Potential applications and pitfalls of Bayesian inference of phylogeny.

By John P. Huelsenbeck, Bret R. Larget, Richard E Miller, Fredrik Ronquist. Systematic Biology, 2002

781 citations recorded by the source corpus.

Subfields: Artificial Intelligence, Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/022df4c48f5a69735751bb68ffcb63e10c649d10

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Citations in the corpus

Plastid and nuclear DNA polymorphism reveals historical processes of isolation and reticulation in the olive tree complex (Olea europaea) (2007, methodology): “These analyses were replicated three times to ensure topological convergence and homogeneity of posterior probabilities (Huelsenbeck et al., 2002).”
Phylogeny and Biogeography of Isophyllous Species of Campanula (Campanulaceae) in the Mediterranean Area (2006, background): “…by determining the posterior probabilities of alternative topologies from the combined set of trees after the burn-in period (see above), considering alternative topologies with posterior probabilities of 0.05 or more as not significantly worse (Huelsenbeck et al. 2002; Steele et al. 2005).”
A review of long‐branch attraction (2005, methodology): “Huelsenbeck et al. (2002a) concluded that the outgroupcriteria for rooting performed better than both a molecular clock and a non-reversible model of DNA substitution.”
Phylogeny in cryptic weevils: molecules, morphology and new genera of western Palaearctic Cryptorhynchinae (Coleoptera : Curculionidae) (2008, background): “Corroborating the burn-in values of the main analyses and excluding the possibility of an attraction to local optima (Huelsenbeck and Bollback 2001, Huelsenbeck et al. 2002), four additional replicates for each dataset (not considered further) were run with a million generations each and with…”
RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees (2005, background): “Furthermore, Figure 4 reveals one of the main problems of MC analysis ( Huelsenbeck et al. 2002 ): When to stop the chain? In the example the run with the random starting tree seems to have reached apparent stationarity, although the tree is far from optimal.”
Gondwanan radiation of the Southern Hemisphere crayfishes (Decapoda: Parastacidae): evidence from fossils and molecules (2010, methodology): “Bayesian topological tests were conducted as described in Huelsenbeck et al. (2002).”
Tyrant flycatchers coming out in the open: phylogeny and ecological radiation of Tyrannidae (Aves, Passeriformes) (2008, background): “The 50% majority rule consensus trees from the individual runs were compared to ensure that the individual runs had converged on the same target distribution (Huelsenbeck et al. 2002).”
Endopterygote systematics – where do we stand and what is the goal (Hexapoda, Arthropoda)? (2006, methodology): “Another recently developed program is MrBayes (Huelsenbeck & Ronquist, 2001; Huelsenbeck et al., 2002), which uses a Markov chain Monte Carlo simulation to approximate the posterior probabilities of trees.”
DNA barcoding: a tool for improved taxon identification and detection of species diversity (2011, methodology): “Posterior probability (PP) distributions of trees were created using the Metropolis-coupled Marcov chain Monte Carlo (MCMCMC) method and the search strategies suggested by Huelsenbeck and Ronquist (2001, 2002).”
Mainland colonization by island lizards (2005, background): “Bayesian posterior probability support of nodes (Huelsenbeck et al., 2002; Suzuki et al., 2002; Wilcox et al., 2002; Alfaro et al., 2003; Douady et al., 2003; Erixon et al., 2003; Simmons et al., 2004).”