphic Nucleus of the Preoptic Area in Rats Exposed to a Maternal High Fat Diet

Mice and rats exposed to a maternal diet high in fat have an increased risk of reproductive system tumors later in life. To test whether a part of the hypothalamus associated with sex differentiation, the sexually dimorphic nucleus of the preoptic area (SDN-POA), might be involved, this nucleus was measured in the offspring of female rats on a high, or low fat diet during pregnancy and nursing. The measurements showed that the SDN-POA was smaller in female offspring exposed to a maternal high fat diet than in female offspring exposed to a maternal low fat diet. This could result in endocrine disturbances and thus provide a possible explanation for the linkage between high fat exposure prenatally and increased female reproductive system cancer.

Multigenerational effects of dietary fat carcinogenesis in mice

The possibility of multigenerational transmission of a carcinogenic effect from exposure to a maternal diet high in fat was tested in mice. Diets with 2.6 or 29% fat (by weight) were fed to strain CD-1 mice during pregnancy. The female offspring were raised on a control diet (10% fat), mated, and continued on the control diet through pregnancy. Their female offspring were raised to terminal illness and autopsied. The total number of reproductive system tumors, pituitary tumors, and metastases was increased in the offspring with ancestral exposure to high dietary fat but to a lesser extent than had been reported previously for direct prenatal exposure to high maternal dietary fat. Because previous work has given evidence against germ cell transmission, a hypothesis based on a maternal effect was offered to explain the multigenerational carcinogenesis. These results have implications for epidemiological studies.

Intensity of multigenerational carcinogenesis from diethylstilbestrol in mice

Mice exposed prenatally to diethylstilbestrol (DES-exposed mice) can transmit a carcinogenic influence to the next generation (DES-lineage mice) when mated to control mice. The persistence of this effect was studied one generation further (DES-lineage-2 mice) by mating DES-lineage female mice to control males. The interaction of maternal dietary fat levels with DES was also tested by feeding high and low levels of dietary fat during the pregnancies that produced the final two generations. DES-lineage-2 mice, exposed to low or high fat maternal diets, had significantly more tumors than control mice with corresponding dietary fat exposure. The frequency of tumors in DES-lineage-2 mice was not significantly lower than in DES-lineage mice from a previous experiment. Thus, the multigenerational effect of DES is relatively intense in mice. If this type of carcinogenesis can occur in the human population, it poses a major threat to future generations.

Combination oral antioxidant supplementation reduces blood pressure

1. Hypertension affects 30% of adults and low intakes of antioxidants have been associated with increased risk of hypertension and cardiovascular disease. To investigate the effect of short-term high-dose antioxidant supplementation on blood pressure in hypertensive and normotensive outpatients, we undertook a randomized, double-blind, crossover design placebo-controlled study. 2. Forty subjects were recruited from medical outpatient clinics, of whom 38 completed the study. Twenty-one were attending for treatment of hypertension and 17 were normotensive, attending for minor gastrointestinal complaints. Subjects were randomly assigned to receive either 8 weeks placebo followed by 2 weeks washout then 8 weeks antioxidants or vice versa. The combination of antioxidants consisted of 200 mg of zinc sulphate, 500 mg of ascorbic acid, 600 mg of alpha-tocopherol (sodium succinate salt) and 30 mg of beta-carotene daily. 3. Systolic blood pressure fell at the end of the antioxidant phase compared with the placebo phase both in subjects receiving anti-hypertensive therapy (P < 0.01) and those who were normotensive (P = 0.067). Circulating levels of beta-carotene and alpha-tocopherol increased in all subjects during supplementation (P < 0.01) and urine nitrite increased in hypertensive patients (P < 0.05). 4. Short-term oral high-dose combination antioxidant therapy reduces blood pressure, possibly via increased availability of nitric oxide. This study may have implications for the innovative use of antioxidants as an adjunct to anti-hypertensive therapy.

Stage of susceptibility to carcinogenicity of prenatal dietary fat exposure tested by blastocyst transfer

A previous experiment with exposure of female mice to a diet high in fat from 4 weeks of age through to the end of pregnancy demonstrated a substantial increase in the frequency of reproductive system tumors in their female offspring. Over this wide period of exposure, one or more specific periods of sensitivity to the carcinogenic effects of dietary fat should exist. To test whether a high fat diet affects maternal germ cells and/or zygote development through to blastocyst formation, two blastocyst transfer experiments were performed. Blastocysts from a dam on high fat were transferred to a pseudopregnant dam on low fat. The reverse type of transfer was performed for contrast. These experiments did not reveal any significant effect of dietary fat on maternal germ cells or zygote development.

The effects of intravenous antioxidants in patients with septic shock

Oxidative stress is implicated in septic shock. We investigated the effect of intravenous antioxidant therapy on antioxidant status, lipid peroxidation, hemodynamics and nitrite in patients with septic shock. Thirty patients randomly received either antioxidants (n-acetylcysteine 150 mg/kg for 30 min then 20 mg/kg/h plus bolus doses of 1 g ascorbic acid and 400 mg alpha-tocopherol) or 5% dextrose. Basal vitamin C was low and redox-reactive iron was elevated in all patients. In the 16 patients receiving antioxidants, vitamin C increased (p = .0002) but total antioxidant capacity was unaffected. Lipid peroxides were elevated in all patients but did not increase further in the patients receiving antioxidants. Plasma total nitrite also increased (p = .007) in the antioxidant group. Heart rate increased in patients receiving antioxidants at 60 min (p = .018) and 120 min (p = .004). Cardiac index also increased at 60 min (p = .007) and 120 min (p = .05). Systemic vascular resistance index decreased at 120 min in the antioxidant treated patients (p = .003). The effect of antioxidants on hemodynamic variables has not previously been reported. Antioxidant administration may be a useful adjunct to conventional approaches in the management of septic shock.

