Population Genetics and Molecular Evolution of DNA Sequences in Transposable Elements. I. A Simulation Framework

Abstract

A population genetic simulation framework is developed to understand the behavior and molecular evolution of DNA sequences of transposable elements. Our model incorporates random transposition and excision of transposable element (TE) copies, two modes of selection against TEs, and degeneration of transpositional activity by point mutations. We first investigated the relationships between the behavior of the copy number of TEs and these parameters. Our results show that when selection is weak, the genome can maintain a relatively large number of TEs, but most of them are less active. In contrast, with strong selection, the genome can maintain only a limited number of TEs but the proportion of active copies is large. In such a case, there could be substantial fluctuations of the copy number over generations. We also explored how DNA sequences of TEs evolve through the simulations. In general, active copies form clusters around the original sequence, while less active copies have long branches specific to themselves, exhibiting a star-shaped phylogeny. It is demonstrated that the phylogeny of TE sequences could be informative to understand the dynamics of TE evolution.

Characterization of a heat-activated retrotransposon in <i>Vigna angularis</i>

“…1 ). The shorter external branches in V. angularis , compared to those in V. radiata , also suggest lesser activities in V. radiata as was also suggested in simulation studies ( Kijima and Innan 2013 , Navarro-Quezada and Schoen 2002 ).…”

Do larger genomes contain more diverse transposable elements?

“…Theoretical investigations have suggested that stronger selection against the deleterious effects of TE insertions results in fewer copies, but also leads to a higher percentage of active elements [ 16 - 18 ]. Inactive (or less active) elements have a lower chance of surviving the selective filter that the host genome presents, possibly winnowing TE diversity over long time periods.…”

Rapid evolution at the Drosophila telomere: transposable element dynamics at an intrinsically unstable locus

“…Second, simulation studies suggest that high rates of TE deletion may drive non-neutral sequence evolution by heightening the strength of selection on transpositional activity [63], as the birth rate of new insertions must compensate for the heightened death rate of preexisting insertions for the family to remain viable. If there are fitness impacts on the organism of excessive telomere elongation [64], which additional observations of telomere trimming suggest may be the case [65,66], this heightened selection on transposition may also intensify conflict among the HTTs as they compete for limited space and transposition machinery.…”