Infinitely long branches and an informal test of common ancestry

Background: The evidence for universal common ancestry (UCA) is vast and persuasive. A phylogenetic test has been proposed for quantifying its odds against independently originated sequences based on the comparison between one versus several trees. This test was successfully applied to a well-supported homologous sequence alignment, which was however criticized on the basis of simulations showing that alignments without any phylogenetic structure could mislead its conclusions.Results: Here we present a simplified version of this same counterexample, which can be interpreted as a tree with arbitrarily long branches, and where the UCA test fails again. We also present another case whereby any sufficiently similar alignment will favour UCA irrespective of the true independent origins for the sequences. Finally, we present a class of frequentist tests that perform better than the purportedly formal UCA test.Conclusion: Despite claims to the contrary, we show that the counterexamples successfully detected a drawback of the original UCA test, of relying on sequence similarity. In light of our own simulations, we therefore conclude that the UCA test as originally proposed should not be trusted unless convergence has already been ruled out a priori.Reviewers: This article was reviewed by Professor Eugene Koonin, Dr. Yuri I. Wolf and Professor William Martin

Computational search for UV radiation resistance strategies in Deinococcus swuensis isolated from Paramo ecosystems

Ultraviolet radiation (UVR) is widely known as deleterious for many organisms since it can cause damage to biomolecules either directly or indirectly via the formation of reactive oxygen species. The goal of this study was to analyze the capacity of high-mountain Espeletia hartwegiana plant phyllosphere microorganisms to survive UVR and to identify genes related to resistance strategies. A strain of Deinococcus swuensis showed a high survival rate of up to 60% after UVR treatment at 800J/m2 and was used for differential expression analysis using RNA-seq after exposing cells to 400J/m2 of UVR (with \u3e95% survival rate). Differentially expressed genes were identified using the R-Bioconductor package NOISeq and compared with other reported resistance strategies reported for this genus. Genes identified as being overexpressed included transcriptional regulators and genes involved in protection against damage by UVR. Non-coding (nc)RNAs were also differentially expressed, some of which have not been previously implicated. This study characterized the immediate radiation response of D. swuensis and indicates the involvement of ncRNAs in the adaptation to extreme environmental conditions

Phylogenomic Analyses of 2,786 Genes in 158 Lineages Support a Root of the Eukaryotic Tree of Life between Opisthokonts and All Other Lineages

Advances in phylogenomics and high-throughput sequencing have allowed the reconstruction of deep phylogenetic relationships in the evolution of eukaryotes. Yet, the root of the eukaryotic tree of life remains elusive. The most popular hypothesis in textbooks and reviews is a root between Unikonta (Opisthokonta + Amoebozoa) and Bikonta (all other eukaryotes), which emerged from analyses of a single-gene fusion. Subsequent, highly cited studies based on concatenation of genes supported this hypothesis with some variations or proposed a root within Excavata. However, concatenation of genes does not consider phylogenetically-informative events like gene duplications and losses. A recent study using gene tree parsimony (GTP) suggested the root lies between Opisthokonta and all other eukaryotes, but only including 59 taxa and 20 genes. Here we use GTP with a duplication-loss model in a gene-rich and taxon-rich dataset (i.e., 2,786 gene families from two sets of 155 and 158 diverse eukaryotic lineages) to assess the root, and we iterate each analysis 100 times to quantify tree space uncertainty. We also contrasted our results and discarded alternative hypotheses from the literature using GTP and the likelihood-based method SpeciesRax. Our estimates suggest a root between Fungi or Opisthokonta and all other eukaryotes; but based on further analysis of genome size, we propose that the root between Opisthokonta and all other eukaryotes is the most likely

Biodiversidad y servicios ecosistémicos en la gestión del suelo-subsuelo

Interactions between the abiotic and biotic components of topsoil and subsoil provide different ecosystem services key to human wellbeing. However, in many cases mining activity avoids the ecological structure as an opportunity and tool to strengthen land use planning strategies, resulting in socioenvironmental conflicts. This situation makes evident the need to take actions to define and harmonize the different instruments on land use planning, in order to take actions for the conservation, restoration, knowledge, sustainable use and risk management of biodiversity and ecosystem services.Las interacciones entre los componentes bióticos y abióticos de suelo y subsuelo proveen diferentes servicios ecosistémicos para el bienestar de la sociedad. No obstante, el desarrollo de actividades mineras ignora la estructura ecológica como herramienta para la planificación territorial, llevando a conflictos socioambientales que ponen de manifiesto la necesidad de establecer acciones de gestión a partir de las sinergias entre políticas y normas intersectoriales que permitan la armonización de instrumentos de gestión territorial, procurando la conservación, la restauración, el conocimiento, el uso sostenible y la gestión del riesgo de la biodiversidad y los servicios ecosistémicos

