Transposable elements: powerful facilitators of evolution

Abstract

Transposable elements (TEs) are powerful facilitators of genome evolution, and hence of phenotypic diversity as they can cause genetic changes of great magnitude and variety. TEs are ubiquitous and extremely ancient, and although harmful to some individuals, they can be very beneficial to lineages. TEs can build, sculpt, and reformat genomes by both active and passive means. Lineages with active TEs or with abundant homogeneous inactive populations of TEs that can act passively by causing ectopic recombination are potentially fecund, adaptable, and taxonate readily. Conversely, taxa deficient in TEs or possessing heterogeneous populations of inactive TEs may be well adapted in their niche, but tend to prolonged stasis and may risk extinction by lacking the capacity to adapt to change, or diversify. Because of recurring intermittent waves of TE infestation, available data indicate a compatibility with punctuated equilibrium, in keeping with widely accepted interpretations of evidence from the fossil record. We propose a general and holistic synthesis on how the presence of TEs within genomes makes them flexible and dynamic, so that genomes themselves are powerful facilitators of their own evolution.

Selfish genetic elements, genetic conflict, and evolutionary innovation

“…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.…”

The Cambrian Explosion and the Origins of Embodied Cognition

“…They marshal evidence that neurohormonal stress can increase levels of genetic transposition, which can increase evolvability (Zeh et al 2009;Oliver and Greene 2009), as well as by destabilizing the genome through changes in epigenetic marks, "which can lead to altered patterns of mitotic and meiotic pairing, to chromosomal re-patterning, to mutation-prone repair, as well as triggering transposition." (Ginsburg and Jablonka 2010) Extant organisms have systems to ameliorate and suppress the genome and epigenome destabilizing effects of stress, but during the Cambrian Explosion, these systems probably had not evolved.…”

Genesis of ancestral haplotypes: RNA modifications and reverse transcription–mediated polymorphisms

“…Spadafora concludes that "RT-mediated machinery operates in sperm cells and is responsible for the genesis and non-Mendelian propagation of new genetic information" [63]. Indeed the role of RT activity from endogenous and exogeneous transposable elements (TEs) shaping genomic diversity has recently been reviewed in the context of RNA-based gene duplications [59] as well as episodic surges in TE activity that could be an explanation for punctuated equilibrium as observed in the paleontological record [64].…”