Effect of urban vs. rural residence on the association between atopy and wheeze in Latin America: findings from a case-control analysis.

BACKGROUND: The association between atopy and asthma is attenuated in non-affluent populations, an effect that may be explained by childhood infections such as geohelminths. OBJECTIVE: To investigate the association between atopy and wheeze in schoolchildren living in urban and rural areas of Ecuador and examine the effects of geohelminths on this association. METHODS: We performed nested case-control studies among comparable populations of schoolchildren living in rural communities and urban neighbourhoods in the Province of Esmeraldas, Ecuador. We detected geohelminths in stool samples, measured recent wheeze and environmental exposures by parental questionnaire, and atopy by specific IgE (sIgE) and skin prick test (SPT) reactivity to aeroallergens. RESULTS: Atopy, particularly sIgE to house dust mite (HDM), was more strongly associated with recent wheeze in urban than rural schoolchildren: (urban, adj. OR 5.19, 95% CI 3.37-8.00, P < 0.0001; rural, adj. OR 1.81, 95%CI 1.09-2.99, P = 0.02; interaction, P < 0.001). The population fractions of wheeze attributable to atopy were approximately two-fold greater in urban schoolchildren: SPT to any allergen (urban 23.5% vs. rural 10.1%), SPT to HDM (urban 18.5% vs. rural 9.6%), and anti-HDM IgE (urban 26.5% vs. rural 10.5%), while anti-Ascaris IgE was related to wheeze in a high proportion of rural (49.7%) and urban (35.4%) children. The association between atopy and recent wheeze was attenuated by markers of geohelminth infections. CONCLUSIONS: Our data suggest that urban residence modifies the association between HDM atopy and recent wheeze, and this effect is explained partly by geohelminth infections

A Natural Language Processing Pipeline to extract phenotypic data from formal taxonomic descriptions with a focus on flagellate plants

Assembling large-scale phenotypic datasets for evolutionary and biodiversity studies of plants can be extremely difficult and time consuming. New semi-automated Natural Language Processing (NLP) pipelines can extract phenotypic data from taxonomic descriptions, and their performance can be enhanced by incorporating information from ontologies, like the Plant Ontology (PO) and the Plant Trait Ontology (TO). These ontologies are powerful tools for comparing phenotypes across taxa for large-scale evolutionary and ecological analyses, but they are largely focused on terms associated with flowering plants. We describe a bottom-up approach to identify terms from flagellate plants (including bryophytes, lycophytes, ferns, and gymnosperms) that can be added to existing plant ontologies. We first parsed a large corpus of electronic taxonomic descriptions using the Explorer of Taxon Concepts tool (http://taxonconceptexplorer.org/) and identified flagellate plant specific terms that were missing from the existing ontologies. We extracted new structure and trait terms, and we are currently incorporating the missing structure terms to the PO and modifying the definitions of existing terms to expand their coverage to flagellate plants. We will incorporate trait terms to the TO in the near future

Chemocoding as an identification tool where morphological- and DNA-based methods fall short:Inga as a case study

This is the author accepted manuscript. The final version is available from Wiley via the DOI in this recordThe need for species identification and taxonomic discovery has led to the development of innovative technologies for large‐scale plant identification. DNA barcoding has been useful, but fails to distinguish among many species in species‐rich plant genera, particularly in tropical regions. Here, we show that chemical fingerprinting, or ‘chemocoding’, has great potential for plant identification in challenging tropical biomes. Using untargeted metabolomics in combination with multivariate analysis, we constructed species‐level fingerprints, which we define as chemocoding. We evaluated the utility of chemocoding with species that were defined morphologically and subject to next‐generation DNA sequencing in the diverse and recently radiated neotropical genus Inga (Leguminosae), both at single study sites and across broad geographic scales. Our results show that chemocoding is a robust method for distinguishing morphologically similar species at a single site and for identifying widespread species across continental‐scale ranges. Given that species are the fundamental unit of analysis for conservation and biodiversity research, the development of accurate identification methods is essential. We suggest that chemocoding will be a valuable additional source of data for a quick identification of plants, especially for groups where other methods fall short