Effect of Different Levels of Calcium Nitrate on Dry Matter Degradation and Methane Production in an in Vitrorumen Fermentation of Kikuyu Grass

RESUMEN: El objetivo de este trabajo fue determinar el efecto de niveles crecientes de nitrato de calcio sobre la degradación de la materia seca y la producción de metano in vitro. Los tratamientos consistieron en la incubación de 500 mg de pasto Kikuyo con cuatro niveles de nitrato de calcio (CaNO3) : 0, 3, 6 y 9% con base en la materia seca incubada. Las variables evaluadas fueron producción acumulada de gases, degradación aparente de la materia seca, producción de ácidos grasos volátiles, producción de metano y concentración de nitrógeno amoniacal. El efecto de los nitratos sobre las variables evaluadas se determinó mediante un análisis de medidas repetidas en el tiempo, considerando un modelo mixto, donde los horarios de incubación y los niveles de nitrato fueron efectos fijos y los animales donadores de inóculo se describieron como un efecto aleatorio. Con 24 horas de incubación, la adición del 6% de nitrato de calcio redujo en un 32% la producción total de gases de la fermentación, en un 17% la degradación de la materia seca y en un 49% la producción de metano con respecto al tratamiento sin nitrato. Las concentraciones de propionato butirato y acetato se redujeron al incrementar el porcentaje de nitrato en el ambiente de fermentación. En este experimento niveles de inclusión de nitrato de calcio superiores al 3% redujeron significativamente la degradación de la materia seca.ABSTRACT: The aim of this study was to determine the effect of increasing levels of calcium nitrate on the in vitro dry matter degradation of Kikuyu grass and on methane production. Treatments consisted of incubating 500 mg of Kikuyu grass (Cenchrus clandestinus Chiov Hochst Ex..) with four levels of calcium nitrate (CaNO3 ): 0, 3, 6 and 9% (dry matter basis). The variables analyzed were cumulative gas production, dry matter degradation, methane production and concentration of ammonia and volatile fatty acids. A repeated measures analysis was conducted considering a mixed model, where incubation times and nitrate levels were fixed effects and animal inoculum donors were described as a random effect. With 24 hours of incubation, the addition of 6% calcium nitrate reduced the total gas production (32%), dry matter degradation (17% ) and methane production (49%). Concentrations of butyrate, propionate and acetate decreased with increasing the nitrate in the fermentation médium. In this experiment, calcium nitrate above 3% significantly reduced the dry matter degradation

Protocol forin vitro propagation of Zingiber officinale Roscoe via organogenesis

Ginger (Zingiber officinale Roscoe) is traditionally propagated by rhizomes and can carrydiseases that decrease production.In vitro propagation allows healthy seed to beobtained, in high volumes and in less time. The objective of this work was to present aprotocol for thein vitro propagation of Z. officinale via organogenesis. Procedures for in vitro establishment from axillary buds of primary rhizomes of field-grown plants areincluded. In addition, thein vitro multiplication and planting in theex vitro acclimatizationphase with high survival rates

Protocolo para la propagación in vitro de Zingiber officinale Roscoe vía organogénesis

Ginger (Zingiber officinale Roscoe) is traditionally propagated by rhizomes and can carry diseases that decrease production. In vitro propagation allows healthy seed to be obtained, in high volumes and in less time. The objective of this work was to present a protocol for the in vitro propagation of Z. officinale via organogenesis. Procedures for in vitro establishment from axillary buds of primary rhizomes of field-grown plants are included. In addition, the in vitro multiplication and planting in the ex vitro acclimatization phase with high survival rates.El jengibre (Zingiber officinale Roscoe), se propaga tradicionalmente por medio de rizomas y se pueden transmitir enfermedades que disminuyen la producción. La propagación in vitro permite obtener semilla sana, en volúmenes elevados y en un menor tiempo. Este trabajo persiguió como objetivo presentar un protocolo para la propagación in vitro de Z. officinale vía organogénesis. Se incluyen procedimientos para el establecimiento in vitro a partir de yemas axilares de rizomas primarios de plantas cultivadas en casa de cultivo. Además, su multiplicación in vitro y la plantación en la fase de aclimatización ex vitro con altos porcentajes de supervivencia

Conclusiones

En una perspectiva normativa se presentaron los antecedentes del actual Estatuto de Protección al Consumidor, observando que ha sido latente la preocupación del legislativo por regular lo concerniente a esta actividad, hecho que se materializó en la Ley 73 (1981), denominada en su momento como Ley del Consumo