The evolution of indel profile, introns, polygamy, polymorphism, and recombination

The first chapter investigates the selective constraints on insertions and deletions in introns due to splicing requirements. Using computer simulations and analytical results, this paper compares the distribution of all possible insertions and deletions to the distribution of insertions and deletions that maintain the original exon structure. The results suggest that introns are subject to selective constraints due to splicing which affects the distribution of insertions and deletions.;The second chapter uses simulations to investigate how introns affect gene evolution and how this effect on gene evolution in turn affects intron evolution. The chapter focuses on the affect that introns have on local rates of recombination. Since the rate of recombination between two bases depends upon the distance between these two bases, an intron greatly increases the rate of recombination between the flanking exons. The results suggest that this increase in recombination helps speed up gene evolution, but is not a strong selective force on introns.;The third chapter places the polygamy threshold model (a model that predicts when an individual should mate polygamously rather than monogamously) in a population genetics context and explores the dynamics of some extensions of this model via simulations and analytical results. The results suggest the validity of the polygamy threshold model in a population genetics context.;Using simulations, the fourth chapter examines the amount of polymorphism that can be maintained and that can evolve given a single locus subject to selection that differs among males and females. The dynamics of this model is then compared to the dynamics for a single locus subject to selection that is identical among males and females. The results suggest that though the amount of polymorphism that can be maintained is greater, the amount that can evolve is less under a model where selection differs among males and females.;The fifth chapter uses simulations to examine a two-locus system in which viability fluctuates stochastically from favoring homozygotes to favoring heterozygotes to determine the fate of alleles at a third locus that modifies the amount of recombination. Interestingly this system still reaches an equilibrium despite the fluctuation in selection.