Modelling heterotachy in phylogenetic inference by reversible-jump Markov chain Monte Carlo

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dc.contributor.author Pagel, Mark
dc.contributor.author Meade, Andrew
dc.date.accessioned 2009-05-21T11:07:54Z
dc.date.available 2009-05-21T11:07:54Z
dc.date.issued 2008-12-27
dc.identifier.citation Pagel , M & Meade , A 2008 , ' Modelling heterotachy in phylogenetic inference by reversible-jump Markov chain Monte Carlo ' Philosophical Transactions of the Royal Society B: Biological Sciences , vol 363 , no. 1512 , pp. 3955-3964 . en
dc.identifier.issn 0962-8436
dc.identifier.other PURE: 102329
dc.identifier.other dspace: 2160/2301
dc.identifier.uri http://hdl.handle.net/2160/2301
dc.identifier.uri http://rstb.royalsocietypublishing.org/content/363/1512/3955.full.pdf+html en
dc.description Pagel, M., Meade, A. (2008). Modelling heterotachy in phylogenetic inference by reversible-jump Markov chain Monte Carlo.  Philosophical Transactions of the Royal Society B, 363 (1512), 3955-3964. IMPF: 05.56 Discussion Meeting Issue ‘Statistical and computational challenges in molecular phylogenetics and evolution’ organized by Ziheng Yang and Nick Goldman Sponsorship: Natural Environment Research Council en
dc.description.abstract The rate at which a given site in a gene sequence alignment evolves over time may vary. This phenomenon—known as heterotachy—can bias or distort phylogenetic trees inferred from models of sequence evolution that assume rates of evolution are constant. Here, we describe a phylogenetic mixture model designed to accommodate heterotachy. The method sums the likelihood of the data at each site over more than one set of branch lengths on the same tree topology. A branch-length set that is best for one site may differ from the branch-length set that is best for some other site, thereby allowing different sites to have different rates of change throughout the tree. Because rate variation may not be present in all branches, we use a reversible-jump Markov chain Monte Carlo algorithm to identify those branches in which reliable amounts of heterotachy occur. We implement the method in combination with our ‘pattern-heterogeneity’ mixture model, applying it to simulated data and five published datasets. We find that complex evolutionary signals of heterotachy are routinely present over and above variation in the rate or pattern of evolution across sites, that the reversible-jump method requires far fewer parameters than conventional mixture models to describe it, and serves to identify the regions of the tree in which heterotachy is most pronounced. The reversible-jump procedure also removes the need for a posteriori tests of ‘significance’ such as the Akaike or Bayesian information criterion tests, or Bayes factors. Heterotachy has important consequences for the correct reconstruction of phylogenies as well as for tests of hypotheses that rely on accurate branch-length information. These include molecular clocks, analyses of tempo and mode of evolution, comparative studies and ancestral state reconstruction. The model is available from the authors' website, and can be used for the analysis of both nucleotide and morphological data. en
dc.format.extent 10 en
dc.language.iso eng
dc.relation.ispartof Philosophical Transactions of the Royal Society B: Biological Sciences en
dc.title Modelling heterotachy in phylogenetic inference by reversible-jump Markov chain Monte Carlo en
dc.type Text en
dc.type.publicationtype Article (Journal) en
dc.identifier.doi http://dx.doi.org/10.1098/rstb.2008.0178
dc.contributor.institution Institute of Biological, Environmental and Rural Sciences en
dc.description.status Peer reviewed en


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