Microsatellites, or simple sequence repeats (SSRs), are common and widespread DNA elements in genomes of many organisms.
However, their dynamics in genome evolution is unclear, whereby they are thought to evolve neutrally. More available genome
sequences along with dated phylogenies allowed for studying the evolution of these repetitive DNA elements along evolutionary time
scales. This could be used to compare rates of genome evolution. We show that SSRs in insects can be retained for several hundred
million years. Different types of microsatellites seem to be retained longer than others. By comparing Dipteran with Hymenopteran
species, we found very similar patterns of SSR loss during their evolution, but both taxa differ profoundly in the rate. Relative to
divergence time,Diptera lost SSRs twice as fast as Hymenoptera.The loss of SSRs on the Drosophila melanogaster X-chromosome was
higher than on the other chromosomes. However, accounting for generation time, the Diptera show an 8.5-fold slower rate of SSR
loss than the Hymenoptera, which, in contrast to previous studies, suggests a faster genome evolution in the latter. This shows that
generation time differences can have a profound effect. A faster genome evolution in these insects could be facilitated by several
factors very different to Diptera, which is discussed in light of our results on the haplodiploid D. melanogaster X-chromosome.
Furthermore, large numbers of SSRs can be found to be in synteny and thus could be exploited as a tool to investigate genome
structure and evolution.