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


Autoria(s): Pagel, Mark; Meade, Andrew
Contribuinte(s)

Institute of Biological, Environmental and Rural Sciences

Data(s)

11/12/2008

11/12/2008

01/08/2004

Resumo

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

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.

Peer reviewed

Formato

11

Identificador

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 . DOI: 10.1080/10635150490468675

1063-5157

PURE: 92454

PURE UUID: bd3d453b-92f0-4749-b8eb-76d2b351fdde

dspace: 2160/1558

http://hdl.handle.net/2160/1558

http://dx.doi.org/10.1080/10635150490468675

Idioma(s)

eng

Relação

Systematic Biology

Tipo

/dk/atira/pure/researchoutput/researchoutputtypes/contributiontojournal/article

Article (Journal)

Direitos