SMARTSNP, an R package for fast multivariate analyses of big genomic data

Abstract Principal component analysis (PCA) is a powerful tool for the analysis of population structure, a genetic property that is essential to understand the evolutionary processes driving biological diversification and (pre)historical colonizations, migrations and extinctions. In the current era of high‐throughput sequencing technologies, population structure can be quantified from scores of genetic markers across hundreds to thousands of genomes. However, these big genomic datasets pose substantial computing and analytical challenges. We present the r package smartsnp for fast and user‐friendly computation of PCA on single‐nucleotide polymorphism (SNP) data. Inspired by the current field‐standard software EIGENSOFT, smartsnp includes appropriate SNP scaling for genetic drift and allows projection of ancient samples onto a modern genetic space while also providing permutation‐based multivariate tests for population differences in genetic diversity (both location and dispersion). Our extensive benchmarks show that smartsnp's PCA is 2–4 times faster than EIGENSOFT's SMARTPCA algorithm across a wide range of sample and SNP sizes. All four smartsnp functions (smart_pca, smart_permanova, smart_permdisp and smart_mva) process datasets with up to 100 samples and 1 million simulated SNPs in less than 30 s and accurately recreate previously published SMARTPCA of ancient‐human and wolf genotypes. The package smartsnp provides fast and robust multivariate ordination and hypothesis testing for big genomic data that is also suitable for ancient and low‐coverage modern DNA. The simple implementation should appeal to biological conservation, evolutionary, ecological and (palaeo)genomic researchers, and be useful for phenotype, ancestry and lineage studies

Forecasting a Language Shift Based on Cellular Automata

Language extinction as a consequence of language shifts is a widespread social phenomenon that affects several million people all over the world today. An important task for social sciences research should therefore be to gain an understanding of language shifts, especially as a way of forecasting the extinction or survival of threatened languages, i.e., determining whether or not the subordinate language will survive in communities with a dominant and a subordinate language. In general, modeling is usually a very difficult task in the social sciences, particularly when it comes to forecasting the values of variables. However, the cellular automata theory can help us overcome this traditional difficulty. The purpose of this article is to investigate language shifts in the speech behavior of individuals using the methodology of the cellular automata theory. The findings on the dynamics of social impacts in the field of social psychology and the empirical data from language surveys on the use of Catalan in Valencia allowed us to define a cellular automaton and carry out a set of simulations using that automaton. The simulation results highlighted the key factors in the progression or reversal of a language shift and the use of these factors allowed us to forecast the future of a threatened language in a bilingual community.Cellular Automata, Computational Simulations, Language, Social Dynamics

Prospectiva de la llengua a Catalunya: simulació amb autòmats cel·lulars

L'artilce aborda l'aplicació d'eines informàtiques de simulació en l'àmbit psicosocial a la situació de la llengua a Catalunya per extreure'n escenaris de futur. En primer lloc, aborda el context metodològic de la simulació social amb autòmats cel·lulars. En segon lloc, s'aplica el mètode i el sistema als resultats de l''Enquesta d'Usos Lingüístics de Població 2008' i se n'extreuen resultats. Finalment, s'apunten algunes conclusions

A new species of Arrhopalites (Collembola, Symphypleona, Arrhopalitidae) from a cave on the Central East Iberian Peninsula

A new species of Collembola, Arrhopalites miravetensis, sp. nov., is described, from a karstic cave in the “Desierto de las Palmas” Nature Park, Castellón, Spain. The new species can be distinguished from all other species in the genus by the combination of the following characters: 2+2 pigmented eyes, rod-like anal appendage with two, relatively long, basal projections, small teeth present in both mucro edges and visible only from posterior view, winged circumanal setae, and no spines on the head. The new species belongs to the A. pygmaeus-group s. str. This species could be a troglophile species as the most of Arrhopalites, although there are too troglobite species

