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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.

• 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.

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.

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.

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. Niche conservatism may link community assembly to biogeographic history. Seido et al. find that the geographic origins of locally co-occurring trees explain 50% of the variation in species’ hydraulic niches, linking local community structure to species distributions millions of years before dispersal.

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.

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.

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.

The effects of historical land use on tropical forest must be examined to understand present forest characteristics and to plan conservation strategies. We compared the effects of past land use, topography, soil type, and other environmental variables on tree species composition in a subtropical wet forest in the Luquillo Mountains, Puerto Rico. The study involved stems ≥10 cm diameter measured at 130 cm above the ground, within the 16-ha Luquillo Forest Dynamics Plot (LFDP), and represents the forest at the time Hurricane Hugo struck in 1989. Topography in the plot is rugged, and soils are variable. Historical documents and local residents described past land uses such as clear-felling and selective logging followed by farming, fruit and coffee production, and timber stand improvement in the forest area that now includes the LFDP. These uses ceased 40-60 yr before the study, but their impacts could be differentiated by percent canopy cover seen in aerial photographs from 1936. Using these photographs, we defined four historic cover classes within the LFDP. These ranged from cover class 1, the least tree-covered area in 1936, to cover class 4, with the least intensive historic land use (selective logging and timber stand improvement). In 1989, cover class 1 had the lowest stem density and proportion of large stems, whereas cover class 4 had the highest basal area, species richness, and number of rare and endemic species. Ordination of tree species composition (89 species, 13 167 stems) produced arrays that primarily corresponded to the four cover classes (i.e., historic land uses). The ordination arrays corresponded secondarily to soil characteristics and topography. Natural disturbances (hurricanes, landslides, and local treefalls) affected tree composition, but these effects did not correlate with the major patterns of species distributions on the plot. Thus, it appears that forest development and natural disturbance have not masked the effects of historical land use in this tropical forest, and that past land use was the major influence on the patterns of tree composition in the plot in 1989. The least disturbed stand harbors more rare and endemic species, and such stands should be protected.

Many of the species classified in Psychotria L. subg. Heteropsychotria Steyerm. (Rubiaceae), including the species of Psychotria ser. Axillares (Hook. f.) Steyerm., have been shown to belong to Palicourea Aubl. based on morphological and molecular characters. This section is now treated as Palicourea sect. Axillares (Hook. f.) Borhidi, and includes 14 species found from southern Central America through the Andes of northwestern and western South America with a center of diversity in eastern Colombia and western Venezuela. This section is characterized by the combination of laminar, well-developed, bilobed stipules and mostly capitate, pseudoaxillary or sometimes terminal, mostly sessile inflorescences with numerous well-developed bracts that enclose the flowers but without enlarged involucral bracts. It is circumscribed differently here than it is by Borhidi. The nomenclatural summary, key, and diagnostic discussions that separate the species included here are based on several new taxonomic circumscriptions. No infraspecific taxa are recognized in Pal. axillaris (Sw.) Borhidi, but one of its varieties from Venezuela is raised to species status as Pal. villipila (Steyerm.) C. M. Taylor. The circumscription of Pal. rosacea (Steyerm.) Borhidi is expanded, and four species are newly described here: Pal. aristata C. M. Taylor from the Andes of southern Ecuador, Pal. quibdoana C. M. Taylor from northwestern Colombia, Pal. santanderiana C. M. Taylor from the Andes of eastern Colombia, and Pal. winfriedii C. M. Taylor from northern Venezuela.