The impact of transposable elements in adaptive evolution

Abstract

The growing knowledge about the influence of transposable elements (TEs) on (a) long-term genome and transcriptome evolution; (b) genomic, transcriptomic and epigenetic variation within populations; and (c) patterns of somatic genetic differences in individuals continues to spur the interest of evolutionary biologists in the role of TEs in adaptive evolution. As TEs can trigger a broad range of molecular variation in a population with potentially severe fitness and phenotypic consequences for individuals, different mechanisms evolved to keep TE activity in check, allowing for a dynamic interplay between the host, its TEs and the environment in evolution. Here, we review evidence for adaptive phenotypic changes associated with TEs and the basic molecular mechanisms by which the underlying genetic changes arise: (a) domestication, (b) exaptation, (c) host gene regulation, (d) TE-mediated formation of intronless gene copies-so-called retrogenes and (e) overall increased genome plasticity. Furthermore, we review and discuss how the stress-dependent incapacitation of defence mechanisms against the activity of TEs might facilitate adaptive responses to environmental challenges and how such mechanisms might be particularly relevant in species frequently facing novel environments, such as invasive, pathogenic or parasitic species.

DeviaTE: Assembly‐free analysis and visualization of mobile genetic element composition

“…TEs are important mutagens, which generate novel phenotypic variation; e.g., in Drosophila melanogaster an estimated 50%–80% of the observed mutations are due to TEs (Ashburner, Golic, & Hawley, ; Drake, Charlesworth, Charlesworth, & Crow, ). Transposons have been implicated in diverse phenomena such as human disease (Burns, ; Kazazian et al., ; Narita et al., ), environmental adaptation (Casacuberta & González, ; Schrader & Schmitz, ), genome evolution (Kazazian, ), quantitative variation (Mackay, Lyman, & Jackson, ) and domestication of important crops (Studer, Zhao, Ross‐Ibarra, & Doebley, ). Understanding TE biology is thus of vital interest for many different research fields.…”

Ecological divergence of DNA methylation patterns at distinct spatial scales

“…2016; Rey et al . 2016; Schrader & Schmitz 2019). The strongest associations between climate and A. thaliana methylation levels were, however, found in CG contexts within or near genes related to abiotic stress responses, development and reproduction (Keller et al .…”

Millipede genomes reveal unique adaptation of genes and microRNAs during myriapod evolution

“…The frequent annotation of TEs in close proximity to genes raises the possibility that TEs may have played a particular role in host evolution in millipedes, since TEs are well known contributors of genomic novelty to host genomes (e.g. Feschotte 2008; Kidwell and Lisch 2000; Schrader and Schmitz 2019). Strikingly, in comparison TEs are largely excluded from genic neighbourhoods in the centipede genome (Figure 4: Repeat Locality).…”