Reliability of Bayesian posterior probabilities and bootstrap frequencies in phylogenetics.

By Per-Olof Erixon, B. Svennblad, Tom Britton, Bengt Oxelman. Systematic Biology, 2003

686 citations recorded by the source corpus.

Subfields: Genetics, Molecular Biology, Paleontology

View Paper: https://www.semanticscholar.org/paper/8edea56cd91accbe440039626d3371fc286c4b28

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

Deciphering the products of evolution at the species level: the need for an integrative taxonomy (2009, background): “Clades with posterior probabilities ≥ 0.95 are considered supported, but we caution that relatively high posterior probabilities for short internodes may be over-estimates of confidence (Alfaro et al. 2003; Erixon et al. 2003).”
Phylogenetic systematics of Glassfrogs (Amphibia: Centrolenidae) and their sister taxon Allophryne ruthveni (2009, background): “…framework, clades with posterior probabilities ≥ 0.95 are considered strongly supported, but we caution that relatively high posterior probabilities for short internodes (particularly those with low bootstrap values) may be over-estimates of confidence (Erixon et al. 2003; Alfaro et al. 2003).”
Partitioned Bayesian analyses, partition choice, and the phylogenetic relationships of scincid lizards. (2005, result): “Unlike nonparametric bootstrap values, which are known to be conservative estimates of clade confidence (Hillis and Bull, 1993), recent simulation studies (e.g., Alfaro et al., 2003; Erixon et al., 2003; Wilcox et al, 2002) have demonstrated that Bayesian posterior probabilities are less biased esti”
Ultraconserved elements show utility in phylogenetic inference of Adephaga (Coleoptera) and suggest paraphyly of ‘Hydradephaga’ (2017, background): “95 are considered strongly supported (Hillis & Bull, 1993; Erixon et al., 2003).”
A 567‐Taxon Data Set for Angiosperms: The Challenges Posed by Bayesian Analyses of Large Data Sets (2007, background): “However, caution must be exercised in the interpretation of high pp values (e.g., Miller et al. 2002; Suzuki et al. 2002; Erixon et al. 2003; Goloboff and Pol 2005).”
A Three-Gene Phylogeny of the Genus Solanum (Solanaceae) (2007, background): “…analyses (cut off at # 95% PP values), but posterior probabilities are known to be inflated relative to bootstrap values (Cummings et al. 2003; Erixon et al. 2003; Simmons et al. 2004) and are more prone to suggest strong support for incorrect phylogenetic hypotheses, particularly when the…”
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).”
Basal Clades and Molecular Systematics of Heteromyid Rodents (2007, neutral): “2; Cummings et al. 2003; Erixon et al. 2003).”
Frequentist properties of Bayesian posterior probabilities of phylogenetic trees under simple and complex substitution models. (2004, background): “…have noted that posterior probabilities on clades tend to be higher than the bootstrap proportions on the same clades (Douady et al., 2003; Erixon et al., 2003; but see Cummings et al., 2003), and Murphy et al. (2001) speculated that posterior probabilities do not suffer from being too…”
Phylogenetic Relationships and Classification of Didelphid Marsupials, an Extant Radiation of New World Metatherian Mammals (2009, background): “…(from MP and ML analyses) and Bayesian posterior probabilities, both of which have respectable statistical pedigrees (Felsenstein, 1985; Efron et al., 1996; Huelsenbeck et al., 2002) despite their imperfect relationship to type I error rates (Erixon et al., 2003; Alfaro and Holder, 2006).”
Progress and challenges toward developing a phylogeny and classification of the hornworts (2007, result): “In general, support levels were much higher than seen with parsimony bootstrapping (Erixon et al. 2003).”
A review of long‐branch attraction (2005, background): “…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., 2003; Goloboff and Pol, 2004; Pickett et al., 2004; Simmons et al., 2004; Huelsenbeck and Rannala, 2004) and they should be taken…”