Sequence evolution of the retrotransposon Ty3 in natural isolates of Saccharomyces cerevisiae and Saccharomyces paradoxus

Transposable elements (TEs) have traditionally been viewed in relation to their effects on their hosts. However, the collection of TEs in a host population can itself be considered a population. This TE population will face the same fundamental evolutionary forces as does the host population. It follows that transposable elements should be subject to natural selection in the same way as other genetic entities. This work seeks to assess the types of natural selection that act on the Saccharomyces transposable element Ty3. A sample of natural isolates of two closely related yeast species, Saccharomyces cerevisiae and Saccharomyces paradoxus, is obtained. The discovery and characterization of Ty3 in S. paradoxus are described. Through sequence analysis, it is determined that this element is closely related to the S. cerevisiae retrotransposon Ty3. A large sample of Ty3 elements are cloned and sequenced from the S. paradoxus and S. cerevisiae isolates. Studying elements from two closely related species allows the examination of both patterns of element diversity within species (including the possible action of purifying selection) and patterns of element divergence between species (including the possible action of positive Darwinian selection). The patterns of nucleotide polymorphism and substitution in the Ty3 elements are also considered. Evidence from sequence analysis suggests that purifying selection, but not positive Darwinian selection, has acted on Ty3, particularly on functional domains of the element. It is observed that Ka/Ks ratios for polymorphisms are elevated relative to Ka/Ks ratios for fixed substitutions. This result may be consistent with the action of either purifying selection or diversifying selection.