This article reviews what is known about mammalian retroelements, which are endogenous components of eukaryotic genomes that are able to amplify to new locations in the genome through an RNA intermediate.
The eukaryotic genome has undergone a series of epidemics of amplification of mobile elements (retroelements) that have resulted in most eukaryotic genomes that contain much more of this "junk" DNA than actual coding DNA. Most of these retroelements appear to amplify in evolutionary waves that insert in the genome and then gradually diverge. Although mobile element insertions cause significant damage to the human genome, unequal recombination events between disperse elements cause even more damage. The authors estimate that at least 0.3 percent of all human genetic diseases are caused by unequal Alu/Alu homologous recombination events that cause moderate-sized deletions or duplications. Because mobile elements are intracellular, they must amplify through a very population-dependent mechanism. The fixation of specific mobile element insertion sites in a species can be used as a distinct character for phylogenetic analysis. If two species share a common retroelement insertion at a given location and a third species does not, the first two species are likely to be more closely related. If several such characters are studied, this provides strong evidence of species relatedness. The current rate of damage by these mobile elements is modest in humans compared to earlier in primate history. Other species, however, are still subject to high mutational loads by active retroelements. These elements represent one of the major forces, both current and past, in the evolution and possibly the overall structure of human genomes. 3 figures and 104 references