Association between Rosacea, Environmental Factors, and Facial Cutaneous Dysbiosis

Background: To investigate the microbiome composition in individuals with and without rosacea and correlate findings to individual factors that may affect facial cutaneous and enteric microbiome composition. Methods: Participants with and without rosacea (as determined by a board-certified dermatologist) were surveyed regarding factors that may affect the facial cutaneous/enteric microbiome. Microbiome samples were collected, analyzed for 16S sequences, and mapped to an optimized version of existing databases. R was used to perform Mann-Whitney/Kruskal-Wallis test for categorical comparisons. Correlation between two continuous variables was determined with linear regression models. Primary Component Analysis (PCoA) plots employed Monte Carlo permutation test to estimate p-values. All p-values are adjusted for multiple comparisons with the false discovery rate (FDR algorithm) using Benjamini-Hochberg. Results: 84 individuals with rosacea and 44 controls were evaluated. Individuals with rosacea were more likely to currently own pets (p = 0.029) and consume more alcohol (p = 0.006). Absolute bacteria abundance were similar in facial cutaneous (p = 0.36) and enteral microbiome (p = 0.29). Facial cutaneous microbiome showed significantly decreased richness and evenness (OTU: p = 0.019; Shannon: p = 0.049) and a three to four-fold decrease in abundance of 8 distinct cutaneous bacterial genera in rosacea. Enteral microbiome analysis showed significant reduction in abundance of Ruminococcaceae (FDR = 0.002) and Blautia (FDR < 0.001) and increase in Prevotellaceae (FDR = 0.024) in rosacea. Conclusion: Environmental factors may alter relative abundances of specific microbial genera and lead to microbiome diversity. Further studies with increased sample sizes and higher severity cases may further elucidate the role of dysbiosis in rosacea.

The Bioindication Evaluation of Ground Beetles (Coleoptera: Carabidae) in Three Forest Biotopes in the Southern Part of Central Slovakia

Ground beetles (Carabidae) were used to evaluate the bio indication environmental incidence. The ground beetle material (2,341 individuals, 30 species) was collected between 2015 and 2017 using pitfall traps in three types of forest habitats with different disturbance rates. The comparison of carabid’s sensitivity as bio indicators has been evaluated by using three methods: (i) community index of ground beetles (IKS), (ii) ellipsoid biovolume (EV) and (iii) flight ability of the carabids. Using the Monte Carlo permutation test, we did not record the statistically significant changes in IKS values, nor does a change in the representation of carabids in the bioindicative group A, E and R. On the contrary, we confirmed the statistically significant changes in the average values of ellipsoid biovolume in biotopes and between biotopes (the Friedman and Kruskal-Wallis test -ANOVA (p-value = 0.00)). A higher number of macropterous species were recorded in biotopes with high disturbance as compared to the biotopes with low disturbance.

Geography shapes the phylogeny of frailejones (Espeletiinae Cuatrec., Asteraceae): a remarkable example of recent rapid radiation in sky islands

BackgroundThe páramo ecosystem, located above the timberline in the tropical Andes, has been the setting for some of the most dramatic plant radiations, and it is one of the world’s fastest evolving and most diverse high-altitude ecosystems. Today 144+ species of frailejones (subtribe Espeletiinae Cuatrec., Asteraceae) dominate the páramo. Frailejones have intrigued naturalists and botanists, not just for their appealing beauty and impressive morphological diversity, but also for their remarkable adaptations to the extremely harsh environmental conditions of the páramo. Previous attempts to reconstruct the evolutionary history of this group failed to resolve relationships among genera and species, and there is no agreement regarding the classification of the group. Thus, our goal was to reconstruct the phylogeny of the frailejones and to test the influence of the geography on it as a first step to understanding the patterns of radiation of these plants.MethodsField expeditions in 70 páramos of Colombia and Venezuela resulted in 555 collected samples from 110 species. Additional material was obtained from herbarium specimens. Sequence data included nrDNA (ITS and ETS) and cpDNA (rpl16), for an aligned total of 2,954 bp. Fragment analysis was performed with AFLP data using 28 primer combinations and yielding 1,665 fragments. Phylogenies based on sequence data were reconstructed under maximum parsimony, maximum likelihood and Bayesian inference. The AFLP dataset employed minimum evolution analyses. A Monte Carlo permutation test was used to infer the influence of the geography on the phylogeny.ResultsPhylogenies reconstructed suggest that most genera are paraphyletic, but the phylogenetic signal may be misled by hybridization and incomplete lineage sorting. A tree with all the available molecular data shows two large clades: one of primarily Venezuelan species that includes a few neighboring Colombian species; and a second clade of only Colombian species. Results from the Monte Carlo permutation test suggests a very strong influence of the geography on the phylogenetic relationships. Venezuelan páramos tend to hold taxa that are more distantly-related to each other than Colombian páramos, where taxa are more closely-related to each other.ConclusionsOur data suggest the presence of two independent radiations: one in Venezuela and the other in Colombia. In addition, the current generic classification will need to be deeply revised. Analyses show a strong geographic structure in the phylogeny, with large clades grouped in hotspots of diversity at a regional scale, and in páramo localities at a local scale. Differences in the degrees of relatedness between sympatric species of Venezuelan and Colombian páramos may be explained because of the younger age of the latter páramos, and the lesser time for speciation of Espeletiinae in them.

Morphological forms of two macrophytes (yellow water-lily and arrowhead) along velocity gradient

We investigated morphological response of yellow water-lily and arrowhead to water velocity gradient in the lowland Wełna river (Western Poland). Percentage cover of floating and submerged forms of yellow water-lily and arrowhead had been measured in randomly selected sites of 16 m2. We analyzed 62 stands of Nuphar lutea and 80 stands of Sagittaria sagittifolia using 13 environmental variables. Redundancy analysis (RDA), the Monte Carlo permutation test, ranges of chemical and hydrological data, Generalized Additive Models (GAMs) and transfer function were used to describe reaction of investigated species to water velocity. Among the analyzed parameters of microhabitats with the floating and submerged forms of investigated species, velocity, pH, water colour, hydration and organic matter in bottom sediments were statistically significant. In S. sagittifolia case, the velocity was the most important parameter, while in N. lutea — both velocity and content of organic matter in river substrate were statistically significant.

Testing the island rule: primates as a case study

The island rule states that after island colonization, larger animals tend to evolve reduced body sizes and smaller animals increased sizes. Recently, there has been disagreement about how often, if ever, this rule applies in nature, and much of this disagreement stems from differences in the statistical tests employed. This study shows, how different tests of the island rule assume different null hypotheses, and that these rely on quite different biological assumptions. Analysis and simulation are then used to quantify the biases in the tests. Many widely used tests are shown to yield false support for the island rule when island and mainland evolution are indistinguishable, and so a Monte Carlo permutation test is introduced that avoids this problem. It is further shown that tests based on independent contrasts lack power to detect the island rule under certain conditions. Finally, a complete reanalysis is presented of recent data from primates. When head–body length is used as the measure of body size, reports of the island rule are shown to stem from methodological artefacts. But when skull length or body mass are used, all tests agree that the island rule does hold in primates.

Kapcom: A Program for the Comparison of Kappa Coefficients Obtained from the Same Sample of Observations

A PC program for comparing two kappa coefficients of agreement obtained from the same sample of observations is described. The program employs a Monte Carlo permutation test to assess the statistical significance of the difference between kappa values.