The role of plant secondary metabolites in shaping regional and local plant community assembly

The outstanding diversity of Amazonian forests is predicted to be the result of several processes. While tree lineages have dispersed repeatedly across the Amazon, interactions between plants and insects may be the principal mechanism structuring the communities at local scales. Using metabolomic and phylogenetic approaches, we investigated the patterns of historical assembly of plant communities across the Amazon based on the Neotropical genus of trees Inga (Leguminosae) at four, widely separated sites. Our results show a low degree of phylogenetic structure and a mixing of chemotypes across the whole Amazon basin, suggesting that although biogeography may play a role, the metacommunity for any local community in the Amazon is the entire basin. Yet, local communities are assembled by ecological processes, with the suite of Inga at a given site more divergent in chemical defences than expected by chance Synthesis. To our knowledge, this is the first study to present metabolomic data for nearly 100 species in a diverse Neotropical plant clade across the whole Amazonia. Our results demonstrate a role for plant–herbivore interactions in shaping the clade's community assembly at a local scale, and suggest that the high alpha diversity in Amazonian tree communities must be due in part to the interactions of diverse tree lineages with their natural enemies providing a high number of niche dimension

Tracking of Host Defenses and Phylogeny During the Radiation of Neotropical Inga-Feeding Sawflies (Hymenoptera; Argidae)

This is the final version. Available from Frontiers Media via the DOI in this recordCoevolutionary theory has long predicted that the arms race between plants and herbivores is a major driver of host selection and diversification. At a local scale, plant defenses contribute significantly to the structure of herbivore assemblages and the high alpha diversity of plants in tropical rain forests. However, the general importance of plant defenses in host associations and divergence at regional scales remains unclear. Here, we examine the role of plant defensive traits and phylogeny in the evolution of host range and species divergence in leaf-feeding sawflies of the family Argidae associated with Neotropical trees in the genus Inga throughout the Amazon, the Guiana Shield and Panama. Our analyses show that the phylogenies of both the sawfly herbivores and their Inga hosts are congruent, and that sawflies radiated at approximately the same time, or more recently than their Inga hosts. Analyses controlling for phylogenetic effects show that the evolution of host use in the sawflies associated with Inga is better correlated with Inga chemistry than with Inga phylogeny, suggesting a pattern of delayed host tracking closely tied to host chemistry. Finally, phylogenetic analyses show that sister species of Inga-sawflies are dispersed across the Neotropics, suggesting a role for allopatric divergence and vicariance in Inga diversification. These results are consistent with the idea that host defensive traits play a key role not only in structuring the herbivore assemblages at a single site, but also in the processes shaping host association and species divergence at a regional scale

Effects of environment on human cytokine responses during childhood in the tropics: role of urban versus rural residence.

BACKGROUND: Environment may have a key role in the development of the immune system in childhood and environmental exposures associated with rural residence may explain the low prevalence of allergic and autoimmune diseases in the rural tropics. We investigated the effects of urban versus rural residence on the adaptive immune response in children living in urban and rural areas in a tropical region of Latin America. METHODS: We recruited school children in either rural communities in the Province of Esmeraldas or in urban neighborhoods in the city of Esmeraldas, Ecuador. We collected data on environmental exposures by questionnaire and on intestinal parasites by examination of stool samples. Peripheral blood leukocytes (PBLs) in whole blood were stimulated with superantigen, parasite antigens and aeroallergens and IFN-γ, IL-5, IL-10, IL-13, and IL-17 were measured in supernatants. RESULTS: We evaluated 440 school children; 210 living in rural communities and 230 in the city of Esmeraldas. Overall, urban children had greater access to piped water (urban 98.7 % vs. rural 1.9 %), were more likely to have a household bathroom (urban 97.4 % vs. rural 54.8 %), and were less likely to be infected with soil-transmitted helminth infections (urban 20.9 % vs. rural 73.5 %). Generally, detectable levels of cytokines were more frequent in blood from children living in urban than rural areas. Urban residence was associated with a significantly greater frequency of IL-10 production spontaneously (adjusted OR 2.56, 95 % CI 1.05-6.24) and on stimulation with Ascaris (adj. OR 2.5, 95 % CI 1.09-5.79) and house dust mite (adj. 2.24, 95 % CI 1.07-4.70) antigens. Analysis of effects of environmental exposures on SEB-induced IL-10 production within urban and rural populations showed that some environmental exposures indicative of poor hygiene (urban - higher birth order, A. lumbricoides infection; rural - no bathroom, more peri-domiciliary animals, and living in a wood/bamboo house) were associated with elevated IL-10. CONCLUSIONS: In our study population, the immune response of children living in an urban environment was associated more frequently with the production of the immune regulatory cytokine, IL-10. Some factors related to poor hygiene and living conditions were associated with elevated IL-10 production within urban and rural populations

