Our genome has several different types of transposons [Transposons: Part I, Transposons: Part II, Retrotransposons/Endogenous Retroviruses]. Most of them are defective in one way or another so they can no longer "jump" to another location but some subfamilies have remained functional and these will spread to new locations. About 44% of our genome consists of active transposons and (mostly) defective transposons [What's in Your Genome?]. Most of these sequences have no function—they are junk DNA.
The development of new, cheap, sequencing technologies and the availability of an annotated standard human genome reference sequence has made it possible to look for new transposon insertions in a large number of individuals. The results can help confirm or refute the idea that most of our genome is junk.
A recently published article in PLoS Genetics describes the results of such an analysis (Stewart et al. 2011). It's part of the 1000 Genomes Project.
They detected a total of 7,310 insertions that were present in only a subset of the 179 genomes that were analyzed. About 85% of these were Alu elements, 12% were L1 LINES, and 3% were SVA's. This is consistent with earlier work that catalogued the number of active transposons in the human genome. As expected, very few of these insertions occurred in exons (39) and only 3 occurred in coding regions. This strongly suggests that there is strong selection against disruptions of coding regions. It implies that most of the detectable insertions occur in regions where disruption of the sequence has no effect on the viability of the the individual. In other words, insertions occur predominantly in junk DNA.
The authors examined the sequences of two families in order to assess the frequency of new transposon insertions. Earlier data indicated that a new insertion arises only once in every twenty births so it's not a surprise to find that the offspring in these two families showed no new insertions relative to their parents.
A data set of this size allows for an assessment of the rate of fixation of various new mobile element insertion (MEI) alleles in the population. The authors conclude,
MEI alleles propagate within population groups much like other predominantly neutral polymorphisms. MEI allele frequency spectra from the low coverage samples are in general agreement with expectations from the standard neutral model for allele drift in a population.What this means is that most (perhaps all) of the insertion alleles are segregating as though they have no effect on the fitness of the individuals that carry them. This is further support for the idea that large parts of the genome are junk.
Stewart, C., Kural, D., Strömberg, M.P., Walker, J.A., Konkel, M.K., Stütz, A.M., Urban, A.E., Grubert, F., Lam, H.Y., Lee, W.P., Busby, M., Indap, A.R., Garrison, E., Huff, C., Xing, J., Snyder, M.P., Jorde, L.B., Batzer, M.A., Korbel, J.O., Marth, G.T. (2011) A comprehensive map of mobile element insertion polymorphisms in humans. PLoS Genet. 2011 Aug;7(8):e1002236. Epub 2011 Aug 18. [doi:10.1371/journal.pgen.1002236]