A target enrichment probe set for resolving phylogenetic relationships in the coffee family, Rubiaceae.

Premise: Rubiaceae is among the most species-rich plant families, as well as one of the most morphologically and geographically diverse. Currently available phylogenies have mostly relied on few genomic and plastid loci, as opposed to large-scale genomic data. Target enrichment provides the ability to generate sequence data for hundreds to thousands of phylogenetically informative, single-copy loci, which often leads to improved phylogenetic resolution at both shallow and deep taxonomic scales; however, a publicly accessible Rubiaceae-specific probe set that allows for comparable phylogenetic inference across clades is lacking. Methods: Here, we use publicly accessible genomic resources to identify putatively single-copy nuclear loci for target enrichment in two Rubiaceae groups: tribe Hillieae (Cinchonoideae) and tribal complex Palicoureeae+Psychotrieae (Rubioideae). We sequenced 2270 exonic regions corresponding to 1059 loci in our target clades and generated in silico target enrichment sequences for other Rubiaceae taxa using our designed probe set. To test the utility of our probe set for phylogenetic inference across Rubiaceae, we performed a coalescent-aware phylogenetic analysis using a subset of 27 Rubiaceae taxa from 10 different tribes and three subfamilies, and one outgroup in Apocynaceae. Results: We recovered an average of 75% and 84% of targeted exons and loci, respectively, per Rubiaceae sample. Probes designed using genomic resources from a particular subfamily were most efficient at targeting sequences from taxa in that subfamily. The number of paralogs recovered during assembly varied for each clade. Phylogenetic inference of Rubiaceae with our target regions resolves relationships at various scales. Relationships are largely consistent with previous studies of relationships in the family with high support (≥0.98 local posterior probability) at nearly all nodes and evidence of gene tree discordance. Discussion: Our probe set, which we call Rubiaceae2270x, was effective for targeting loci in species across and even outside of Rubiaceae. This probe set will facilitate phylogenomic studies in Rubiaceae and advance systematics and macroevolutionary studies in the family.

Use of Herbarium Voucher Specimens To Investigate Phytochemical Composition in Poisonous Plant Research.

Poisonous plants cause large losses to the livestock industry through death, reduced production efficiency, reproductive dysfunction, and compromised harvesting of rangeland and pasture forages. Research investigating poisonous plants is complex because there are hundreds of genera of toxic plants representing thousands of species. To investigate the effects of poisonous plants on livestock, a clear understanding of the taxonomic identity of the plant and the ability to collect the plant in sufficient quantities for scientific studies is required. Subsequently, the active principles must be defined and investigated in the taxa of interest to better predict risk and make recommendations to reduce losses. Herbaria are collections of preserved plant specimens and are an important resource in poisonous plant research. Voucher specimens have often been used in the identification of the plant for the experimental reproduction of suspected livestock poisoning associated with a spontaneous case. More recently, herbarium specimens have been used to investigate the chemical composition of toxic plants as well as the distribution of different chemotypes over the landscape. The primary purpose of this review is to highlight the chemical analysis of herbarium specimens in poisonous plant research.

Phylogenetic and geographic distribution of nickel hyperaccumulation in neotropical Psychotria.

PREMISE: Hyperaccumulation of heavy metals in plants has never been documented from Central America or Mexico. Psychotria grandis, P. costivenia, and P. glomerata (Rubiaceae) have been reported to hyperaccumulate nickel in the Greater Antilles, but they also occur widely across the neotropics. The goals of this research were to investigate the geographic distribution of hyperaccumulation in these species and explore the phylogenetic distribution of hyperaccumulation in this clade by testing related species. METHODS: Portable x-ray fluorescence (XRF) spectroscopy was used to analyze 565 specimens representing eight species of Psychotria from the Missouri Botanical Garden herbarium. RESULTS: Nickel hyperaccumulation was found in specimens of Psychotria costivenia ranging from Mexico to Costa Rica and in specimens of P. grandis from Guatemala to Ecuador and Venezuela. Among related species, nickel hyperaccumulation is reported for the first time in P. lorenciana and P. papantlensis, but no evidence of hyperaccumulation was found in P. clivorum, P. flava, or P. pleuropoda. Previous reports of hyperaccumulation in P. glomerata appear to be erroneous, resulting from taxonomic synonymy and specimen misidentification. CONCLUSIONS: Hyperaccumulation of nickel by Psychotria is now known to occur widely from southern Mexico through Central America to northwestern South America, including some areas not known to have ultramafic soils. Novel aspects of this research include the successful prediction of new hyperaccumulator species based on molecular phylogeny, use of XRF technology to nondestructively obtain elemental data from herbarium specimens, and documentation of previously unknown areas of ultramafic or nickel-rich soil based on such data.

