| I study the evolution of solidification fronts propagating in undercooled liquids, the evolution of microbial communities through diversification fronts propagating along microbial genomes, the evolution of the universality and optimality of the genetic code, and the emergence of genome biases.;I present a phase-field model of solidification which allows efficient computations in the regime when interface kinetic effects dominate over capillary effects.;I model the competition between homologous recombination and point mutation in microbial genomes, and present evidence for two distinct phases, one uniform and the other genetically diverse. I find that global sequence divergence can be mediated by fronts propagating along the genome, whose characteristic signature is elucidated, and apparently observed in closely related genomes from the Bacillus cereus group. Front propagation provides an emergent, generic mechanism for microbial "speciation," and suggests a classification of microorganisms on the basis of their propensity to support propagating fronts.;I propose that selection on the speed, accuracy and energy efficiency of template-directed synthesis processes, such as translation, transcription and replication, can lead to the spontaneous emergence of genome biases. Selection on translation leads to codon usage bias; selection on transcription or replication leads to nucleotide composition biases such as the GC content. These biases result from the generic tradeoffs inherent to template-directed synthesis and occur even in the absence of biased mutation or direct selection on the nucleotide composition.;Then, I show that the coevolution between tRNA expression levels and codon usage provides an efficient mechanism for optimization of genetic codes, even if, as the frozen accident theory assumes, every amino acid substitution is lethal at least at some genome sites.;Finally, I investigate the proposition that genetic exchange dominating the early evolution of life naturally leads to a common genetic code for all organisms. I present three possible mechanisms through which HGT brings universality---communal advantage of popular codes, HGT of translational components and HGT of protein coding regions. A possible consequence of the interplay of these mechanisms is the concerted evolution towards optimality of a community of organisms sharing the same genetic code and having compatible translational machineries. |
