On the estimation of the insertion time of LTR retrotransposable elements

Abstract

It has been proposed that the insertion time of a long terminal repeat (LTR) retrotransposon can be estimated by the divergence between the two LTRs at the both ends because their sequences were identical at the insertion event. This method is based on the assumption that the two LTRs accumulate point mutations independently; therefore, the divergence reflects the time since the insertion event. However, if gene conversion occurs between LTRs, the nucleotide divergence will be much smaller than expected with the assumption of the independent accumulation of point mutations. To examine this assumption, we investigated the extent of gene conversion between LTRs by applying a comparative genomic approach to primates (humans and rhesus macaques) and rodents (mice and rats). We found that gene conversion plays a significant role in the molecular evolution of LTRs in primates and rodents, but the extent is quite different. In rodents, most LTRs are subject to extensive gene conversion that reduces the divergence, so that the divergence-based method results in a serious underestimation of the insertion time. In primates, this effect is limited to a small proportion of LTRs. The most likely explanation of the difference involves the minimum length of the interacting sequence (minimal efficient processing segment [MEPS]) for interlocus gene conversion. An empirical estimate of MEPS in human is 300-500 bp, which exceeds the length of most of the analyzed LTRs. In contrast, MEPS for mice should be much smaller. Thus, MEPS can be an important factor to determine the susceptibility of LTRs to gene conversion, although there are many other factors involved. It is concluded that the divergence method to estimate the insertion time should be applied with special caution because at least some LTRs undergo gene conversion.