1,8-Substituted anthraquinones, anthrones and bianthrones as potential non-azole leads against fungal infections.

The synthesis of a variety of 1,8-substituted anthraquinones, anthrones and bianthrones and their potential as antifungal agents is evaluated. Preliminary screening against Schizosaccharomyces pombe (S. pombe), a fission yeast, and Saccharomyces cerevisiae (S. cerevisiae), a budding yeast, is reported. Both these yeast species demonstrate close homologue to a number of pathogenic fungi.

Sensor systems for bacterial reactors: A new flavin-phenol composite film for the in situ voltammetric measurement of pH.

Monitoring pH within microbial reactors has become an important requirement across a host of applications ranging from the production of functional foods (probiotics) to biofuel cell systems. An inexpensive and scalable composite sensor capable of monitoring the pH within the demanding environments posed by microbial reactors has been developed. A custom designed flavin derivative bearing an electropolymerisable phenol monomer was used to create a redox film sensitive to pH but free from the interferences that can impede conventional pH systems. The film was integrated within a composite carbon-fibre-polymer laminate and was shown to exhibit Nernstian behaviour (55 mV/pH) with minimal drift and robust enough to operate within batch reactors.

Amazon plant diversity revealed by a taxonomically verified species list.

Recent debates on the number of plant species in the vast lowland rain forests of the Amazon have been based largely on model estimates, neglecting published checklists based on verified voucher data. Here we collate taxonomically verified checklists to present a list of seed plant species from lowland Amazon rain forests. Our list comprises 14,003 species, of which 6,727 are trees. These figures are similar to estimates derived from nonparametric ecological models, but they contrast strongly with predictions of much higher tree diversity derived from parametric models. Based on the known proportion of tree species in neotropical lowland rain forest communities as measured in complete plot censuses, and on overall estimates of seed plant diversity in Brazil and in the neotropics in general, it is more likely that tree diversity in the Amazon is closer to the lower estimates derived from nonparametric models. Much remains unknown about Amazonian plant diversity, but this taxonomically verified dataset provides a valid starting point for macroecological and evolutionary studies aimed at understanding the origin, evolution, and ecology of the exceptional biodiversity of Amazonian forests.

Determination of toxicity in rabbits and corresponding detection of monofluoroacetate in four Palicourea (Rubiaceae) species from the Amazonas state, Brazil.

Numerous monofluoroacetate (MFA)-containing plants in Brazil cause sudden death syndrome precipitated by exercise in livestock, which is characterized by loss of balance, ataxia, labored breathing, muscle tremors, and recumbence leading to death. Four species of Palicourea collected at six farms were tested for the presence of MFA and their toxicity to rabbits. Palicourea longiflora and Palicourea barraensis contained MFA and caused sudden death in the rabbits. Palicourea croceoides and Palicourea nitidella did not contain MFA and were not toxic to rabbits. P. longiflora and P. barraensis were collected at three farms with a history of sudden death in their cattle. This is the first report of toxicity in regard to these two species.

Problematic specimens turn out to be two undescribed species of Bignonia (Bignoniaceae).

Bignonia comprises 29 species of lianas characterized by eight phloem wedges, leaves usually 2-foliolate, mostly simple tendrils and opaque seed wings. The analysis of herbarium specimens in preparation for a taxonomic revision of the genus led to the recognition of two new species: (i) Bignonia cararensis from Costa Rica, characterized by a thyrse with lateral compound dichasia and lack of interpetiolar ridge, and (ii) Bignonia sanctae-crucis from Bolivia and Brazil, distinguishable by its membranous leaflets, membranous calyx and small fruits. We provide detailed descriptions, illustrations, distribution maps, initial conservation status assessments, and comparisons of the newly described taxa with closely related species.

Estimating species diversity and distribution in the era of Big Data: to what extent can we trust public databases?

