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Reconstructing the Evolutionary History of Transposable Elements

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 copie...

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Detalles Bibliográficos
Autores principales: Le Rouzic, Arnaud, Payen, Thibaut, Hua-Van, Aurélie
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2013
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3595040/
https://www.ncbi.nlm.nih.gov/pubmed/23275488
http://dx.doi.org/10.1093/gbe/evs130
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author Le Rouzic, Arnaud
Payen, Thibaut
Hua-Van, Aurélie
author_facet Le Rouzic, Arnaud
Payen, Thibaut
Hua-Van, Aurélie
author_sort Le Rouzic, Arnaud
collection PubMed
description 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.
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spelling pubmed-35950402013-03-12 Reconstructing the Evolutionary History of Transposable Elements Le Rouzic, Arnaud Payen, Thibaut Hua-Van, Aurélie Genome Biol Evol Research Article 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. Oxford University Press 2013 2012-12-29 /pmc/articles/PMC3595040/ /pubmed/23275488 http://dx.doi.org/10.1093/gbe/evs130 Text en © The Author(s) 2012. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. http://creativecommons.org/licenses/by-nc/3.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0/), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Article
Le Rouzic, Arnaud
Payen, Thibaut
Hua-Van, Aurélie
Reconstructing the Evolutionary History of Transposable Elements
title Reconstructing the Evolutionary History of Transposable Elements
title_full Reconstructing the Evolutionary History of Transposable Elements
title_fullStr Reconstructing the Evolutionary History of Transposable Elements
title_full_unstemmed Reconstructing the Evolutionary History of Transposable Elements
title_short Reconstructing the Evolutionary History of Transposable Elements
title_sort reconstructing the evolutionary history of transposable elements
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3595040/
https://www.ncbi.nlm.nih.gov/pubmed/23275488
http://dx.doi.org/10.1093/gbe/evs130
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