The roles of natural selection and germline gene expression in primate genome evolution

In this dissertation I focus on two questions that arise from patterns of variation in the human genome. First, why does primate nucleotide divergence vary so dramatically across the genome? Second, why do intergenic and genic regions differ in their composition and evolution? I first describe how mutation, selection and demography may cause these patterns and review the existing literature. I then analyze regional variation in hominid divergence and conclude that most of it is explained by natural selection. I next examine how gene expression is associated with crossover rate, transposable element density and strand-asymmetric substitution. All of these features are more strongly associated with gene expression in germline tissues than in somatic tissues indicating that they are a neutral by-product of transcription, rather than a consequence of natural selection. I conclude by discussing the implications of these findings and future directions for research.