A Better Understanding of the Ecological Conditions for Leontopodium alpinum Cassini in the Swiss Alps

Although Leontopodium alpinum is considered to be threatened in many countries, only limited scientific information about its autecology is available. In this study, we aim to define the most important ecological factors which influence the distribution of L. alpinum in the Swiss Alps. These were assessed at the national scale using species distribution models based on topoclimatic predictors and at the community scale using exhaustive plant inventories. The latter were analysed using hierarchical clustering and principal component analysis, and the results were interpreted using ecological indicator values. Leontopodium alpinum was found almost exclusively on base-rich bedrocks (limestone and ultramafic rocks). The species distribution models showed that available moisture (dry regions, mostly in the Inner Alps), elevation (mostly above 2,000 m a.s.l.) and slope (mostly >30°) were the most important predictors. The relevés showed that L. alpinum is present in a wide range of plant communities, all subalpine-alpine open grasslands, with a low grass cover. As a light-demanding and short species, L. alpinum requires light at ground level; hence, it can only grow in open, nutrient-poor grasslands. These conditions are met in dry conditions (dry, summer-warm climate, rocky and draining soil, south-facing aspect and/or steep slope), at high elevations, on oligotrophic soils and/or on windy ridges. Base-rich soils appear to also be essential, although it is still unclear whether this corresponds to physiological or ecological (lower competition) requirements

Density-based hierarchical clustering of pyro-sequences on a large scale—the case of fungal ITS1

Motivation: Analysis of millions of pyro-sequences is currently playing a crucial role in the advance of environmental microbiology. Taxonomy-independent, i.e. unsupervised, clustering of these sequences is essential for the definition of Operational Taxonomic Units. For this application, reproducibility and robustness should be the most sought after qualities, but have thus far largely been overlooked. Results: More than 1 million hyper-variable internal transcribed spacer 1 (ITS1) sequences of fungal origin have been analyzed. The ITS1 sequences were first properly extracted from 454 reads using generalized profiles. Then, otupipe, cd-hit-454, ESPRIT-Tree and DBC454, a new algorithm presented here, were used to analyze the sequences. A numerical assay was developed to measure the reproducibility and robustness of these algorithms. DBC454 was the most robust, closely followed by ESPRIT-Tree. DBC454 features density-based hierarchical clustering, which complements the other methods by providing insights into the structure of the data. Availability: An executable is freely available for non-commercial users at ftp://ftp.vital-it.ch/tools/dbc454. It is designed to run under MPI on a cluster of 64-bit Linux machines running Red Hat 4.x, or on a multi-core OSX system. Contact: [email protected] or [email protected]

Annual Risk of Tuberculous Infection Using Different Methods in Communities with a High Prevalence of TB and HIV in Zambia and South Africa

BACKGROUND: The annual risk of tuberculous infection (ARTI) is a key epidemiological indicator of the extent of transmission in a community. Several methods have been suggested to estimate the prevalence of tuberculous infection using tuberculin skin test data. This paper explores the implications of using different methods to estimate prevalence of infection and ARTI. The effect of BCG vaccination on these estimates is also investigated. METHODOLOGY/PRINCIPAL FINDINGS: Tuberculin surveys among school children in 16 communities in Zambia and 8 in South Africa (SA) were performed in 2005, as part of baseline data collection and for randomisation purposes of the ZAMSTAR study. Infection prevalence and ARTI estimates were calculated using five methods: different cut-offs with or without adjustments for sensitivity, the mirror method, and mixture analysis. A total of 49,835 children were registered for the surveys, of which 25,048 (50%) had skin tests done and 22,563 (90%) of those tested were read. Infection prevalence was higher in the combined SA than Zambian communities. The mirror method resulted in the least difference of 7.8%, whereas that estimated by the cut-off methods varied from 12.2% to 17.3%. The ARTI in the Zambian and SA communities was between 0.8% and 2.8% and 2.5% and 4.2% respectively, depending on the method used. In the SA communities, the ARTI was higher among the younger children. BCG vaccination had little effect on these estimates. CONCLUSIONS/SIGNIFICANCE: ARTI estimates are dependent on the calculation method used. All methods agreed that there were substantial differences in infection prevalence across the communities, with higher rates in SA. Although TB notification rates have increased over the past decades, the difference in cumulative exposure between younger and older children is less dramatic and a rise in risk of infection in parallel with the estimated incidence of active tuberculosis cannot be excluded