Nutrients cause grassland biomass to outpace herbivory

Human activities are transforming grassland biomass via changing climate, elemental nutrients, and herbivory. Theory predicts that food-limited herbivores will consume any additional biomass stimulated by nutrient inputs ('consumer-controlled'). Alternatively, nutrient supply is predicted to increase biomass where herbivores alter community composition or are limited by factors other than food ('resource-controlled'). Using an experiment replicated in 58 grasslands spanning six continents, we show that nutrient addition and vertebrate herbivore exclusion each caused sustained increases in aboveground live biomass over a decade, but consumer control was weak. However, at sites with high vertebrate grazing intensity or domestic livestock, herbivores consumed the additional fertilization-induced biomass, supporting the consumer-controlled prediction. Herbivores most effectively reduced the additional live biomass at sites with low precipitation or high ambient soil nitrogen. Overall, these experimental results suggest that grassland biomass will outstrip wild herbivore control as human activities increase elemental nutrient supply, with widespread consequences for grazing and fire risk

Comprehensive phylogenomic time tree of bryophytes reveals deep relationships and uncovers gene incongruences in the last 500 million years of diversification

Premise: Bryophytes form a major component of terrestrial plant biomass, structuring ecological communities in all biomes. Our understanding of the evolutionary history of hornworts, liverworts, and mosses has been significantly reshaped by inferences from molecular data, which have highlighted extensive homoplasy in various traits and repeated bursts of diversification. However, the timing of key events in the phylogeny, patterns, and processes of diversification across bryophytes remain unclear. Methods: Using the GoFlag probe set, we sequenced 405 exons representing 228 nuclear genes for 531 species from 52 of the 54 orders of bryophytes. We inferred the species phylogeny from gene tree analyses using concatenated and coalescence approaches, assessed gene conflict, and estimated the timing of divergences based on 29 fossil calibrations. Results: The phylogeny resolves many relationships across the bryophytes, enabling us to resurrect five liverwort orders and recognize three more and propose 10 new orders of mosses. Most orders originated in the Jurassic and diversified in the Cretaceous or later. The phylogenomic data also highlight topological conflict in parts of the tree, suggesting complex processes of diversification that cannot be adequately captured in a single gene-tree topology. Conclusions: We sampled hundreds of loci across a broad phylogenetic spectrum spanning at least 450 Ma of evolution; these data resolved many of the critical nodes of the diversification of bryophytes. The data also highlight the need to explore the mechanisms underlying the phylogenetic ambiguity at specific nodes. The phylogenomic data provide an expandable framework toward reconstructing a comprehensive phylogeny of this important group of plantsFunding was provided by the NSF collaborative project “Building a Comprehensive Evolutionary History of Flagellate Plants” (DEB #1541506 to J.G. Burleigh, E.C. Davis, S.F. McDaniel, and E.B. Sessa, and #1541545 to M von Konrat). B.G. acknowledges DEB‐1753811. J.C.V.A. acknowledges the Canada Research Chair (950‐232698); the CRNSG‐RGPIN 05967–2016 and the Canadian Foundation for Innovation (projects 36781, 39135). The authors thank the two anonymous reviewers and the Associate Editor for their constructive comments on previous versions of the manuscrip