Simulation of genome-wide evolution under heterogeneous substitution models and complex multispecies coalescent histories

Genomic evolution can be highly heterogeneous. Here, we introduce a new framework to simulate genome-wide sequence evolution under a variety of substitution models that may change along the genome and the phylogeny, following complex multispecies coalescent histories that can include recombination, demographics, longitudinal sampling, population subdivision/species history, and migration. A key aspect of our simulation strategy is that the heterogeneity of the whole evolutionary process can be parameterized according to statistical prior distributions specified by the user. We used this framework to carry out a study of the impact of variable codon frequencies across genomic regions on the estimation of the genome-wide nonsynonymous/synonymous ratio. We found that both variable codon frequencies across genes and rate variation among sites and regions can lead to severe underestimation of the global dN/dS values. The program SGWE—Simulation of Genome-Wide Evolution—is freely available from http://code.google.com/p/sgwe-project/, including extensive documentation and detailed examples.Ministerio de Ciencia e Innovación | Ref. JCI-2011-1045

Characterization of Reticulate Networks Based on the Coalescent with Recombination

Phylogenetic networks aim to represent the evolutionary history of taxa. Within these, reticulate networks are explicitly able to accommodate evolutionary events like recombination, hybridization, or lateral gene transfer. Although several metrics exist to compare phylogenetic networks, they make several assumptions regarding the nature of the networks that are not likely to be fulfilled by the evolutionary process. In order to characterize the potential disagreement between the algorithms and the biology, we have used the coalescent with recombination to build the type of networks produced by reticulate evolution and classified them as regular, tree sibling, tree child, or galled trees. We show that, as expected, the complexity of these reticulate networks is a function of the population recombination rate. At small recombination rates, most of the networks produced are already more complex than regular or tree sibling networks, whereas with moderate and large recombination rates, no network fit into any of the standard classes. We conclude that new metrics still need to be devised in order to properly compare two phylogenetic networks that have arisen from reticulating evolutionary process

Argumentación o retórica, una de las piezas claves para la construcción de la realidad social

Este artículo busca mostrar que es la retórica, y no la argumentación, la prácticahumana decisiva en la construcción y sostenimiento de la realidad social. Es lacapacidad de persuadir a auditorios lo que constituye los principios rectores de lasinstituciones sociales, y no el debate crítico y argumentado de ideas. Para esto, enla primera parte se distinguirá entre argumentación y retórica. Se mostrará que enla argumentación prima la demostración de verdades, mientras que en la retórica,el consentimiento o persuasión de auditorios. Sobre esta idea, y desde las tesisdel filósofo del lenguaje John Searle acerca de la construcción de la realidad social,se mostrará que es el lenguaje persuasivo el que permite la constitución de laintencionalidad colectiva, y con ella, de los hechos institucionales, estos últimos,las unidades básicas de la realidad social. Brevemente, este artículo desarrollará elargumento: en tanto la realidad social se constituye en la intencionalidad colectiva, yla intencionalidad colectiva se forma a través del lenguaje retórico, la realidad socialse constituye en el lenguaje retórico

Characterization of phylogenetic networks with NetTest

<p>Abstract</p> <p>Background</p> <p>Typical evolutionary events like recombination, hybridization or gene transfer make necessary the use of phylogenetic networks to properly depict the evolution of DNA and protein sequences. Although several theoretical classes have been proposed to characterize these networks, they make stringent assumptions that will likely not be met by the evolutionary process. We have recently shown that the complexity of simulated networks is a function of the population recombination rate, and that at moderate and large recombination rates the resulting networks cannot be categorized. However, we do not know whether these results extend to networks estimated from real data.</p> <p>Results</p> <p>We introduce a web server for the categorization of explicit phylogenetic networks, including the most relevant theoretical classes developed so far. Using this tool, we analyzed statistical parsimony phylogenetic networks estimated from ~5,000 DNA alignments, obtained from the NCBI PopSet and Polymorphix databases. The level of characterization was correlated to nucleotide diversity, and a high proportion of the networks derived from these data sets could be formally characterized.</p> <p>Conclusions</p> <p>We have developed a public web server, <it>NetTest </it>(freely available from the software section at <url>http://darwin.uvigo.es</url>), to formally characterize the complexity of phylogenetic networks. Using NetTest we found that most statistical parsimony networks estimated with the program TCS could be assigned to a known network class. The level of network characterization was correlated to nucleotide diversity and dependent upon the intra/interspecific levels, although no significant differences were detected among genes. More research on the properties of phylogenetic networks is clearly needed.</p

