A Phylogenetic Mixture Model for Detecting Pattern-Heterogeneity in Gene Sequence or Character-State Data

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dc.contributor.author Pagel, Mark
dc.contributor.author Meade, Andrew
dc.date.accessioned 2008-12-11T16:28:26Z
dc.date.available 2008-12-11T16:28:26Z
dc.date.issued 2004-08-01
dc.identifier.citation Pagel , M & Meade , A 2004 , ' A Phylogenetic Mixture Model for Detecting Pattern-Heterogeneity in Gene Sequence or Character-State Data ' Systematic Biology , vol 53 , no. 4 , pp. 571-581 . , 10.1080/10635150490468675 en
dc.identifier.issn 1063-5157
dc.identifier.other PURE: 92454
dc.identifier.other dspace: 2160/1558
dc.identifier.uri http://hdl.handle.net/2160/1558
dc.identifier.uri http://www.informaworld.com/smpp/content?content=10.1080/10635150490468675 en
dc.description Mark Pagel, Andrew Meade (2004). A phylogenetic mixture model for detecting pattern-heterogeneity in gene sequence or character-state data. Systematic Biology, 53(4), 571-581. RAE2008 en
dc.description.abstract We describe a general likelihood-based 'mixture model' for inferring phylogenetic trees from gene-sequence or other character-state data. The model accommodates cases in which different sites in the alignment evolve in qualitatively distinct ways, but does not require prior knowledge of these patterns or partitioning of the data. We call this qualitative variability in the pattern of evolution across sites “pattern-heterogeneity” to distinguish it from both a homogenous process of evolution and from one characterized principally by differences in rates of evolution. We present studies to show that the model correctly retrieves the signals of pattern-heterogeneity from simulated gene-sequence data, and we apply the method to protein-coding genes and to a ribosomal 12S data set. The mixture model outperforms conventional partitioning in both these data sets. We implement the mixture model such that it can simultaneously detect rate- and pattern-heterogeneity. The model simplifies to a homogeneous model or a rate-variability model as special cases, and therefore always performs at least as well as these two approaches, and often considerably improves upon them. We make the model available within a Bayesian Markov-chain Monte Carlo framework for phylogenetic inference, as an easy-to-use computer program. en
dc.format.extent 11 en
dc.language.iso eng
dc.relation.ispartof Systematic Biology en
dc.title A Phylogenetic Mixture Model for Detecting Pattern-Heterogeneity in Gene Sequence or Character-State Data en
dc.type Text en
dc.type.publicationtype Article (Journal) en
dc.identifier.doi http://dx.doi.org/10.1080/10635150490468675
dc.contributor.institution Institute of Biological, Environmental and Rural Sciences en
dc.description.status Peer reviewed en


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