Efeitos de usos alternativos do solo sobre a população de fungos micorrízicos arbusculares na Amazônia.

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Rabifier2: an improved bioinformatic classifier of Rab GTPases

SUMMARY: The Rab family of small GTPases regulates and provides specificity to the endomembrane trafficking system; each Rab subfamily is associated with specific pathways. Thus, characterization of Rab repertoires provides functional information about organisms and evolution of the eukaryotic cell. Yet, the complex structure of the Rab family limits the application of existing methods for protein classification. Here, we present a major redesign of the Rabifier, a bioinformatic pipeline for detection and classification of Rab GTPases. It is more accurate, significantly faster than the original version and is now open source, both the code and the data, allowing for community participation. AVAILABILITY AND IMPLEMENTATION: Rabifier and RabDB are freely available through the web at http://rabdb.org. The Rabifier package can be downloaded from the Python Package Index at https://pypi.python.org/pypi/rabifier, the source code is available at Github https://github.com/evocell/rabifier

Immunization for complex network based on the effective degree of vertex

The basic idea of many effective immunization strategies is first to rank the importance of vertices according to the degrees of vertices and then remove the vertices from highest importance to lowest until the network becomes disconnected. Here we define the effective degrees of vertex, i.e., the number of its connections linking to un-immunized nodes in current network during the immunization procedure, to rank the importance of vertex, and modify these strategies by using the effective degrees of vertices. Simulations on both the scale-free network models with various degree correlations and two real networks have revealed that the immunization strategies based on the effective degrees are often more effective than those based on the degrees in the initial network.Comment: 16 pages, 5 figure

Daphnia revisited: Local stability and bifurcation theory for physiologically structured population models explained by way of an example

We consider the interaction between a general size-structured consumer population and an unstructured resource. We show that stability properties and bifurcation phenomena can be understood in terms of solutions of a system of two delay equations (a renewal equation for the consumer population birth rate coupled to a delay differetial equation for the resource concentration). As many results for such systems are available, we can draw rigorous conclusions concerning dynamical behaviour from an analysis of a characteristic equation. We derive the characteristic equation for a fairly general class of population models, including those based on the Kooijman-Metz Daphnia model and a model introduced by Gurney-Nisbet and Jones et al., and next obtain various ecological insights by analytical or numerical studies of special cases

Accurate age estimation in small-scale societies

Precise estimation of age is essential in evolutionary anthropology, especially to infer population age structures and understand the evolution of human life history diversity. However, in small-scale societies, such as hunter-gatherer populations, time is often not referred to in calendar years, and accurate age estimation remains a challenge. We address this issue by proposing a Bayesian approach that accounts for age uncertainty inherent to fieldwork data. We developed a Gibbs sampling Markov chain Monte Carlo algorithm that produces posterior distributions of ages for each individual, based on a ranking order of individuals from youngest to oldest and age ranges for each individual. We first validate our method on 65 Agta foragers from the Philippines with known ages, and show that our method generates age estimations that are superior to previously published regression-based approaches. We then use data on 587 Agta collected during recent fieldwork to demonstrate how multiple partial age ranks coming from multiple camps of hunter-gatherers can be integrated. Finally, we exemplify how the distributions generated by our method can be used to estimate important demographic parameters in small-scale societies: here, age-specific fertility patterns. Our flexible Bayesian approach will be especially useful to improve cross-cultural life history datasets for small-scale societies for which reliable age records are difficult to acquire

Parking functions, labeled trees and DCJ sorting scenarios

In genome rearrangement theory, one of the elusive questions raised in recent years is the enumeration of rearrangement scenarios between two genomes. This problem is related to the uniform generation of rearrangement scenarios, and the derivation of tests of statistical significance of the properties of these scenarios. Here we give an exact formula for the number of double-cut-and-join (DCJ) rearrangement scenarios of co-tailed genomes. We also construct effective bijections between the set of scenarios that sort a cycle and well studied combinatorial objects such as parking functions and labeled trees.Comment: 12 pages, 3 figure

Introductory Editorial: Evolutionary Genomics

This supplement is intended to focus on evolutionary genomics. Evolutionary Bioinformatics aims to provide researchers working in this complex, quickly developing field with online, open access to highly relevant scholarly articles by leading international researchers. In a field where the literature is ever-expanding, researchers increasingly need access to up-to-date, high quality scholarly articles on areas of specific contemporary interest. This supplement aims to address this by presenting high-quality articles that allow readers to distinguish the signal from the noise. The editor in chief hopes that through this effort, practitioners and researchers will be aided in finding answers to some of the most complex and pressing issues of our time

Palaeoecological and genetic evidence for Neanderthal power locomotion as an adaptation to a woodland environment

The prevailing explanation for Neanderthal body form is the cold (glacial) adaptation hypothesis. However, palaeoecological associations appear to indicate a less cold woodland environment. Under such conditions, encounter and ambush (rather than pursuit) hunting e and thus muscular power and sprint (rather than endurance) capacity e would have been favoured. We hypothesise that the highly muscular Neanderthal body form reflects an adaptation to hunting conditions rather than cold, and here both review the palaeoecological evidence that they inhabited a mainly woodland environment, and present preliminary genetic analyses in support of this new hypothesis

Oscillations in low-dimensional cyclic differential delay systems

Nonlinear autonomous N-dimensional systems of cyclic differential equations with delays and overall negative feedback are considered. Such systems serve as mathematical models of numerous real world phenomena in physics and laser optics, physiology and mathematical biology, economics and life sciences among others. In the case of lower dimensions and sufficient conditions are derived for the oscillation of all solutions about the unique equilibrium. Open problems and conjectures are discussed for the higher dimensional case and for more convoluted sign feedbacks. © 2018, Springer Nature Switzerland AG