Mobile DNA and the TE-Thrust hypothesis: supporting evidence from the primates

Building on the groundbreaking work of McClintock [1] and numerous others [2-14], we further advanced the proposition of transposable elements (TEs) as powerful facilitators of evolution [15] and now formalise this into 'The TE-Thrust hypothesis'. In this paper, we present much specific evidence in support of this hypothesis, which we suggest may have great explanatory power. We focus mainly on the well-studied higher primate (monkey, ape and human) lineages. We emphasize the part played by the retro-TEs, especially the primate-specific non-autonomous Alu short interspersed element (SINE), together with its requisite autonomous partner long interspersed element (LINE)-1 or L1 (Figure 1A). In addition, both ancient and recent endogenizations of exogenous retroviruses (endogenous retroviruses (ERVs)/solo long terminal repeats (sLTRs) have been very important in primate evolution (Figure 1A). The Alu element has been particularly instrumental in the evolution of primates by TE-Thrust. This suggests that, at least in some mammalian lineages, specific SINE-LINE pairs have a large influence on the trajectory and extent of evolution on the different clades within that lineage.The ubiquitous, very diverse, and mostly extremely ancient TEs are powerful facilitators of genome evolution, and therefore of phenotypic diversity. TE-Thrust acts to build, sculpt and reformat genomes, either actively by TE transposition and integration (active TE-Thrust), or passively, because after integration, TEs become dispersed homologous sequences that facilitate ectopic DNA recombination (passive TE-Thrust). TEs can cause very significant and/or complex coding, splicing, regulatory and karyotypic changes to genomes, resulting in phenotypes that can adapt well to biotic or environmental challenges, and can often invade new ecological niches. TEs are usually strongly controlled in the soma, where they can be damaging [16,17], but they are allowed some limited mobility in the germline and early