Frequentist properties of Bayesian posterior probabilities of phylogenetic trees under simple and complex substitution models.

By John P. Huelsenbeck, Bruce Rannala. Systematic Biology, 2004

881 citations recorded by the source corpus.

Subfields: Genetics, Molecular Biology, Paleontology

View Paper: https://www.semanticscholar.org/paper/7b6f6d19cc4813a678400e2248a19906f77a64f2

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Citations in the corpus

Molecular phylogenetics of Vespoidea indicate paraphyly of the superfamily and novel relationships of its component families and subfamilies (2008, background): “One situation where PPs may be unreliable (inflated) is when the model is too simple (Erixon et al. 2003; Huelsenbeck & Rannala 2004; Lemmon & Moriarty 2004); overparameterization, however, seems to have no adverse effects (Huelsenbeck & Rannala 2004).”
The phylogeny and evolution of Figitidae (Hymenoptera: Cynipoidea) (2007, background): “The advantages of a Bayesian analysis are the straightforward (theoretical) interpretation of probabilities (Huelsenbeck and Rannala, 2004) and the way uncertainties in trees and parameter values can be accommodated: instead of basing conclusions on point estimates, uncertainty in tree topology can ”
Renewing Felsenstein’s Phylogenetic Bootstrap in the Era of Big Data (2018, background): “4, ED3) and could be extended to parametric bootstrap 2 and Bayesian branch supports 14 .”
Discordant mitochondrial and nuclear gene phylogenies in emydid turtles: implications for speciation and conservation (2010, methodology): “Clades with posterior probabilities (Pp) 0.95 were considered as strongly supported (Wilcox et al., 2002; Alfaro, Zoller & Lutzoni, 2003; Erixon et al., 2003; Huelsenbeck & Rannala, 2004).”
Phylogenomics and the reconstruction of the tree of life (2005, methodology): “Therefore, methods that focus on the most reliable characters have been developed to reduce the impact of inconsistency. a | Purine–pyrimidine coding (RY coding).”
Correlating viral phenotypes with phylogeny: accounting for phylogenetic uncertainty. (2008, methodology): “In addition, Bayesian MCMC methods are thought to provide a better estimate of phylogenetic accuracy than the bootstrap or jacknife methods commonly used to assess ML trees (Alfaro et al., 2003; Huelsenbeck and Rannala, 2004).”
A review of long‐branch attraction (2005, background): “…2002; Suzuki et al., 2002; Whittingham et al., 2002; Wilcox et al., 2002; Alfaro et al., 2003; Cummings et al., 2003; Douady et al., 2003; Erixon et al., 2003; Goloboff and Pol, 2004; Pickett et al., 2004; Simmons et al., 2004; Huelsenbeck and Rannala, 2004) and they should be taken with caution.”
A subfamily‐level classification of mealybugs (Hemiptera: Pseudococcidae) based on integrated molecular and morphological data (2008, methodology): “1 (Ronquist & Huelsenbeck, 2003). The data were partitioned by data type (DNA and Morphology), by gene, and by codon position for Ef-1a. The mk1 model, with gamma-distributed rates and coding set to variable, was applied to the morphological dataset (Lewis, 2001). Because simulation by Huelsenbeck &”
A molecular phylogenetic study of armoured scale insects (Hemiptera: Diaspididae) (2005, methodology): “This model was chosen a priori as a result of the different substitution constraints facing each defined partition and to err on the side of a more complicated model, which is very important in Bayesian analyses (Huelsenbeck & Rannala, 2004).”
Survey of Branch Support Methods Demonstrates Accuracy, Power, and Robustness of Fast Likelihood-based Approximation Schemes (2011, background): “This nice property, however, is often affected by model violations (Huelsenbeck and Rannala 2004).”
Incorporating molecular evolution into phylogenetic analysis, and a new compilation of conserved polymerase chain reaction primers for animal mitochondrial DNA (2006, methodology): “F or p er so na l u se o nl y. ANRV292-ES37-20 ARI 17 October 2006 7:32 proportions because the former give a more direct measure of confidence in a node (e.g., Huelsenbeck & Rannala 2004).”
A review of the tribes of Deltocephalinae (Hemiptera: Auchenorrhyncha: Cicadellidae) (2013, methodology): “Selected references Linnavuori (1979b), Hayashi (1996), Li & Chen (1998), Knight & Webb (2002), Chen et al.”