La filiacion y la fecundacion "in vitro"

Las tecnicas de reproduccion asistida no solo representan una solucion para ayudar a superar problemas de esterilidad, sino que su practica conlleva problemas eticos y juridicos. Esta Tesis analiza los problemas que plantea la fecundacion "in vitro", desde el punto de vista de la filiacion, para determinar la paternidad y maternidad cuando se utilizan los gametos de la pareja o de un tercero. Desde este punto de vista, se estudian la situacion juridica del tercero -llamado donante- y de las madres subrogadas, asi como las acciones de filiacion Tambien se examina la problematica que plantea la congelacion de semen y embriones, al poder un hombre engendrar un hijo despues de muerto. Entre las fuentes que se analizan estan los principales informes extranjeros que han estudiado la problematica de estas tecnicas, asi como el Informe especial de..

Data from: Predicting spatial patterns of plant species richness: a comparison of direct macroecological and species stacking modelling approaches

PLEASE NOTE, THESE DATA ARE ALSO REFERRED TO IN TWO OTHER PUBLICATIONS. PLEASE SEE http://dx.doi.org/10.1111/j.1365-2486.2008.01766.x AND http://dx.doi.org/10.1111/2041-210X.12222 FOR MORE INFORMATION. Aim: This study compares the direct, macroecological approach (MEM) for modelling species richness (SR) with the more recent approach of stacking predictions from individual species distributions (S-SDM). We implemented both approaches on the same dataset and discuss their respective theoretical assumptions, strengths and drawbacks. We also tested how both approaches performed in reproducing observed patterns of SR along an elevational gradient. Location: Two study areas in the Alps of Switzerland. Methods: We implemented MEM by relating the species counts to environmental predictors with statistical models, assuming a Poisson distribution. S-SDM was implemented by modelling each species distribution individually and then stacking the obtained prediction maps in three different ways – summing binary predictions, summing random draws of binomial trials and summing predicted probabilities – to obtain a final species count. Results: The direct MEM approach yields nearly unbiased predictions centred around the observed mean values, but with a lower correlation between predictions and observations, than that achieved by the S-SDM approaches. This method also cannot provide any information on species identity and, thus, community composition. It does, however, accurately reproduce the hump-shaped pattern of SR observed along the elevational gradient. The S-SDM approach summing binary maps can predict individual species and thus communities, but tends to overpredict SR. The two other S-SDM approaches – the summed binomial trials based on predicted probabilities and summed predicted probabilities – do not overpredict richness, but they predict many competing end points of assembly or they lose the individual species predictions, respectively. Furthermore, all S-SDM approaches fail to appropriately reproduce the observed hump-shaped patterns of SR along the elevational gradient. Main conclusions: Macroecological approach and S-SDM have complementary strengths. We suggest that both could be used in combination to obtain better SR predictions by following the suggestion of constraining S-SDM by MEM predictions

Data from: Predicting spatial patterns of plant species richness: a comparison of direct macroecological and species stacking modelling approaches

