Thesis (Ph.D.) - Indiana University, Department of Biology and School of Informatics, Computing, and Engineering/University Graduate School, 2019All genetic variation originates as a mutation in the DNA sequence of a single individual. The rate at which mutations arise is a parameter of utmost importance both for human health and evolutionary studies. While it is known that mutation and substitution rates vary between species, whether this is due to natural selection or some other phenomena remains unclear. Recent studies have shown that in mammals the rate of new nucleotide mutations is dependent almost entirely on the age of the father. This is likely due to errors accruing during DNA replication during spermatogenesis in the male parent. Based on these observations, I have developed a model of the single nucleotide mutation rate that incorporates parental age into estimates of both the mutation rate and substitution rate. To test this model, I sequenced the genomes of several families of owl monkeys and macaques, primates closely related to humans. I found that, in primates, variation in nucleotide mutation rates can be explained almost entirely by variation in the generation time and puberty age of the species considered. I also show that, for larger structural variants, parental age likely plays no role in the rate of these mutations. This stands in contrast to the paternal age effect of single nucleotide mutations and is in accordance with the accepted mechanism of formation for structural variants. Finally, since genome sequencing is still error-prone, mutation and substitution rate estimates are likely conflated by false positives. To remedy this, I developed a method to assign an intuitive quality score to genome assemblies that takes into account underlying sequence and mapping quality. This method can be used to annotate a genome assembly and subsequently correct or filter out low quality positions, thus reducing the number of false positive variants found. This in turn will lead to more accurate estimates of the mutation rate and substitution rate in any species.