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Bacteria and their bacteriophages are the most abundant, widespread and diverse groups of biological entities on the planet. In an attempt to understand how the interactions between bacteria, virulent phages and temperate phages might affect the diversity of these groups, we developed a novel stochastic network model for examining the co-evolution of these ecologies. In our approach, nodes represent whole species or strains of bacteria or phages, rather than individuals, with speciation and extinction modelled by duplication and removal of nodes. Phage-bacteria links represent host-parasite relationships and temperate-virulent phage links denote prophage-encoded resistance. The effect of horizontal transfer of genetic information between strains was also included in the dynamical rules. The observed networks evolved in a highly dynamic fashion but the ecosystems were prone to collapse (one or more entire groups going extinct). Diversity could be stably maintained in the model only if the probability of speciation was independent of the diversity. Such an effect could be achieved in real ecosystems if the speciation rate is primarily set by the availability of ecological niches.
Some bacteria and archaea possess an immune system, based on the CRISPR-Cas mechanism, that confers adaptive immunity against phage. In such species, individual bacteria maintain a cassette of viral DNA elements called spacers as a memory of past inf
During last years theoretical works shed new light and proposed new hypothesis on the mechanisms which regulate the time behaviour of biological populations in different natural systems. Despite of this, the role of environmental variables in ecologi
Levy flights in the space of mutations model time evolution of bacterial DNA. Parameters in the model are adjusted in order to fit observations coming from the Long Time Evolution Experiment with E. Coli.
This thesis is aimed at studying mutations, understood as trajectories in the DNA configuration space. An evolutive model of mutations in terms of Levy flights is proposed. The parameters of the model are estimated by means of data from the Long-Term
I compare two quantum-theoretical approaches to the phenomenon of adaptive mutations, termed here Q-cell and Q-genome. I use fluctuation trapping model as a general framework. I introduce notions of R-error and D-error and argue that the fluctuation