PLEASE NOTE, THESE DATA ARE ALSO REFERRED TO IN TWO OTHER PUBLICATIONS. PLEASE SEE http://dx.doi.org/10.1111/j.1365-2486.2008.01766.x AND http://dx.doi.org/10.1111/2041-210X.12222 FOR MORE INFORMATION. Aim: This study compares the direct, macroecological approach (MEM) for modelling species richness (SR) with the more recent approach of stacking predictions from individual species distributions (S-SDM). We implemented both approaches on the same dataset and discuss their respective theoretical assumptions, strengths and drawbacks. We also tested how both approaches performed in reproducing observed patterns of SR along an elevational gradient. Location: Two study areas in the Alps of Switzerland. Methods: We implemented MEM by relating the species counts to environmental predictors with statistical models, assuming a Poisson distribution. S-SDM was implemented by modelling each species distribution individually and then stacking the obtained prediction maps in three different ways – summing binary predictions, summing random draws of binomial trials and summing predicted probabilities – to obtain a final species count. Results: The direct MEM approach yields nearly unbiased predictions centred around the observed mean values, but with a lower correlation between predictions and observations, than that achieved by the S-SDM approaches. This method also cannot provide any information on species identity and, thus, community composition. It does, however, accurately reproduce the hump-shaped pattern of SR observed along the elevational gradient. The S-SDM approach summing binary maps can predict individual species and thus communities, but tends to overpredict SR. The two other S-SDM approaches – the summed binomial trials based on predicted probabilities and summed predicted probabilities – do not overpredict richness, but they predict many competing end points of assembly or they lose the individual species predictions, respectively. Furthermore, all S-SDM approaches fail to appropriately reproduce the observed hump-shaped patterns of SR along the elevational gradient. Main conclusions: Macroecological approach and S-SDM have complementary strengths. We suggest that both could be used in combination to obtain better SR predictions by following the suggestion of constraining S-SDM by MEM predictions

Flore vasculaire et communautés végétale du Bois de Chênes

A la suite des Journées de la biodiversité qui ont eu lieu en juin 2015, les différents documents, articles et bases de données concernant la flore du Bois de Chênes ont été réunis dans le but de dresser une liste aussi complète que possible des espèces et milieux naturels. Actuellement, 591 taxons sont connus sur les 2,13 km2 protégés, 482 ayant été observés durant les Journées de la biodiversité, dont 159 mentionnés pour la première fois et 36 autres confirmés après plus de 20 ans sans observation. Trente-sept espèces connues au Bois de Chênes sont considérées comme menacées en Suisse (CR, EN ou VU selon la Liste rouge). La surface abrite également 21 types de milieux naturels, plusieurs se déclinant en 2-3 associations. Douze milieux sont considérés comme menacés en Suisse selon la Liste rouge, la végétation ségétale (Caucalidion), les prairies à molinie (Molinion) et l’aulnaie noire (Alnion glutinosae) étant les plus intéressants. Malgré sa petite taille, le Bois de Chênes conserve une biodiversité floristique importante, comportant beaucoup de milieux et d'espèces devenus rares sur le Plateau. La poursuite des mesures de conservation mises en place, en particulier pour les marais, prairies maigres et adventices de cultures, est donc essentielle pour le maintien de cette richesse

Butterfly distribution and environmental data in the western Swiss Alps

Butterfly species (presence-absence records) and environmental data for each of the 192 plots. The Scherrer et al. (2018, Methods in Ecology and Evolution) paper uses the associated Dryas dataset of plant species distribution data and environmental predictors to compare a number of thresholding methods for stacked species distribution models (S-SDMs) and how to best evaluate them with an appropriate cross-validation framework. Subsets of these data have also been used in previous works by the same research group: Pellisier et al. (2012, Ecography), D’Amen et al. (2015, Global Ecology and Biogeography) and others (see full publication list under http://www.unil.ch/ecospat)

Variation in habitat suitability does not always relate to variation in species' plant functional traits

Habitat suitability models, which relate species occurrences to environmental variables, are assumed to predict suitable conditions for a given species. If these models are reliable, they should relate to change in plant growth and function. In this paper, we ask the question whether habitat suitability models are able to predict variation in plant functional traits, often assumed to be a good surrogate for a species' overall health and vigour. Using a thorough sampling design, we show a tight link between variation in plant functional traits and habitat suitability for some species, but not for others. Our contrasting results pave the way towards a better understanding of how species cope with varying habitat conditions and demonstrate that habitat suitability models can provide meaningful descriptions of the functional niche in some cases, but not in others