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Disentangling the determinants of transposable elements dynamics in vertebrate genomes using empirical evidences and simulations
In PLOS Genetics
Bourgeois, Ruggiero, Hariyani, and Boissinot
Author Summary
Transposable elements (TEs) are mobile DNA sequences that can replicate and insert in genomes. By doing so, they can disrupt gene function and meiotic process, but also generate evolutionary novelties. It is however unclear how different processes such as varying rates of transposition, selection on TEs, linked selection and genome properties interact with each other. Here, we use the green anole (Anolis carolinensis) as a model, since it harbors one of the highest diversities of TEs found in a vertebrate (including non-LTR retrotransposons, LTR-Retrotransposons, DNA transposons and SINEs). By studying the population genomics of these different categories of TEs within the same species, we are able to disentangle processes that are specific to TE clades from general processes related to drift and selection. To do so, we use simulations of TEs in their genomic context to provide an interpretation of associations between recombination rate and statistics summarizing TE diversity and abundance. Our results highlight clear differences in TE dynamics across clades, with a clear dichotomy between SINEs/DNA-transposons and LTR-Retrotransposons/long LINEs. These differences can be mostly explained by changes in the relative impact of selection against TEs, linked selection, and insertional preferences.
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