Abstract
Transposable elements (TEs) are a key component of eukaryotic genomes. TEs can copy themselves independently of the host genome, thus are often considered to be selfish genomic elements. However, TE dynamics within genomes have contributed to adaptive evolution leading to speculation that natural selection preserves TE expression. Here we used experimental evolution of C. elegans to study the dynamics of TE expression over 400 generations in population sizes maintained at 1, 10 and 100 individuals. We demonstrate increased TE expression relative to the ancestral population, with the largest increases corresponding to smaller population sizes. Using high-throughput small RNA sequencing we show that the transcriptional activation of TEs within active regions of the genome is associated with loss of piRNA-mediated silencing, whilst desilenced TEs in repressed chromatin domains retain small RNAs. Additionally, we find that the sequence context of the surrounding region influences the propensity of TEs to lose silencing through failure of small RNA-mediated silencing. Together, our results show that natural selection in C. elegans is responsible for maintaining low levels of TE expression, and provide new insights into the epigenomic features responsible.