Forecasting a language shift based on cellular automata

Language extinction as a consequence of language shifts is a widespread social phenomenon that affects several million people all over the world today. An important task for social sciences research should therefore be to gain an understanding of language shifts, especially as a way of forecasting the extinction or survival of threatened languages, i.e., determining whether or not the subordinate language will survive in communities with a dominant and a subordinate language. In general, modeling is usually a very difficult task in the social sciences, particularly when it comes to forecasting the values of variables. However, the cellular automata theory can help us overcome this traditional difficulty. The purpose of this article is to investigate language shifts in the speech behavior of individuals using the methodology of the cellular automata theory. The findings on the dynamics of social impacts in the field of social psychology and the empirical data from language surveys on the use of Catalan in Valencia allowed us to define a cellular automaton and carry out a set of simulations using that automaton. The simulation results highlighted the key factors in the progression or reversal of a language shift and the use of these factors allowed us to forecast the future of a threatened language in a bilingual community

Statistical Language Backs Conservatism in Climate-Change Assessments

The scientific evidence for anthropogenic climate change is empirically settled, but communicating it to nonscientific audiences remains challenging. To be explicit about the state of knowledge on climate science, the Intergovernmental Panel on Climate Change (IPCC) has adopted a vocabulary that ranks climate findings through certainty-calibrated qualifiers of confidence and likelihood. In this article, we quantified the occurrence of knowns and unknowns about “The Physical Science Basis” of the IPCC's Fifth Assessment Report by counting the frequency of calibrated qualifiers. We found that the tone of the IPCC's probabilistic language is remarkably conservative (mean confidence is medium, and mean likelihood is 66%–100% or 0–33%), and emanates from the IPCC recommendations themselves, complexity of climate research, and exposure to politically motivated debates. Leveraging communication of uncertainty with overwhelming scientific consensus about anthropogenic climate change should be one element of a wider reform, whereby the creation of an IPCC outreach working group could enhance the transmission of climate science to the panel's audiences.Salvador Herrando-Pérez, Corey J A Bradshaw, Stephan Lewandowsky, David R Vieite

Un Camino de Aprendizaje hacia la Profesión Docente

Agrupar una experiencia de aprendizaje a través del Máster en Profesorado de Educación Secundaria Obligatoria, Bachillerato, Formación Profesional y Enseñanzas de Idiomas, Artísticas y Deportivas que ofrece la Facultad de Educación de la Universidad de Zaragoza, dar una visión general. Fue un camino dirigido sobre todo a alcanzar las competencias necesarias para ejercer la docencia. En este camino relaciono mi experiencia laboral con lo aprendido, como un aprendizaje significativo. Hablo de la Formación Profesional, de su relación con el aprendizaje de competencias y de la evolución que está experimentando para ser parte de un mundo tecnológico donde la innovación y la creatividad tiene un peso crucial. Describo actividades realizadas que me han resultado especialmente inspiradoras por lo aprendido en ellas, por lo prácticas que me resultaron y porque el hacerlas incrementó mi motivación.También se destaca la importancia que tiene para la profesión docente, seguir formándose a lo largo de la vida.<br /

Girardia festae (Borelli, 1898) (Platyhelminthes: Tricladida: Dugesiidae): Distribution extension in a high-altitude lake from Colombia

We revise the Neotropical distribution of Girardia festae (Platyhelminthes, Dugesiidae) following a new record in a Colombian high-altitude lake. G. festae is a freshwater planarian known mainly in the Andean Cordillera from Venezuela to Argentina. The species' key reproductive features include: ventral testes, bottle-like penis papilla, and sperm ducts joining to the penis bulb latero-dorsally.Fil: Brusa, Francisco. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata; Argentina. Universidad Nacional de La Plata. Facultad de Ciencias Naturales y Museo. División de Zoología Invertebrados; ArgentinaFil: Negrete, Lisandro Hector Luis. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata; Argentina. Universidad Nacional de La Plata. Facultad de Ciencias Naturales y Museo. División de Zoología Invertebrados; ArgentinaFil: Herrera Martínez, Yimy. Universidad Pedagógica Nacional de Colombia.; ColombiaFil: Herrando Pérez, Salvador. University of Adelaide; Australia. Bioestudios Saganta; Españ