The embedding problem for markov models of nucleotide substitution.

Continuous-time Markov processes are often used to model the complex natural phenomenon of sequence evolution. To make the process of sequence evolution tractable, simplifying assumptions are often made about the sequence properties and the underlying process. The validity of one such assumption, ti...

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Autores principales:	Klara L Verbyla, Von Bing Yap, Anuj Pahwa, Yunli Shao, Gavin A Huttley
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2013
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/e418da09653146ba84de9bb0611ebffa
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spelling	oai:doaj.org-article:e418da09653146ba84de9bb0611ebffa2021-11-18T09:02:03ZThe embedding problem for markov models of nucleotide substitution.1932-620310.1371/journal.pone.0069187https://doaj.org/article/e418da09653146ba84de9bb0611ebffa2013-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23935949/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203Continuous-time Markov processes are often used to model the complex natural phenomenon of sequence evolution. To make the process of sequence evolution tractable, simplifying assumptions are often made about the sequence properties and the underlying process. The validity of one such assumption, time-homogeneity, has never been explored. Violations of this assumption can be found by identifying non-embeddability. A process is non-embeddable if it can not be embedded in a continuous time-homogeneous Markov process. In this study, non-embeddability was demonstrated to exist when modelling sequence evolution with Markov models. Evidence of non-embeddability was found primarily at the third codon position, possibly resulting from changes in mutation rate over time. Outgroup edges and those with a deeper time depth were found to have an increased probability of the underlying process being non-embeddable. Overall, low levels of non-embeddability were detected when examining individual edges of triads across a diverse set of alignments. Subsequent phylogenetic reconstruction analyses demonstrated that non-embeddability could impact on the correct prediction of phylogenies, but at extremely low levels. Despite the existence of non-embeddability, there is minimal evidence of violations of the local time homogeneity assumption and consequently the impact is likely to be minor.Klara L VerbylaVon Bing YapAnuj PahwaYunli ShaoGavin A HuttleyPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 8, Iss 7, p e69187 (2013)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Klara L Verbyla Von Bing Yap Anuj Pahwa Yunli Shao Gavin A Huttley The embedding problem for markov models of nucleotide substitution.
description	Continuous-time Markov processes are often used to model the complex natural phenomenon of sequence evolution. To make the process of sequence evolution tractable, simplifying assumptions are often made about the sequence properties and the underlying process. The validity of one such assumption, time-homogeneity, has never been explored. Violations of this assumption can be found by identifying non-embeddability. A process is non-embeddable if it can not be embedded in a continuous time-homogeneous Markov process. In this study, non-embeddability was demonstrated to exist when modelling sequence evolution with Markov models. Evidence of non-embeddability was found primarily at the third codon position, possibly resulting from changes in mutation rate over time. Outgroup edges and those with a deeper time depth were found to have an increased probability of the underlying process being non-embeddable. Overall, low levels of non-embeddability were detected when examining individual edges of triads across a diverse set of alignments. Subsequent phylogenetic reconstruction analyses demonstrated that non-embeddability could impact on the correct prediction of phylogenies, but at extremely low levels. Despite the existence of non-embeddability, there is minimal evidence of violations of the local time homogeneity assumption and consequently the impact is likely to be minor.
format	article
author	Klara L Verbyla Von Bing Yap Anuj Pahwa Yunli Shao Gavin A Huttley
author_facet	Klara L Verbyla Von Bing Yap Anuj Pahwa Yunli Shao Gavin A Huttley
author_sort	Klara L Verbyla
title	The embedding problem for markov models of nucleotide substitution.
title_short	The embedding problem for markov models of nucleotide substitution.
title_full	The embedding problem for markov models of nucleotide substitution.
title_fullStr	The embedding problem for markov models of nucleotide substitution.
title_full_unstemmed	The embedding problem for markov models of nucleotide substitution.
title_sort	embedding problem for markov models of nucleotide substitution.
publisher	Public Library of Science (PLoS)
publishDate	2013
url	https://doaj.org/article/e418da09653146ba84de9bb0611ebffa
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The embedding problem for markov models of nucleotide substitution.

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