Abstract:

The general focus of this thesis is on the molecular evolution and population genetics of the D. melanogaster subgroup. The work can be viewed as having two main sections. The first section deals with the evolutionary dynamics of gene families. The second section deals with the evolution and population genetics of the fourth chromosomes of D. melanogaster, D. simulans, and D. yakuba .

One of the most salient results of comparative genomics is the disparity in gene content, due to both evolutionary changes of existing gene families as well as the generation of new ones. The ability to alter the coding portions of genomes, either through duplicating the whole genome or though smaller duplication events, immediately seemed to be a rapid way to bring about evolutionary change, and considerable interest was focused on studying them. The introductory chapter will introduce this field of research, and then introduce the work on gene families in this thesis. The research contains two parts (comprised of three chapters): (1) The evolutionary dynamics of young dispersed gene families and (2) the evolution of olfactory and gustatory receptors gene families (Ors and Grs , respectively).

The second section follows up previous work on the fourth chromosome that has resulted in potentially conflicting conclusions. The fourth chromosome has long been thought to be a nonrecombining chromosome, devoid of nucleotide variation. Previous population genetic surveys of limited loci that supported this view, stood in agreement with tens of thousands of crosses that never had resulted in a visible cross over for this chromosome either. However, the most recent polymorphism data sets revealed surprising diversity and levels of recombination. These latter sets had their own limitations due to distant SNP markers, and thus an inability to describe fine-scale population characteristics, and possibly leading to inflated estimates. The research in this section analyses a new and expanded polymorphism data set with the goal of providing a fine-scale map of diversity and recombination along this chromosome.