Mejora en el proceso de empaque de chocolate en polvo en sobres de 20 gramos en una empresa de chocolates de la región

La actualización, cambio o compra de un nuevo equipo de producción es algo muy común dentro de las organizaciones que tienen como objetivo ser cada vez más competitivas en el mercado global; dichos equipos son fabricados bajo normas y estándares que cumplen con los reglamentos nacionales e internacionales para garantizar la calidad de sus productos el cuidado del medio ambiente y las personas, no obstante en ocasiones llegan desde fabrica con desajustes paramétricos que alteran el correcto desempeño de una línea productiva generando pérdidas significativas que ameritan un control inmediato garantizando la viabilidad del proyecto en términos económicos. El presente análisis busca optimizar, controlar y mejorar las variables que influyen en un equipo de empaque vertical de sobres de chocolate en polvo de 20 gramos donde por ser una nueva máquina que entra a la línea productiva carece de estandarización y mejoras que lleven a dicho proceso a la eficiencia y rentabilidad esperada al momento de su adquisición, vale la pena resaltar que actualmente se presentan una serie de inconvenientes que no solo afectan la rentabilidad del producto sino también la percepción y fidelización de los clientes por un producto que puede no salir en óptimas condiciones al mercado.The update, change or purchase of a new production equipment is something very common within organizations that aim to be increasingly competitive in the global market; such equipment is manufactured under norms and standards that comply with national and international regulations to ensure the quality of their products, the care of the environment and people, however sometimes they arrive from the factory with parametric mismatches that alter the correct performance of a production line generating significant losses that merit immediate control ensuring the viability of the project in economic terms. The present analysis seeks to optimize, control and improve the variables that influence a vertical packaging equipment of 20 grams chocolate powder sachets, where as a new machine that enters the production line lacks standardization and improvements that lead the process to the efficiency and profitability expected at the time of its acquisition, it is worth noting that currently there are a number of problems that not only affect the profitability of the product but also the perception and customer loyalty for a product that may not come out in optimal conditions to the market.Rionegr

CodABC:A computational framework to coestimate recombination, substitution, and molecular adaptation rates by approximate bayesian computation

The estimation of substitution and recombination rates can provide important insights into the molecular evolution of protein-coding sequences. Here, we present a new computational framework, called "CodABC," to jointly estimate recombination, substitution and synonymous and nonsynonymous rates from coding data. CodABC uses approximate Bayesian computation with and without regression adjustment and implements a variety of codon models, intracodon recombination, and longitudinal sampling. CodABC can provide accurate joint parameter estimates from recombining coding sequences, often outperforming maximum-likelihood methods based on more approximate models. In addition, CodABC allows for the inclusion of several nuisance parameters such as those representing codon frequencies, transition matrices, heterogeneity across sites or invariable sites. CodABC is freely available from http://code.google.com/p/codabc/, includes a GUI, extensive documentation and ready-to-use examples, and can run in parallel on multicore machines.This work was supported by the Spanish Government with the “Juan de la Cierva” fellowship JCI-2011-10452 to M.A., the European Research Council (ERC Grant Agreement No. 617457) to D.P., and Fundac¸~ao para a Ci^encia e a Tecnologia (FCT) (grant EXCL/BIA-ANM/0549/2012) to J.S.L.Peer reviewe

Protein evolution along phylogenetic histories under structurally constrained substitution models

