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Vetsigian, Kalin 2012-11-19T16:30:31Z 2012-11-19T16:30:31Z 10000-01-01 2005 In this dissertation, 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 new phase-field model of solidification which allows efficient computations in the regime when interface kinetic effects dominate over capillary effects. The asymptotic analysis required to relate the parameters in the phase-field with those of the original sharp interface model is straightforward, and the resultant phase-field model can be used for a wide range of material parameters. I model the competition between homologous recombination and point mutation in microbial genomes, and present evidence for two distinct phases, one uniform, the other genetically diverse. Depending on the specifics of homologous recombination, I find that global sequence divergence can be mediated by fronts propagating along the genome, whose characteristic signature on genome structure 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 coming from, say, DNA or mRNA stability. In the case of translation, it is the coevolution between codon usage and tRNA expression levels that creates a fitness landscape that enforces quasi-stable patterns of codon usage. Occasional transitions between patterns are expected, due to genetic drift or hitchhiking of slightly deleterious adjustments of the translational system on other beneficial traits. Then, I show that the above coevolutionary dynamics 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. This research shows that it is possible to account for the optimality of the code within the framework of translation as a standardized competition between tRNA adaptors. Finally, I investigate the proposition that genetic exchange dominating the early evolution of life naturally leads to a common genetic code for all organisms, while promoting their incredible diversity in all other aspects. 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. Submitted by Elias Lopez (erlopez2@illinois.edu) on 2012-11-19T16:30:31Z No. of bitstreams: 1 Vetsigian_Kalin.pdf: 1119047 bytes, checksum: f3739b85db5de92583dc06131698d4c7 (MD5) Made available in DSpace on 2012-11-19T16:30:31Z (GMT). No. of bitstreams: 1 Vetsigian_Kalin.pdf: 1119047 bytes, checksum: f3739b85db5de92583dc06131698d4c7 (MD5) Previous issue date: 2005 Restriction data tranferred 2014-07-01T11:35:22-05:00 Original Data Group with Access UIUC Users [automated] Release Date: none Reason: Student has not yet granted open access permission Item marked as restricted to the 'UIUC Users [automated]' Group (id=2) by Elias Lopez (erlopez2@illinois.edu) on 2012-11-19T16:30:32Z Item is restricted indefinitely. Student has not yet granted open access permission U of I Only http://hdl.handle.net/2142/35234 en 2005 Vetsigian © microbial genome microbial genomes asymtotic homologous recombination speciation Deoxyribonucleic acid (DNA) Transfer ribonucleic acid (tRNA) Messenger Ribonucleic Acid (mRNA) Bacillus microogranism genetic drift deleterius Horizontal Gene Transfer (HGT) phase-feild model invasion-equilibrium cycle amino acid fitness noise Collective Evolution of Biological and Physical Systems Dissertation / Thesis text Physics Physics University of Illinois at Urbana-Champaign Dissertation Ph.D.