A Brief History of the Status of Transposable Elements: From Junk DNA to Major Players in Evolution

Abstract

The idea that some genetic factors are able to move around chromosomes emerged more than 60 years ago when Barbara McClintock first suggested that such elements existed and had a major role in controlling gene expression and that they also have had a major influence in reshaping genomes in evolution. It was many years, however, before the accumulation of data and theories showed that this latter revolutionary idea was correct although, understandably, it fell far short of our present view of the significant influence of what are now known as ''transposable elements'' in evolution. In this article, I summarize the main events that influenced my thinking about transposable elements as a young scientist and the influence and role of these specific genomic elements in evolution over subsequent years. Today, we recognize that the findings about genomic changes affected by transposable elements have considerably altered our view of the ways in which genomes evolve and work.

Selfish genetic elements, genetic conflict, and evolutionary innovation

“…These observations are consistent with the parasitic hypothesis, and no additional conditions are needed to explain the persistence of TEs over evolutionary time or their widespread occurrence. In contrast, there is much less direct evidence supporting the argument that TEs persist in evolution because they enhance the evolvability of organisms or play some vital role in ecosystems (81,83).…”

“…Note that the parasite hypothesis does not preclude TE insertions evolving beneficial functions in the host (i.e., domestication) but argues that this is a consequence of TEs rather than the "reason" for the existence of TEs. There has been a recent resurgence of articles either implicitly or explicitly stating that an important evolutionary "function" of TEs is to promote genetic innovation and evolvability (81)(82)(83)(84). For example, Aziz et al (83) argue that the ubiquity of TEs is proof that they must exist to provide benefits in evolution.…”

“…A more reasonable hypothesis for maintenance of TEs attributable to long-term benefits is based on clade selection (i.e., competition among lineages of species) (81,84). The clade selection hypothesis is that those clades (e.g., species, genera) with active TE elements are more likely to persist and radiate because of their ability to evolve to changing environments or to evolve innovations.…”

“…A theme in some recent papers is that although TEs were "dismissed" over the past several decades as mere selfish DNA, new evidence now shows that they have evolved functions within the genome (81,83). Although perhaps a useful literary foil, these statements are not very accurate.…”

What's in a genome? The C-value enigma and the evolution of eukaryotic genome content

“…[15,[37][38][39][40]). The results of this study confirm that repeat content in general and TE content in particular are strongly positively correlated with genome size (figure 3).…”