Bayesian Analysis of Correlated Evolution of Discrete Characters by Reversible‐Jump Markov Chain Monte Carlo

By Mark Pagel, Andrew Meade. American Naturalist, 2006

934 citations recorded by the source corpus.

Subfields: Genetics, Molecular Biology, Paleontology

View Paper: https://www.semanticscholar.org/paper/5148c279d131cce3d40cd6fb3f5c57fc675ea6da

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Citations in the corpus

A Phylogenetic Analysis of the Evolution of Wind Pollination in the Angiosperms (2008, background): “This is supported by the observation that most ambophilous taxa are pollinated by generalist pollinators (e.g., Salix: Peeters and Totland 1999; Tamura and Kudo 2000; Piper: De Figueiredo and Sazima 2000; Linanthus: Goodwillie 1999; Thalictrum: Kaplan and Mulcahy 1971; Schiedea: Weller et al. 1998, ”
Global stingless bee phylogeny supports ancient divergence, vicariance, and long distance dispersal (2009, methodology): “To account for phylogenetic uncertainty and branch length in the analyses, we explored BAYESTRAITS, version 1.0 (Pagel, Meade & Barker, 2004; Pagel & Meade, 2006), which has been used in other studies to infer ancestral geographic range (Praz et al., 2008; Xiang & Thomas, 2008).”
Genome Size Dynamics and Evolution in Monocots (2010, methodology): “The two statistical modeling programs used for analysis were BayesTraits [168–170] and Brownie [171].”
Territoriality, Social Bonds, and the Evolution of Communal Signaling in Birds (2016, positive): “We ran each BayesTraits model for 1.1 × 10 7 iterations, discarding an initial burn-in of 10 6 and sampling the chain every 10,000 iterations, resulting in a sample of 1000 per model/per tree.”
The evolution of food sharing in primates (2011, methodology): “Rather than testing the BF against a distribution such as chi square, by convention, a BF >2 is taken as positive evidence for dependent evolution, BF >5 as strong positive evidence, and BF >10 as very strong positive evidence (Pagel and Meade 2006).”
General quantitative genetic methods for comparative biology: phylogenies, taxonomies and multi‐trait models for continuous and categorical characters (2010, methodology): “…also, using MCMC. Alternative methods exist, mainly based around models of substitutions in DNA sequences (Pagel, 1994; Huelsenbeck et al., 2003; Pagel & Meade, 2006), but Felsenstein (2005) gives a persuasive argument as to why the quantitative genetic approach is to be preferred for the…”
Maximum likelihood inference of geographic range evolution by dispersal, local extinction, and cladogenesis. (2008, background): “, Schluter, 1997; Pagel, 1994, 1999) and Bayesian (e.g., Huelsenbeck and Bollback, 2001; Huelsenbeck et al., 2003; Pagel et al., 2004; Pagel and Meade, 2006) inference methods has been especially active, yielding a rich statistical tool set for investigating a wide range of macroevolutionary questio”
Ecology of plant speciation (2010, background): “Future extensions of the Duminil & al. study should use the more powerful tests of correlated evolution now available (e.g., Pagel, 1999; Pagel & Meade, 2006).”
Prospects and challenges for parametric models in historical biogeographical inference (2009, methodology): “…(see Sullivan & Joyce, 2005, for a review), and new approaches such as mixture models (Pagel & Meade, 2004), model averaging (Posada & Buckley, 2004) and reversible-jump Markov chain Monte Carlo methods (Pagel & Meade, 2006) allow ancestral inference without the need to apply a specific model.”
MODELING STABILIZING SELECTION: EXPANDING THE ORNSTEIN–UHLENBECK MODEL OF ADAPTIVE EVOLUTION (2012, methodology): “As with Huelsenbeck et al. (2004) and Pagel and Meade (2006), a reversible jump MCMC approach could also be used to get the posterior probabilities of various models, ranging from BM1 to OUMVA, in a single analysis.”
Phylogenetic trees do not reliably predict feature diversity (2014, background): “…1953) in which rates of change decline over time; (Harmon et al., 2010)], whether change in one feature is conditional upon the state of others (e.g. Pagel & Meade, 2006) and whether the likelihood and magnitude of change are conditional on the state of the feature at the time (e.g.…”
Why are there so many plant species in the Neotropics (2011, methodology): “Phylogenetic correlation analyses (e.g., Pagel & Meade, 2006; Freckleton & al., 2008) could be increasingly used to test whether increases in diversification rates can be associated with specific events, such as dispersal into a new region or acquisition of a morphological “key innovation” (e.g.,…”
Changing philosophies and tools for statistical inferences in behavioral ecology (2009, background): “Moreover, in a comparative study of trait variation across species, the application of the Bayesian approach can treat uncertainties about estimating phylogenetic relationships (Pagel et al. 2004; Pagel and Meade 2006).”
Assembling the Tree of the Monocotyledons: Plastome Sequence Phylogeny and Evolution of Poales1 (2010, methodology): “BayesDiscrete tests for significant patterns of correlated evolution of two binary traits by comparing the fit (ln likelihood) to models that assume their independent versus dependent evolution on the phylogeny provided using continuous- time Markov models (Pagel & Meade, 2006).”
Historical biogeography and life‐history evolution of Andean Puya (Bromeliaceae) (2013, methodology): “Second, we employed ancestral state reconstruction using the MultiState program implemented in BayesTraits ver.”