As the scientific community increases its knowledge about the genomes of various organisms, the study of the molecular basis of phenotypic variation within and between species has become possible.  In 1975 King and Wilson postulated that most evolutionary changes occur by changes in protein expression rather than protein structure based on the fact that proteins are conserved between species.  In support of this, various microarray studies have shown that there is a large amount of genetic variation in gene expression levels.  A significant problem that remains is the lack of knowledge about regulatory sequences within most organisms’ genome.  With the sequencing of the S. cerevisiae genome and that of six other yeast species, gene regulatory sites have been shown to be conserved between species. Five genes, CCA1, CYT1, MLS1, PDR10, and ZDS2 and their promoters, were randomly chosen from all divergently transcribed intergenic sequences upstream of functionally annotated genes to be sequenced in 81 strains for a polymorphism survey.  The rate of polymorphism in the MLS1 and PDR10 promoters was higher than that at synonymous sites.  There are three possible explanations for this occurrence.  The first is that there is a higher mutation rate in this area, but if that is the case then the divergence rate should be higher as well.  The second is that natural selection is acting on the sites.  The third possibility is that the synonymous sites are not in fact neutral, but this seems unlikely because the divergence and polymorphism rates are normal, or as expected.  If the mutation rate is high no change in gene expression is expected.  If natural selection is the cause, then it is likely that the sites will affect gene regulation.  To test the hypothesis that these polymorphic sites affect gene expression, the promoter of PDR10 was isolated from13 different yeast strains and cloned into a Bgal reporter construct.  Future work will include transforming the vector into yeast and measuring gene expression using a Bgal assay.