Search results for "Models of DNA evolution"
showing 5 items of 5 documents
Set Membership (In) Validation of nonlinear positive models for biological systems
2006
The complexity of biology needs quantitative tools in order to support and validate biologists intuition and traditional qualitative descriptions. In this paper, Nonlinear Positive models with constraints for biological systems are validated/invalidated in a worst-case deterministic setting. These models are usefull for the analysis of the DNA and RNA evolution and for the description of the population dynamics of viruses and bacteria. The conditional central estimate and the Uncertainty Intervals are determined in order to validate/invalidate the model. The effectiveness of the proposed procedure has been illustrated by means of simulation experiments.
Temperature-dependent mutational robustness can explain faster molecular evolution at warm temperatures, affecting speciation rate and global pattern…
2015
Distribution of species across the Earth shows strong latitudinal and altitudinal gradients with the number of species decreasing with declining temperatures. While these patterns have been recognized for well over a century, the mechanisms generating and maintaining them have remained elusive. Here, we propose a mechanistic explanation for temperature-dependent rates of molecular evolution that can influence speciation rates and global biodiversity gradients. Our hypothesis is based on the effects of temperature and temperature-adaptation on stability of proteins and other catalytic biomolecules. First, due to the nature of physical forces between biomolecules and water, stability of biomo…
Concerted Evolution of Multigene Families and Homoeologous Recombination
2012
The dynamism of genomes is one of the most thoroughly documented paradigms in the genomic era, envisaged by the cytogenetic school during middle decades of the twentieth century. Such dynamism refers not just to the evolutionary changes that take place across deep time but also to the myriad changes at different levels (from SNPs to large structural rearrangements) that shape and adjust genomes over a smaller time scale. This chapter reviews two of the many forces that provide genome dynamism in plants. These two forces, concerted evolution of multigene families and homoeologous recombination of hybridized genomes, in principle contribute to shape the plant genomes through opposite effects …
Identification of Replicator Mutator models
2006
The complexity of biology literally calls for quantitative tools in order to support and validate biologists intuition and traditional qualitative descriptions. In this paper, the Replicator-Mutator models for Evolutionary Dynamics are validated/invalidated in a worst-case deterministic setting. These models analyze the DNA and RNA evolution or describe the population dynamics of viruses and bacteria. We identify the Fitness and the Replication Probability parameters of a genetic sequences, subject to a set of stringent constraints to have physical meaning and to guarantee positiveness. The conditional central estimate is determined in order to validate/invalidate the model. The effectivene…
Application of model quality evaluation to systems biology
2008
Application of model quality evaluation to the quasispecies models is presented. These models are useful for the analysis of the DNA and RNA evolution and for the description of the population dynamics of viruses and bacteria. An estimate of the parameters together with their interval of variability is computed and the quality evaluation is tested on the basis of the model prediction error capability.