Relaxed phylogenetics and dating with confidence.

In phylogenetics, the unrooted model of phylogeny and the strict molecular clock model are two extremes of a continuum. Despite their dominance in phylogenetic inference, it is evident that both are biologically unrealistic and that the real evolutionary process lies between these two extremes. Fort...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Alexei J Drummond, Simon Y W Ho, Matthew J Phillips, Andrew Rambaut
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2006
Materias:	Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/5d6eec81957d4d0eba2721544a384951
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:5d6eec81957d4d0eba2721544a384951
record_format	dspace
spelling	oai:doaj.org-article:5d6eec81957d4d0eba2721544a3849512021-12-02T19:54:32ZRelaxed phylogenetics and dating with confidence.1544-91731545-788510.1371/journal.pbio.0040088https://doaj.org/article/5d6eec81957d4d0eba2721544a3849512006-05-01T00:00:00Zhttps://doi.org/10.1371/journal.pbio.0040088https://doaj.org/toc/1544-9173https://doaj.org/toc/1545-7885In phylogenetics, the unrooted model of phylogeny and the strict molecular clock model are two extremes of a continuum. Despite their dominance in phylogenetic inference, it is evident that both are biologically unrealistic and that the real evolutionary process lies between these two extremes. Fortunately, intermediate models employing relaxed molecular clocks have been described. These models open the gate to a new field of "relaxed phylogenetics." Here we introduce a new approach to performing relaxed phylogenetic analysis. We describe how it can be used to estimate phylogenies and divergence times in the face of uncertainty in evolutionary rates and calibration times. Our approach also provides a means for measuring the clocklikeness of datasets and comparing this measure between different genes and phylogenies. We find no significant rate autocorrelation among branches in three large datasets, suggesting that autocorrelated models are not necessarily suitable for these data. In addition, we place these datasets on the continuum of clocklikeness between a strict molecular clock and the alternative unrooted extreme. Finally, we present analyses of 102 bacterial, 106 yeast, 61 plant, 99 metazoan, and 500 primate alignments. From these we conclude that our method is phylogenetically more accurate and precise than the traditional unrooted model while adding the ability to infer a timescale to evolution.Alexei J DrummondSimon Y W HoMatthew J PhillipsAndrew RambautPublic Library of Science (PLoS)articleBiology (General)QH301-705.5ENPLoS Biology, Vol 4, Iss 5, p e88 (2006)
institution	DOAJ
collection	DOAJ
language	EN
topic	Biology (General) QH301-705.5
spellingShingle	Biology (General) QH301-705.5 Alexei J Drummond Simon Y W Ho Matthew J Phillips Andrew Rambaut Relaxed phylogenetics and dating with confidence.
description	In phylogenetics, the unrooted model of phylogeny and the strict molecular clock model are two extremes of a continuum. Despite their dominance in phylogenetic inference, it is evident that both are biologically unrealistic and that the real evolutionary process lies between these two extremes. Fortunately, intermediate models employing relaxed molecular clocks have been described. These models open the gate to a new field of "relaxed phylogenetics." Here we introduce a new approach to performing relaxed phylogenetic analysis. We describe how it can be used to estimate phylogenies and divergence times in the face of uncertainty in evolutionary rates and calibration times. Our approach also provides a means for measuring the clocklikeness of datasets and comparing this measure between different genes and phylogenies. We find no significant rate autocorrelation among branches in three large datasets, suggesting that autocorrelated models are not necessarily suitable for these data. In addition, we place these datasets on the continuum of clocklikeness between a strict molecular clock and the alternative unrooted extreme. Finally, we present analyses of 102 bacterial, 106 yeast, 61 plant, 99 metazoan, and 500 primate alignments. From these we conclude that our method is phylogenetically more accurate and precise than the traditional unrooted model while adding the ability to infer a timescale to evolution.
format	article
author	Alexei J Drummond Simon Y W Ho Matthew J Phillips Andrew Rambaut
author_facet	Alexei J Drummond Simon Y W Ho Matthew J Phillips Andrew Rambaut
author_sort	Alexei J Drummond
title	Relaxed phylogenetics and dating with confidence.
title_short	Relaxed phylogenetics and dating with confidence.
title_full	Relaxed phylogenetics and dating with confidence.
title_fullStr	Relaxed phylogenetics and dating with confidence.
title_full_unstemmed	Relaxed phylogenetics and dating with confidence.
title_sort	relaxed phylogenetics and dating with confidence.
publisher	Public Library of Science (PLoS)
publishDate	2006
url	https://doaj.org/article/5d6eec81957d4d0eba2721544a384951
work_keys_str_mv	AT alexeijdrummond relaxedphylogeneticsanddatingwithconfidence AT simonywho relaxedphylogeneticsanddatingwithconfidence AT matthewjphillips relaxedphylogeneticsanddatingwithconfidence AT andrewrambaut relaxedphylogeneticsanddatingwithconfidence
_version_	1718375901550346240

Relaxed phylogenetics and dating with confidence.

Ejemplares similares