Conceptual and empirical investigations of eukaryotic transposable element evolution
Transposable elements (TEs), mobile pieces of self-replicating DNA, are one of the driving forces behind genomic evolution in eukaryotic organisms. Their contribution to genome size variation and as mutagens has led researchers to pursue their study in the hope of better understanding the evolution of genomic properties and organismal phenotypes But TEs can also be thought of in a multi-level evolutionary context, with TEs best understood as evolving populations residing within (and interacting with) the host genome. I argue, with empirical evidence from the literature, that the multi-level approach advocated by the classic “selfish DNA” papers of 1980 has become less commonly invoked over the past 35 years, in a favour of a strictly organism-centric view. I also make the case that an exploration of evolution at the level of TEs within genomes is required, one which articulates the similarities and differences between a TE population and a traditional population of organisms. A comprehensive analysis of sequenced eukaryote genomes outlines the landscape of how TE superfamilies are distributed, but also reveals that how TEs are reported needs to be addressed. A proper exploration of evolution at the TE level will require a dramatic change to how TE information is annotated, curated, and stored, and I make several specific recommendations in this regard.