A phylogenetic mixture model for detecting pattern-heterogeneity in gene sequence or character-state data.

By Mark Pagel, Andrew Meade. Systematic Biology, 2004

506 citations recorded by the source corpus.

Subfields: Political Science and International Relations, Safety Research

View Paper: https://www.semanticscholar.org/paper/4f63b3c05e228ff303d66da3cbb60862843ca345

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Citations in the corpus

The influence of rate heterogeneity among sites on the time dependence of molecular rates. (2012, background): “However, more general mixture-models have recently been shown to outperform the discrete gamma model, particularly when multi-modal heterogeneity is present (Lartillot and Philippe 2004; Pagel and Meade 2004; Huelsenbeck and Suchard 2007).”
Molecular phylogenetics of Vespoidea indicate paraphyly of the superfamily and novel relationships of its component families and subfamilies (2008, methodology): “Journal compilation © 2008 The Norwegian Academy of Science and Letters • Zoologica Scripta, 37, 5, September 2008, pp 539–560 545 model using MRBAYES; (ii) genes partitioned and unlinked under the GTR + I + Γ model with the covarion-like model (Tuffley & Steel 1998) applied using MRBAYES (the covar”
Incorporating molecular evolution into phylogenetic analysis, and a new compilation of conserved polymerase chain reaction primers for animal mitochondrial DNA (2006, background): “Furthermore, within a stem the pattern of variation may differ depending on the identity of the base; tertiary structure and protein interactions also add complexity (Gutell et al. 2002, Hickson et al. 1996, Pagel & Meade 2004).”
Computing Bayes factors using thermodynamic integration. (2006, methodology): “These methods are now applied extensively in molecular phylogenetics (Huelsenbeck and Ronquist, 2001; Larget and Simon, 1999; Lartillot and Philippe, 2004; Pagel and Meade, 2004; Suchard, 2001).”
The Pleasures and Perils of Darwinizing Culture (with Phylogenies) (2007, methodology): “However, methods that can identify pattern heterogeneity, such as the aforementioned mixture models (Pagel and Meade 2004), do not require a priori partitioning of data, and are thus ideally suited for the analysis of complex histories.”
Detecting and overcoming systematic errors in genome-scale phylogenies. (2007, background): “, 1992), and site-heterogeneous nucleotide/ amino acid replacement (Lartillot and Philippe, 2004; Pagel and Meade, 2004).”
High-Throughput Genomic Data in Systematics and Phylogenetics (2013, background): “More appropriate levels of model complexity can be obtained through mixture models (Pagel & Meade 2004) or data partitioning (Yang 1996).”
Bayesian estimation of ancestral character states on phylogenies. (2004, background): “A Markov chain is constructed, the states of which are different phylogenetic trees (Rannala and Yang, 1996; Wilson and Balding, 1998; Larget and Simon, 1999; Mau et al., 1999; Lutzoni et al., 2001; Huelsenbeck et al., 2001; Pagel and Lutzoni, 2002; Pagel and Meade, 2004).”
Selecting optimal partitioning schemes for phylogenomic datasets (2014, methodology): “However, partitioning remains the most widely-used method to account for variation in rates and patterns of substitution among sites [9,17,20,21].”
Suppression of long-branch attraction artefacts in the animal phylogeny using a site-heterogeneous model (2007, unknown): “Mixture models have also been implemented at this level [32], and they may display a similar robustness agains systematic artefacts.”
Bayesian Analysis of Correlated Evolution of Discrete Characters by Reversible‐Jump Markov Chain Monte Carlo (2006, methodology): “Markov chain Monte Carlo methods are now widely used in phylogenetic inference (e.g., Rannala and Yang 1996; Wilson and Balding 1998; Larget and Simon 1999; Huelsenbeck et al. 2001; Lutzoni et al. 2001; Pagel and Lutzoni 2002; Pagel and Meade 2004).”
Partitionfinder: combined selection of partitioning schemes and substitution models for phylogenetic analyses. (2012, methodology): “Although mixture models are implemented in an increasing variety of phylogenetic software (e.g., Pagel and Meade 2004; Stamatakis 2006; Le et al. 2008), partitioning remains by far the most common approach to incorporating heterogeneity in evolutionary processes among sites (Blair and Murphy 2011).”
Mutational dynamics and phylogenetic utility of noncoding chloroplast DNA (2009, background): “Bayesian and likelihood approaches will play an increasingly important role in phylogenetic inference because they allow the use of mixed models or relaxed parameters (Pagel and Meade 2004; Kelchner and Thomas 2007).”
PhyloBayes MPI: phylogenetic reconstruction with infinite mixtures of profiles in a parallel environment. (2013, methodology): “Mixture models have been proposed as a natural and simple approach for modeling site-specific effects and have been applied to nucleotides (Pagel and Meade 2004; Evans and Sullivan 2012), amino acids (Koshi and Goldstein 1998, 2001; Lartillot and Philippe 2004; Le et al.”