Bayesian Inference of Phylogeny and Its Impact on Evolutionary Biology

By John P. Huelsenbeck, Fredrik Ronquist, Rasmus Nielsen, Jonathan P. Bollback. Science, 2001

2,789 citations recorded by the source corpus.

Subfields: Genetics, Molecular Biology, Paleontology

View Paper: https://www.semanticscholar.org/paper/3d6e5f2caa50a415cee56acf5860905022250e6a

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Citations in the corpus

Advances in Protein Chemistry and Structural Biology (2010, methodology): “These can be computed using maximum likelihood method or Bayesian method (Adachi and Hasegawa, 1996; Huelsenbeck et al., 2001; Yang, 1997).”
Comparison of site-specific rate-inference methods for protein sequences: empirical Bayesian methods are superior. (2004, methodology): “In cases where this is not the case, one might use the Markov chain Monte Carlo technique to take the uncertainty of the tree topology into account (Huelsenbeck et al. 2001).”
Natural Delineation, Molecular Phylogeny and Floral Evolution in Campanula (2008, methodology): “The models and the resulting parameter estimates were then used in BI analyses conducted with MrBayes 3.1 (Huelsenbeck et al. 2001; Ronquist and Huelsenbeck 2003).”
Taxonomy of Gambierdiscus including four new species, Gambierdiscus caribaeus, Gambierdiscus carolinianus, Gambierdiscus carpenteri and Gambierdiscus ruetzleri (Gonyaulacales, Dinophyceae) (2009, neutral): “0b4 (Huelsenbeck et al. 2001).”
FROM WORDS TO DATES: WATER INTO WINE, MATHEMAGIC OR PHYLOGENETIC INFERENCE? (2005, methodology): “First, character-based stochastic models of evolution retain phylogenetic information from the source data and allow us to reconstruct phylogeny accurately, even under conditions of rate heterogeneity (Huelsenbeck et al., 2001).”
Diet predicts intestine length in Lake Tanganyika’s cichlid fishes (2009, methodology): “After editing and aligning sequence data, we used Bayesian phylogenetic methods implemented in MR.BAYES 3.1.2 ( Huelsenbeck et al. 2001; Ronquist & Huelsenbeck 2003) to construct a phylogeny using the complete ND2 and cytb gene sequences for each species (Fig. 1). We ran MR.BAYES for two runs of 2 ”
A synopsis of the South Asian fishes referred to Puntius (Pisces: Cyprinidae) (2012, methodology): “We used the frequencies of clades in trees that were sampled every ten generations from the last 250 000 generations as estimates of the posterior probabilities of those clades (Huelsenbeck et al., 2001).”
Twelve new species of Cyrtodactylus Gray (Squamata: Gekkonidae) from isolated limestone habitats in east-central and southern Myanmar demonstrate high localized diversity and unprecedented microendemism (2018, background): “95 and above were considered well-supported (Huelsenbeck et al., 2001; Wilcox et al., 2002).”
A new subfamilial and tribal classification of the pantropical flowering plant family Annonaceae informed by molecular phylogenetics (2012, positive): “Bayesian inference Bayesian analysis was performed on the combined dataset using MrBayes 3.2 (Huelsenbeck et al., 2001; Ronquist & Huelsenbeck, 2003).”
Incorporating molecular evolution into phylogenetic analysis, and a new compilation of conserved polymerase chain reaction primers for animal mitochondrial DNA (2006, methodology): “Bayesian phylogenetic analysis (Huelsenbeck et al. 2001, Larget & Simon 1999, Yang & Rannala 1997) was rapidly embraced once MrBayes became available (Huelsenbeck & Ronquist 2001).”
Language-tree divergence times support the Anatolian theory of Indo-European origin (2003, methodology): “(MCMC) methods in which the frequency distribution of the sample approximates the posterior probability distribution of the tree”
Phylogenomics and the reconstruction of the tree of life (2005, methodology): “Bayesian methods 106 derive the distribution of trees according to their posterior probability,using Bayes’mathematical formula to combine the likelihood function with PRIOR PROBABILITIES on trees.”