Improved integration time estimation of endogenous retroviruses with phylogenetic data.

<h4>Background</h4>Endogenous retroviruses (ERVs) are genetic fossils of ancient retroviral integrations that remain in the genome of many organisms. Most loci are rendered non-functional by mutations, but several intact retroviral genes are known in mammalian genomes. Some have been ado...

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Autores principales:	Hugo Martins, Palle Villesen
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2011
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/2f2a5037a3cf43bb92252a31d9e069bd
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spelling	oai:doaj.org-article:2f2a5037a3cf43bb92252a31d9e069bd2021-11-18T06:57:47ZImproved integration time estimation of endogenous retroviruses with phylogenetic data.1932-620310.1371/journal.pone.0014745https://doaj.org/article/2f2a5037a3cf43bb92252a31d9e069bd2011-03-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/21394200/?tool=EBIhttps://doaj.org/toc/1932-6203<h4>Background</h4>Endogenous retroviruses (ERVs) are genetic fossils of ancient retroviral integrations that remain in the genome of many organisms. Most loci are rendered non-functional by mutations, but several intact retroviral genes are known in mammalian genomes. Some have been adopted by the host species, while the beneficial roles of others remain unclear. Besides the obvious possible immunogenic impact from transcribing intact viral genes, endogenous retroviruses have also become an interesting and useful tool to study phylogenetic relationships. The determination of the integration time of these viruses has been based upon the assumption that both 5' and 3' Long Terminal Repeats (LTRs) sequences are identical at the time of integration, but evolve separately afterwards. Similar approaches have been using either a constant evolutionary rate or a range of rates for these viral loci, and only single species data. Here we show the advantages of using different approaches.<h4>Results</h4>We show that there are strong advantages in using multiple species data and state-of-the-art phylogenetic analysis. We incorporate both simple phylogenetic information and Monte Carlo Markov Chain (MCMC) methods to date the integrations of these viruses based on a relaxed molecular clock approach over a Bayesian phylogeny model and applied them to several selected ERV sequences in primates. These methods treat each ERV locus as having a distinct evolutionary rate for each LTR, and make use of consensual speciation time intervals between primates to calibrate the relaxed molecular clocks.<h4>Conclusions</h4>The use of a fixed rate produces results that vary considerably with ERV family and the actual evolutionary rate of the sequence, and should be avoided whenever multi-species phylogenetic data are available. For genome-wide studies, the simple phylogenetic approach constitutes a better alternative, while still being computationally feasible.Hugo MartinsPalle VillesenPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 6, Iss 3, p e14745 (2011)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Hugo Martins Palle Villesen Improved integration time estimation of endogenous retroviruses with phylogenetic data.
description	<h4>Background</h4>Endogenous retroviruses (ERVs) are genetic fossils of ancient retroviral integrations that remain in the genome of many organisms. Most loci are rendered non-functional by mutations, but several intact retroviral genes are known in mammalian genomes. Some have been adopted by the host species, while the beneficial roles of others remain unclear. Besides the obvious possible immunogenic impact from transcribing intact viral genes, endogenous retroviruses have also become an interesting and useful tool to study phylogenetic relationships. The determination of the integration time of these viruses has been based upon the assumption that both 5' and 3' Long Terminal Repeats (LTRs) sequences are identical at the time of integration, but evolve separately afterwards. Similar approaches have been using either a constant evolutionary rate or a range of rates for these viral loci, and only single species data. Here we show the advantages of using different approaches.<h4>Results</h4>We show that there are strong advantages in using multiple species data and state-of-the-art phylogenetic analysis. We incorporate both simple phylogenetic information and Monte Carlo Markov Chain (MCMC) methods to date the integrations of these viruses based on a relaxed molecular clock approach over a Bayesian phylogeny model and applied them to several selected ERV sequences in primates. These methods treat each ERV locus as having a distinct evolutionary rate for each LTR, and make use of consensual speciation time intervals between primates to calibrate the relaxed molecular clocks.<h4>Conclusions</h4>The use of a fixed rate produces results that vary considerably with ERV family and the actual evolutionary rate of the sequence, and should be avoided whenever multi-species phylogenetic data are available. For genome-wide studies, the simple phylogenetic approach constitutes a better alternative, while still being computationally feasible.
format	article
author	Hugo Martins Palle Villesen
author_facet	Hugo Martins Palle Villesen
author_sort	Hugo Martins
title	Improved integration time estimation of endogenous retroviruses with phylogenetic data.
title_short	Improved integration time estimation of endogenous retroviruses with phylogenetic data.
title_full	Improved integration time estimation of endogenous retroviruses with phylogenetic data.
title_fullStr	Improved integration time estimation of endogenous retroviruses with phylogenetic data.
title_full_unstemmed	Improved integration time estimation of endogenous retroviruses with phylogenetic data.
title_sort	improved integration time estimation of endogenous retroviruses with phylogenetic data.
publisher	Public Library of Science (PLoS)
publishDate	2011
url	https://doaj.org/article/2f2a5037a3cf43bb92252a31d9e069bd
work_keys_str_mv	AT hugomartins improvedintegrationtimeestimationofendogenousretroviruseswithphylogeneticdata AT pallevillesen improvedintegrationtimeestimationofendogenousretroviruseswithphylogeneticdata
_version_	1718424091900248064

Improved integration time estimation of endogenous retroviruses with phylogenetic data.

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