Patterns of selection in the evolution of a transposable element

Abstract

Transposable elements (TEs) are a major component of most eukaryotic genomes. Here, we present a new approach which allows us to study patterns of natural selection in the evolution of TEs over short time scales. The method uses the alignment of all elements with intact gag/pol genes of a TE family from a single genome. We predict that the ratio of non-synonymous to synonymous variants (vN/vS) in the alignment should decrease as a function of the frequency of the variants, because elements with non-synonymous variants that reduce transposition will have fewer progeny. We apply our method to Sirevirus LTR retrotransposons that are abundant in maize and other plant species and show that vN/vS declines as variant frequency increases, indicating that negative selection is acting strongly on the Sirevirus genome. The asymptotic value of vN/vS suggests that at least 85% of all non-synonymous mutations in the TE reduce transposition. Crucially, these patterns in vN/vS are only predicted to occur if the gene products from a particular TE insertion preferentially promote the transposition of the same insertion. Overall, this study is the first to use large numbers of intact elements to shed new light on the selective processes that act on TEs.