On specific scenarios in molecular evolution: Theoretical and computer simulation approaches

This dissertation uses computer simulations and mathematical models to examine several scenarios in Molecular evolution. In each study individual based computer simulations were combined with statistical estimations (chapter 2) or a population genetic model (chapters 3, 4, 5, 6) to provide support or motivation for the mathematical results. In brief the non-introduction chapters study the following scenarios: (Chapter 2) The time required to fix an advantageous allele, with arbitrary dominance, in a population is obtained via simulations and an approximation for this time obtained. This approximation is shown to be superior to the most commonly used alternative and is used to make additional population genetic predictions. (Chapter 3) A model of adaptive evolution utilizing gene conversion between duplicates is studied to determine parameter values for which this pathway is feasible. (Chapter 4) A model of compensatory evolution in enhancers sequences is derived and studied to explain an apparent discrepancy in the mode of enhancer evolution between vertebrates and non-vertebrates. Results suggest that population size alone may explain the observed discrepancy. (Chapter 5) A similar mathematical model is used to show that the influential “shifting balance theory” is not needed to explain simple fitness landscape peak shifts if the intermediate alleles are recessive. (Chapter 6) Two pathways for the evolutionary origin of functionally novel loci via gene duplication are compared using simulations and a model that incorporates both pathways. Results suggest that the traditional pathway is often not the most likely under the conditions of the model.