Overcredibility of molecular phylogenies obtained by Bayesian phylogenetics

By Yoshiyuki Suzuki, Galina V. Glazko, Masatoshi Nei. Proceedings of the National Academy of Sciences of the United States of America, 2002

635 citations recorded by the source corpus.

Subfields: Genetics, Molecular Biology, Paleontology

View Paper: https://www.semanticscholar.org/paper/532119590512d790feb30d4c3acc2e5cddafff68

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Genetics

In Molecular Biology

In Paleontology

Citations in the corpus

Phylogenetic analysis and a time tree for a large drosophilid data set (Diptera: Drosophilidae) (2013, background): “Furthermore, Bayesian analyses are known to inflate clade support, and their statistical support may not hold if more consistent statistical tests are performed (Suzuki et al. 2002).”
A phylogeny of legumes (Leguminosae) based on analysis of the plastid matK gene resolves many well-supported subclades within the family. (2004, background): “Within Fabales, pairwise distances (calculated across all sites as uncorrected p values in PAUP*) in matK sequences ranged from a maximum of nearly 17% among outgroups and caesalpinioids, to nearly 7% among mimosoids, 12% among caesalpinioids, and just over 19% among papilionoids.”
Phylogenetic Relationships in Fagales Based on DNA Sequences from Three Genomes (2004, background): “However, PP values may be inflated relative to bootstrap values (Suzuki et al. 2002).”
Bayesian phylogenetic analysis of combined data. (2004, background): “Recent computer simulations have shown that with certain types of extreme model deviations, Bayesian inference can result in excessively high posterior probabilities for clades (Suzuki et al., 2002).”
A Dated Phylogeny of Marsupials Using a Molecular Supermatrix and Multiple Fossil Constraints (2008, background): “Studies indicate that posterior probabilities may be misleadingly high, whereas bootstrap values are more conservative (Suzuki et al. 2002; Taylor and Piel 2004).”
Bayesian Analysis of Molecular Evolution Using MrBayes (2005, background): “The posterior probabilities are usually compared to the nonparametric bootstrap proportions, and many workers have reached the conclusion that the posterior probabilities on clades are too high, or that the posterior probabilities do not have an easy interpretation (Suzuki et al, 2002).”
Phylogenetic Analysis of the Lythraceae Based on Four Gene Regions and Morphology (2005, methodology): “MP analyses were performed in PAUP* 4.0b10 (Swofford 2002) using heuristic search algorithms with random addition and 1000 replicates and holding 10 trees to search for islands of equally most parsimonious trees.”
A review of long‐branch attraction (2005, background): “…values of clades has been extensively debated in the recent literature (Huelsenbeck et al., 2002b; Leaché and Reeder, 2002; Reed et al., 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.,…”
Reliability of Bayesian posterior probabilities and bootstrap frequencies in phylogenetics. (2003, background): “Suzuki et al. (2002) showed that BAYES often gives high support values for groups, even with completely uninformative data.”
Evolutionary studies of ectomycorrhizal fungi: recent advances and future directions (2004, background): “Finally, the lack of correspondence between bootstrap values and posterior probabilities is reason for concern (Suzuki et al. 2002; Alfaro et al. 2003; Douady et al. 2003).”
Molecular phylogenetics of Vespoidea indicate paraphyly of the superfamily and novel relationships of its component families and subfamilies (2008, methodology): “The tendency of Bayesian techniques to find significant support (high PP) for clades where bootstrap support is lacking, however, has caused some to question the reliability of this approach (Suzuki et al. 2002; Cummings et al. 2003; Douady et al. 2003; Simmons et al. 2004).”
PHYLOGENETIC RELATIONSHIPS WITHIN IGUANIDAE INFERRED USING MOLECULAR AND MORPHOLOGICAL DATA AND A PHYLOGENETIC TAXONOMY OF IGUANIAN LIZARDS (2003, result): “Comparison of branch support, as assessed using parsimony, and Bayesian criteria is consistent with the suggestion that Bayesian posterior probabilities generally overestimate support for branches in the tree (Suzuki et al., 2002).”
Molecular phylogenetics: principles and practice (2012, background): “Posterior probabilities for trees and clades that have been calculated from real data sets often appear to be too high 66,78–80 .”
Phylogeny of Aristolochiaceae based on parsimony, likelihood, and Bayesian analyses of trnL-trnF sequences (2004, positive): “Lewis 1998, Swofford et al. 1996) and, thus, confidence in the results found with ML and Bayesian inference is higher than in MP. However, PPs are known to frequently overestimate confidence in a given clade (Huelsenbeck et al. 2002, Suzuki et al. 2002 ), and should at least be treated with more ca”