Bayes or bootstrap? A simulation study comparing the performance of Bayesian Markov chain Monte Carlo sampling and bootstrapping in assessing phylogenetic confidence.

By Michael E. Alfaro, Stefan Zoller, F. Lutzoni. Molecular biology and evolution, 2003

1,103 citations recorded by the source corpus.

Subfields: Genetics, Molecular Biology, Paleontology

View Paper: https://www.semanticscholar.org/paper/d21f9d92299d1df18a237bcb1d5848f32e1d3191

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Citations in the corpus

Phylogenetic analysis of Tylenchida Thorne, 1949 as inferred from D2 and D3 expansion fragments of the 28S rRNA gene sequences (2006, background): “On the other hand, BI may often provide more accurate estimates of phylogeny than parsimony because it incorporates explicit models of DNA sequence evolution and may be less sensitive to long-branch attraction (Alfaro et al., 2003).”
Missing data and the accuracy of Bayesian phylogenetics (2008, methodology): “Although the performance of Bayesian phylogenetic methods has become relatively well understood through a large number of simulation studies (e.g., Suzuki et al., 2002; Wilcox et al., 2002; Alfaro et al., 2003; Cummings et al., 2003; Douady et al., 2003; Erixon et al., 2003; Huelsenbeck & Rannala,”
Assembling the fungal tree of life: progress, classification, and evolution of subcellular traits. (2004, background): “…can be obtained for wrong topological bipartitions with current programs implementing Bayesian MCMC, especially when internodes are very short (Alfaro et al., 2003; Buckley et al., 2002; Douady et al., 2003; Erixon et al., 2003; Kauff and Lutzoni, 2002; Leaché and Reeder, 2002; Suzuki et…”
Morphological and molecular data reveal cryptic speciation in Lasiodiplodia theobromae. (2008, background): “High support typically refers to bootstrap support values ≥ 70% and Bayesian posterior probabilities ≥ 95% (Alfaro et al., 2003).”
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).”
A molecular phylogenetic assessment of the advanced Asiatic and Malesian didymocarpoid Gesneriaceae with focus on non-monophyletic and monotypic genera (2011, background): “They are not strictly comparable to bootstrap values (Mo ¨ller et al. 2009), but are indicators of clade robustness (Lewis 2001; Alfaro et al. 2003; but see Cummings et al. 2003; Erixon et al. 2003).”
Frequentist properties of Bayesian posterior probabilities of phylogenetic trees under simple and complex substitution models. (2004, methodology): “A similar result is seen in Figure 4 of Alfaro et al. (2003).”
Developmental Gene Evolution and the Origin of Grass Inflorescence Diversity (2006, background): “Only branches supported by 0.95 or greater posterior probability were considered well supported, based on published simulation studies (Alfaro et al., 2003), although other studies have noted that Bayesian phylogenetic analyses can overestimate clade credibility values (Simmons et al., 2004).”
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): “…(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., 2003; Goloboff and Pol, 2004; Pickett et al., 2004; Simmons et al.,…”
Reliability of Bayesian posterior probabilities and bootstrap frequencies in phylogenetics. (2003, result): “Alfaro et al. (2003) argued that because data are parameterized differently in BAYES and MLBOOT, the methods are expected to give different results.”