AIM: Massive digitalization of natural history collections is now leading to a steep accumulation of publicly available species distribution data. However, taxonomic errors and geographical uncertainty of species occurrence records are now acknowledged by the scientific community - putting into question to what extent such data can be used to unveil correct patterns of biodiversity and distribution. We explore this question through quantitative and qualitative analyses of uncleaned versus manually verified datasets of species distribution records across different spatial scales. LOCATION: The American tropics. METHODS: As test case we used the plant tribe Cinchoneae (Rubiaceae). We compiled four datasets of species occurrences: one created manually and verified through classical taxonomic work, and the rest derived from GBIF under different cleaning and filling schemes. We used new bioinformatic tools to code species into grids, ecoregions, and biomes following WWF's classification. We analysed species richness and altitudinal ranges of the species. RESULTS: Altitudinal ranges for species and genera were correctly inferred even without manual data cleaning and filling. However, erroneous records affected spatial patterns of species richness. They led to an overestimation of species richness in certain areas outside the centres of diversity in the clade. The location of many of these areas comprised the geographical midpoint of countries and political subdivisions, assigned long after the specimens had been collected. MAIN CONCLUSION: Open databases and integrative bioinformatic tools allow a rapid approximation of large-scale patterns of biodiversity across space and altitudinal ranges. We found that geographic inaccuracy affects diversity patterns more than taxonomic uncertainties, often leading to false positives, i.e. overestimating species richness in relatively species poor regions. Public databases for species distribution are valuable and should be more explored, but under scrutiny and validation by taxonomic experts. We suggest that database managers implement easy ways of community feedback on data quality.

Phylogeny and generic limits in the sister tribes Psychotrieae and Palicoureeae (Rubiaceae): Evolution of schizocarps in Psychotria and origins of bacterial leaf nodules of the Malagasy species.

• Premise of the study: The pantropical, species-rich Psychotrieae and Palicoureeae are sister tribes of mostly drupe-bearing and nonbacterial leaf-nodulating species with problematic generic limits. This problem is more complicated in Psychotrieae due to the paraphyly of the genus Psychotria, the lack of diagnostic characters for some major lineages, and the poor sampling from some biodiversity hotspots. Schizocarps and bacterial leaf nodules have been used for recognizing formal groups in Psychotrieae, but their evolution and taxonomic value have not been studied using a robust phylogeny of the tribe.• Methods: We analyzed 287 samples from the entire ranges of the tribes, with particular emphasis on the Western Indian Ocean region, with the Bayesian Markov chain Monte Carlo method.• Key results: All allied Psychotria genera investigated are nested within a paraphyletic Psychotria. Schizocarps evolved independently two times within Psychotria, and one reversal back to the drupaceous condition is inferred. The Malagasy leaf-nodulated Psychotrieae (except Apomuria bullata) and the Comorian non-leaf-nodulated Psychotria conocarpa are nested within the (African) leaf-nodulated clade. Within Palicoureeae, Chassalia is paraphyletic with respect to Geophila sensu stricto, and the Malagasy Geophila gerrardii and the African Hymenocoleus are closely related.• Conclusions: A widely circumscribed Psychotria encompassing the entire Psychotrieae is supported. Within Psychotria, two separate origins of schizocarps from drupes, one reversal back to the drupaceous condition, and two independent origins of the Malagasy leaf-nodulated species are inferred. A new genus Puffia is described to accommodate Geophila gerrardii, and a narrow circumscription of Chassalia is adopted. Thirty-two new combinations, two lectotypifications, and 25 new names are presented.

Monofluoroacetate-containing plants that are potentially toxic to livestock.

Many plants worldwide contain monofluoroacetate and cause sudden death in livestock. These plants are primarily found in the southern continents of Africa, Australia, and South America, where they negatively affect livestock production. This review highlights past and current research investigating (1) the plants reported to contain monofluoroacetate and cause sudden death; (2) the mode of action, clinical signs, and pathology associated with poisoning by monofluoroacetate-containing plants; (3) chemical methods for the analysis of monofluoroacetate in plants; (4) the coevolution of native flora and fauna in Western Australia with respect to monofluoroacetate-containing plants; and (5) methods to mitigate livestock losses caused by monofluoroacetate-containing plants.

Detection of toxic monofluoroacetate in Palicourea species.

