Acelerando o processo de detecção de espécies ameaçadas através de avaliações expeditas.

Disponível online. Resumo

Contributions of protein-coding and regulatory change to adaptive molecular evolution in murid rodents

The contribution of regulatory versus protein change to adaptive evolution has long been controversial. In principle, the rate and strength of adaptation within functional genetic elements can be quantified on the basis of an excess of nucleotide substitutions between species compared to the neutral expectation or from effects of recent substitutions on nucleotide diversity at linked sites. Here, we infer the nature of selective forces acting in proteins, their UTRs and conserved noncoding elements (CNEs) using genome-wide patterns of diversity in wild house mice and divergence to related species. By applying an extension of the McDonald-Kreitman test, we infer that adaptive substitutions are widespread in protein-coding genes, UTRs and CNEs, and we estimate that there are at least four times as many adaptive substitutions in CNEs and UTRs as in proteins. We observe pronounced reductions in mean diversity around nonsynonymous sites (whether or not they have experienced a recent substitution). This can be explained by selection on multiple, linked CNEs and exons. We also observe substantial dips in mean diversity (after controlling for divergence) around protein-coding exons and CNEs, which can also be explained by the combined effects of many linked exons and CNEs. A model of background selection (BGS) can adequately explain the reduction in mean diversity observed around CNEs. However, BGS fails to explain the wide reductions in mean diversity surrounding exons (encompassing ~100 Kb, on average), implying that there is a substantial role for adaptation within exons or closely linked sites. The wide dips in diversity around exons, which are hard to explain by BGS, suggest that the fitness effects of adaptive amino acid substitutions could be substantially larger than substitutions in CNEs. We conclude that although there appear to be many more adaptive noncoding changes, substitutions in proteins may dominate phenotypic evolution

SimiVal, a multi-criteria map comparison tool for land-change model projections

The multiple uses of land-cover models have led to validation with choice metrics or an ad hoc choice of the validation metrics available. To address this, we have identified the major dimensions of land-cover maps that ought to be evaluated and devised a Similarity Validation (SimiVal) tool. SimiVal uses a linear regression to test a modelled projection against benchmark cases of, perfect, observed and systematic-bias, calculated by rescaling the metrics from a random case relative to the observed, perfect case. The most informative regression coefficients, p-value and slope, are plot on a ternary graph of ‘similarity space’ whose extremes are the three benchmark cases. SimiVal is tested on projections of two deliberately contrasting land-cover models to show the similarity between intra- and inter-model parameterisations. We find metrics of landscape structure are important in distinguishing between different projections of the same model. Predictive and exploratory models can benefit from the tool

Dynamical continuous time random walk

© 2015, EDP Sciences, SIF, Springer-Verlag Berlin Heidelberg. We consider a continuous time random walk model in which each jump is considered to be dynamical process. Dissipative launch velocity and hopping time in each jump is the key factor in this model. Within the model, normal diffusion and anomalous diffusion is realized theoretically and numerically in the force free potential. Besides, external potential can be introduced naturally, so the random walker’s behavior in the linear potential and quartic potential is discussed, especially the walker with Lévy velocity in the quartic potential, bimodal behavior of the spatial distribution is observed, it is shown that due to the inertial effect induced by damping term, there exists transition from unimodality to bimodality for the walker’s spatial stationary distribution