The processes of speciation and reproductive isolation are complex, and are not well understood. Transposons are an important force in evolution - I would like to investigate their role in the mysterious route to speciation. One of the initial steps in speciation, postzygotic reproductive isolation, is a phenomena where, after the egg and sperm meet, the zygote is unable to complete development, or dies soon after birth. Postzygotic isolation is critical to prevent the breakdown of speciation, because closely related species may still be geographically close to one another, and are still physically able to copulate. Epigenetic modifications are thought to be relatively less stable than the nucleotide sequence, and may be important in postzygotic isolation. Transposons, which make up 35% of the human genome, have been hypothesized to be critical for proper epigenetic gene regulation, and in proper silencing of the X chromosome in mammals. Many transposons are close to genes, and even when they lack transposable activity they may still have intact promoter/enhancer elements, may form gene/transposon fusions, and may affect genes indirectly by being targeted for methylation.
To investigate their importance in speciation events I would like to use a bioinformatics approach to look at the similarity of sequence and location of LINEs, SINEs, and DNA transposons at a genomic level. Pairs of closely related species would be compared, to see if there are significant differences in sequence and location of transposons within pairs that can have viable offspring vs. those that cannot. I suggest comparing humans and chimps to Mus musculus and Mus spretus, the latter of which can still have viable offspring.
Mills RE, Bennett EA, Iskow RC, Luttig CT, Tsui C, Pittard WS, Devine SE. 2006. Recently mobilized transposons in the human and chimpanzee genomes. Am J Hum Genet. 78(4):671-9.