Journal Article

Reconstructing the Evolutionary History of Transposable Elements

Arnaud Le Rouzic, Thibaut Payen and Aurélie Hua-Van

in Genome Biology and Evolution

Published on behalf of Society for Molecular Biology and Evolution

Volume 5, issue 1, pages 77-86
Published in print January 2013 |
Published online December 2012 | e-ISSN: 1759-6653 | DOI: http://dx.doi.org/10.1093/gbe/evs130

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The impact of transposable elements (TEs) on genome structure, plasticity, and evolution is still not well understood. The recent availability of complete genome sequences makes it possible to get new insights on the evolutionary dynamics of TEs from the phylogenetic analysis of their multiple copies in a wide range of species. However, this source of information is not always fully exploited. Here, we show how the history of transposition activity may be qualitatively and quantitatively reconstructed by considering the distribution of transposition events in the phylogenetic tree, along with the tree topology. Using statistical models developed to infer speciation and extinction rates in species phylogenies, we demonstrate that it is possible to estimate the past transposition rate of a TE family, as well as how this rate varies with time. This methodological framework may not only facilitate the interpretation of genomic data, but also serve as a basis to develop new theoretical and statistical models.

Keywords: transposition activity; phylogeny; branching process; repeated sequences

Journal Article.  5509 words.  Illustrated.

Subjects: Bioinformatics and Computational Biology ; Evolutionary Biology ; Genetics and Genomics

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