Numerous plant species worldwide including some Palicourea (Rubiaceae), Tanaecium (Bignoniaceae), and Amorimia (Malpighiaceae) species in Brazil cause sudden death and are known to contain monofluoroacetate (MFA). Two species of Palicourea, Palicourea aenofusca and Palicourea marcgravii, cause sudden death and are reported to contain MFA while other Palicourea species are reported to cause sudden death in livestock and are suspected to contain MFA due to the similarity in clinical signs. Using an HPLC-APCI-MS method to detect MFA, herbarium specimens representing 46 Palicourea taxa were screened for the presence of MFA. Additionally we screened five Psychotria taxa that are closely related to Palicourea species. Ten species of Palicourea were identified that contained MFA, two previously reported and eight newly reported here; these are closely related to each other, though some other related species did not contain MFA.

Fine-scale niche structure of Neotropical forests reflects a legacy of the Great American Biotic Interchange.

The tendency of species to retain their ancestral niches may link processes that determine community assembly with biogeographic histories that span geological time scales. Biogeographic history is likely to have had a particularly strong impact on Neotropical forests because of the influence of the Great American Biotic Interchange, which followed emergence of a land connection between North and South America ~3 Ma. Here we examine the community structure, ancestral niches and ancestral distributions of the related, hyperdiverse woody plant genera Psychotria and Palicourea (Rubiaceae) in Panama. We find that 49% of the variation in hydraulic traits, a strong determinant of community structure, is explained by species' origins in climatically distinct biogeographic regions. Niche evolution models for a regional sample of 152 species indicate that ancestral climatic niches are associated with species' habitat distributions, and hence local community structure and composition, even millions of years after dispersal into new geographic regions.

Diagnostic performance of rapid diagnostic tests versus blood smears for malaria in US clinical practice.

BACKGROUND: Approximately 4 million US travelers to developing countries are ill enough to seek health care, with 1500 malaria cases reported in the United States annually. The diagnosis of malaria is frequently delayed because of the time required to prepare malaria blood films and lack of technical expertise. An easy, reliable rapid diagnostic test (RDT) with high sensitivity and negative predictive value (NPV), particularly for Plasmodium falciparum, would be clinically useful. The objective of this study was to determine the diagnostic performance of a RDT approved by the US Food and Drug Administration compared with traditional thick and thin blood smears for malaria diagnosis. METHODS: This prospective study tested 852 consecutive blood samples that underwent thick and thin smears and blinded malaria RDTs at 3 hospital laboratories during 2003-2006. Polymerase chain reaction verified positive test results and discordant results. RESULTS: Malaria was noted in 95 (11%) of the 852 samples. The RDT had superior performance than the standard Giemsa thick blood smear (p = .003). The RDT's sensitivity for all malaria was 97% (92 of 95 samples), compared with 85% (81 of 95) for the blood smear, and the RDT had a superior NPV of 99.6%, compared with 98.2% for the blood smear (p = .001). The P. falciparum performance was excellent, with 100% rapid test sensitivity, compared with only 88% (65 of 74) by blood smear (p = .003). CONCLUSIONS: This operational study demonstrates that the US Food and Drug Administration-approved RDT for malaria is superior to a single set of blood smears performed under routine US clinical laboratory conditions. The most valuable clinical role of the RDT is in the rapid diagnosis or the exclusion of P. falciparum malaria, which is particularly useful in outpatient settings when evaluating febrile travelers.

Evolutionary time for dispersal limits the extent but not the occupancy of species' potential ranges in the tropical plant genus Psychotria (Rubiaceae).

Explaining the diversity in geographic range sizes among species is a central goal of ecological and evolutionary studies. We tested species age as an explanation of range size variation within a group of understory shrubs in the Neotropics (Psychotria subgenus Psychotria, Rubiaceae). We distinguish between range occupancy (filling an occupied area) and range extent (maximum distances dispersed). We used Bayesian relaxed-clock dating of molecular sequence data to estimate the relative age of species, and we used species distribution modeling to predict species' potential ranges. If the range sizes of species are limited by time for dispersal, we hypothesize that older species should have (1) larger realized range occupancies and realized range extents than younger species, (2) filled a greater proportion of their potential range occupancies, and (3) colonized a greater proportion of their potential range extents. We found (1) a significant but weak positive relationship between species age versus both realized range occupancy and realized range extent, (2) no relationship between species age and filling of potential range occupancies, but (3) that older species had colonized a significantly greater proportion of their potential range extents than younger species. Our results indicate that a time-for-dispersal effect can limit the extent of ranges of species but not necessarily their occupancies.