A phylogenetic perspective on sequence evolution in microsatellite loci

We examined the evolution of the repeat regions of three noncoding microsat ellite loci in 58 species of the Polistinae, a subfamily of wasps that dive rged over 140 million years ago. A phylogenetic approach allows two new kin ds of approaches to studying microsatellite evolution: character mapping an d comparative analysis. The basic repeat structure of the loci was highly c onserved, but was often punctuated with imperfections that appear to be phy logenetically informative. Repeat numbers evolved more rapidly than other c hanges in the repeat region. Changes in number of repeats among species see m consistent with the stepwise mutation model, which is based on slippage d uring replication as the main source of mutations. Changes in repeat number s can occur even when there are very few tandem repeats but longer repeats, especially perfect repeats led to greater rates of evolutionary change. Sp ecies phylogenetically closer to the one from which we identified the loci had longer stretches of uninterrupted repeats and more different motifs, bu t not longer total repeat regions. The number of perfect repeats increased more often than it decreased. However, there was no evidence that some spec ies have consistently greater numbers of repeats across loci than other spe cies have, once ascertainment bias is eliminated. We also found no evidence for a population size effect posited by one form of the directionality hyp othesis. Overall, phylogenetic variation in repeat regions can be explained by adding neutral evolution to what is already known about the mutation pr ocess. The life cycle of microsatellites appears to reflect a balance betwe en growth by slippage and degradation by an essentially irreversible accumu lation of imperfections.