Congestive cardiac failure following laxative withdrawal

We report the case of a 60-year-old woman who presented with weakness and hypokalaemia due to excessive use of laxatives. When the laxatives were withdrawn, she developed severe congestive cardiac failure requiring treatment with a diuretic and angiotensin-converting enzyme inhibitor. There was no underlying cardiac abnormality, and these drugs were eventually stopped with no recurrence of the cardiac failure. The possible mechanisms of heart failure following laxative withdrawal is discussed.

Effects of fostering on the increased tumor incidence produced by a maternal diet high in fat

Previous work has shown that female offspring of mice fed a diet high in fat during pregnancy developed more reproductive system tumors and metastases than offspring of pregnant mice fed a low-fat diet. The purpose of the current experiment was to use fostering to test whether the sensitive period for this cancer effect involved the early postnatal period. Strain CD-1 female mice were placed on a diet of 2.6% fat or 29% fat from corn oil at 4 weeks of age and bred at 6-10 weeks of age. The special diets were discontinued at birth, and litters from dams that had been fed the low-fat diet were fostered to dams previously fed the high-fat diet, and vice versa. The offspring were raised to terminal illness and autopsied. There was no difference in age at terminal illness or in the number of the common nonreproductive system tumors between the two fostered groups. Tumor metastases appeared in both groups. However, the combined frequency of reproductive tract tumors and mammary tumors was significantly higher in mice exposed prenatally to a low-fat diet and fostered to dams that had consumed a high-fat diet during pregnancy than in mice exposed prenatally to a high-fat diet and fostered to a dam fed a low-fat diet. Thus the most sensitive period for a cancer effect from high fat was early postnatal, even though the special diets had been discontinued at birth. This matches the period of greatest sensitivity for sex differentiation of the hypothalamus.

Regulation of nitric oxide synthase activity in cultured human endothelial cells: effect of antioxidants

Nitric oxide release is induced in many cells, including vascular endothelium, as part of the host response to inflammation. Nitric oxide synthase activity is increased in patients with sepsis, associated with increased oxidant demands and decreased antioxidant protection. We used a human vascular endothelial cell line to investigate the influence of antioxidants on nitric oxide synthase activity. Cells were cultured to confluence and incubated with interferon gamma, tumor necrosis factor, and lipopolysaccharide in the combined presence of the antioxidants ascorbic acid, Trolox, catalase, or superoxide dismutase, singly and in combination, for 48 h. Additionally, some cells were incubated with hypoxanthine-xanthine oxidase or a nitric oxide donor. Nitric oxide synthase activity was upregulated by cytokine exposure (p < .0005). Ascorbic acid and superoxide dismutase/ catalase resulted in decreased enzyme activity (p < .05). Superoxide anion release from xanthine oxidase caused increased activity (p < .05) and exogenous nitric oxide tended to suppress synthase activity. We suggest that antioxidants scavenge superoxide anion, enabling feedback inhibition of nitric oxide synthase activity by nitric oxide, and thus reducing enzyme activity. Exogenous nitric oxide also has a similar effect. Superoxide generation suppresses this feedback inhibition. This study has important implications in patients with sepsis in whom nitric oxide synthase inhibitor therapy is currently under investigation.

Increased reproductive tract tumors in the female offspring of mice fed a high fat diet during the fetal stage of pregnancy

In a previous study, female offspring of mice consuming a high fat diet throughout pregnancy developed reproductive system tumors and tumor metastases with a frequency significantly higher than offspring of mice on a low fat diet. To test for the sensitive period more specifically, the feeding of a high fat diet was restricted to the fetal period of pregnancy in the present experiment. The offspring were raised to terminal illness and autopsied. The total number of ovarian, uterine and mammary tumors was 14 among 74 mice exposed prenatally to low fat and 34 among 75 mice exposed prenatally to high fat (P < 0.002). In mice exposed to high fat during the fetal period 13 tumors produced metastases, but no metastases were identified after exposure to low fat (P < 0.001). Thus, a maternal diet high in fat during the fetal period of pregnancy was sufficient to increase reproductive system tumors and metastases in the female offspring.

Total antioxidant capacity and lipid peroxidation during liver transplantation

1. We assessed plasma total antioxidant capacity using enhanced chemiluminescence and plasma lipid peroxides in eight patients undergoing orthotopic liver transplantation and 26 healthy control subjects. 2. The antioxidant capacity of plasma decreased significantly on reperfusion of the donor liver (P < 0.05) during liver transplantation, although levels were not lower in patients than in control subjects. 3. Pre-reperfusion antioxidant capacity correlated negatively with the concentration of lipid peroxidation products appearing in the plasma by the end of the transplant (P < 0.02), but did not correlate with vitamin A or E concentrations. 4. This study provides evidence of oxidant stress during liver transplantation, as shown by antioxidant utilization associated with increased lipid peroxidation.