TN5 transposase complexed with transposon end DNA (1F3I)

Daphnia pulex

return to Lynch Lab main page

Sarah Schaack
Graduate Student
schaack(at)indiana.edu
(812) 856-0115

Since their discovery, transposable elements (TEs) have been found to be dynamic and widespread components of the genetic architecture in most eukaryotes. Their ability to move and replicate within the genome suggests they are a significant source of new mutations and, subsequently, generate genetic variation upon which selection might act. Transposable elements have been characterized as both genomic “parasites” and functional “mutualists.” At the genome level, TEs may facilitate significant reductions (e.g. pufferfish; Neafsey and Palumbi 2003) or explain expansions (Lynch and Conery 2003) in overall genome size. As a result, there is considerable interest in how TEs influence the way populations and species evolve over long and short time periods. Given that the portion of the genome represented by TEs varies widely among taxa, even for the same element (e.g. L1 in mammals vs. teleosts; Duvernell et al. 2004), it appears that TE proliferation is explained not only by properties of different element families, but in many cases by aspects of the host genomes themselves.

The aim of my dissertation is to examine how recombination in the host genome influences the short- and long-term dynamics of TE proliferation. Recombination may provide a means by which TEs can be either mobilized or purged by host genomes, making it a mechanism of special interest for understanding patterns of TE proliferation. For my dissertation, I am performing two major comparisons using the cyclic parthenogen D. pulex. The recent sequencing and imminent release of the full genome for D. pulex will make it possible to identify TEs in the genome of this cyclic parthenogen (Part I). By comparing the TE profiles among natural populations and laboratory-reared lines that vary in the frequency with which they reproduce via sex, I hope to gain insight into the role of recombination in TE proliferation. The natural comparison among populations of obligately asexual and facultative parthenogens will reveal long-term patterns of TE accumulation in the presence and absence of sex (Part II). The lab experiment will reduce the number of confounding variables associated with the natural comparison, eliminate negative selection against TEs, and thereby allow for the assessment of TE profiles among sexually- and asexually-reproducing lineages of the same starting clone (Part III).