Motivation: Models of molecular evolution aim at describing the evolutionary processes at the molecular level. However, current models rarely incorporate information from protein structure. Conversely, structure-based models of protein evolution have not been commonly applied to simulate sequence evolution in a phylogenetic framework, and they often ignore relevant evolutionary processes such as recombination. A simulation evolutionary framework that integrates substitution models that account for protein structure stability should be able to generate more realistic in silico evolved proteins for a variety of purposes. Results: We developed a method to simulate protein evolution that combines models of protein folding stability, such that the fitness depends on the stability of the native state both with respect to unfolding and misfolding, with phylogenetic histories that can be either specified by the user or simulated with the coalescent under complex evolutionary scenarios, including recombination, demographics and migration. We have implemented this framework in a computer program called ProteinEvolver. Remarkably, comparing these models with empirical amino acid replacement models, we found that the former produce amino acid distributions closer to distributions observed in real protein families, and proteins that are predicted to be more stable. Therefore, we conclude that evolutionary models that consider protein stability and realistic evolutionary histories constitute a better approximation of the real evolutionary process.Ministerio de Ciencia e Innovación | Ref. BFU2011-24595Ministerio de Economía y Competitividad | Ref. BFU2012-40020Ministerio de Ciencia e Innovación | Ref. JCI-2011-1045

CodABC: a computational framework to coestimate recombination, substitution, and molecular adaptation rates by approximate Bayesian computation

The estimation of substitution and recombination rates can provide important insights into the molecular evolution of protein-coding sequences. Here, we present a new computational framework, called CodABC, to jointly estimate recombination, substitution and synonymous and non-synonymous rates from coding data. CodABC uses approximate Bayesian computation (ABC) with and without regression adjustment and implements a variety of codon models, intracodon recombination and longitudinal sampling. CodABC can provide accurate joint parameter estimates from recombining coding sequences, often outperforming maximum likelihood methods based on more approximate models. In addition, CodABC allows for the inclusion of several nuisance parameters such as those representing codon frequencies, transition matrices, heterogeneity across sites or invariable sites. CodABC is freely available from http://code.google.com/p/codabc/, includes a GUI, extensive documentation and ready-touse examples, and can run in parallel on multicore machines.Ministerio de Ciencia e Innovación | Ref. JCI-2011-10452Fundação para a Ciência e a Tecnologia | Ref. EXCL/BIA-ANM/0549/201

Factores relacionados con la violencia laboral vistos desde la perspectiva de la salud ocupacional

La presente revisión bibliográfica pretende presentar una contextualización acerca de factores relacionados con la violencia laboral vistos desde la perspectiva de la salud Ocupacional, así como sus características y consecuencias, los tipos de violencia que se pueden presentar en una empresa entre las que se encuentran, el acoso, que puede presentarse como psicológico, moral y laboral; y algunas de las leyes que respaldan estas condiciones a nivel mundial y en Colombia. Para poder llevar a cabo esta monografía fue necesaria la revisión de artículos, teniendo como preferencia aquellas investigaciones que fueron realizadas los últimos quince años. Como conclusión se observó que las investigaciones realizadas en cuanto a Factores Relacionados con la violencia laboral vistos desde la perspectiva de la salud ocupacional muestran nuevas medidas a tomar y nuevos enfoques, además apunta a confirmar que tan protegidos dentro de las organización se sienten los empleados sobre las situaciones y riesgos a los que se ven expuestos a diario en los sitios de trabajo dentro de la EmpresaIncluye bibliografí

Argumentación o retórica, una de las piezas claves para la construcción de la realidad social

Este artículo busca mostrar que es la retórica, y no la argumentación, la prácticahumana decisiva en la construcción y sostenimiento de la realidad social. Es lacapacidad de persuadir a auditorios lo que constituye los principios rectores de lasinstituciones sociales, y no el debate crítico y argumentado de ideas. Para esto, enla primera parte se distinguirá entre argumentación y retórica. Se mostrará que enla argumentación prima la demostración de verdades, mientras que en la retórica,el consentimiento o persuasión de auditorios. Sobre esta idea, y desde las tesisdel filósofo del lenguaje John Searle acerca de la construcción de la realidad social,se mostrará que es el lenguaje persuasivo el que permite la constitución de laintencionalidad colectiva, y con ella, de los hechos institucionales, estos últimos,las unidades básicas de la realidad social. Brevemente, este artículo desarrollará elargumento: en tanto la realidad social se constituye en la intencionalidad colectiva, yla intencionalidad colectiva se forma a través del lenguaje retórico, la realidad socialse constituye en el lenguaje retórico