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

Systematic Biology
John Huelsenbeck, Bruce Rannala


What does the posterior probability of a phylogenetic tree mean?This simulation study shows that Bayesian posterior probabilities have the meaning that is typically ascribed to them; the posterior probability of a tree is the probability that the tree is correct, assuming that the model is correct. At the same time, the Bayesian method can be sensitive to model misspecification, and the sensitivity of the Bayesian method appears to be greater than the sensitivity of the nonparametric bootstrap method (using maximum likelihood to estimate trees). Although the estimates of phylogeny obtained by use of the method of maximum likelihood or the Bayesian method are likely to be similar, the assessment of the uncertainty of inferred trees via either bootstrapping (for maximum likelihood estimates) or posterior probabilities (for Bayesian estimates) is not likely to be the same. We suggest that the Bayesian method be implemented with the most complex models of those currently available, as this should reduce the chance that the method will concentrate too much probability on too few trees.


Oct 1, 1982·Genetical Research·L D Mueller, F J Ayala
Jan 1, 1981·Journal of Molecular Evolution·J Felsenstein
Mar 1, 1995·Molecular Phylogenetics and Evolution·A Zharkikh, W H Li
Feb 1, 1993·Journal of Molecular Evolution·N Goldman
Jul 1, 1993·International Journal for Parasitology·A G Rodrigo
Jan 1, 1996·Molecular Biology and Evolution·J Felsenstein, G A Churchill
Nov 12, 1996·Proceedings of the National Academy of Sciences of the United States of America·B EfronS Holmes
Dec 24, 1997·Mathematical Biosciences·C Tuffley, M Steel
Apr 4, 2000·Genetics·J P HuelsenbeckD Swofford
Aug 29, 2001·Bioinformatics·J P Huelsenbeck, F Ronquist
Nov 5, 2002·Molecular Phylogenetics and Evolution·Thomas P WilcoxDavid M Hillis
Nov 27, 2002·Proceedings of the National Academy of Sciences of the United States of America·Yoshiyuki SuzukiMasatoshi Nei
Feb 25, 2003·Molecular Biology and Evolution·Christophe J DouadyEmmanuel J P Douzery
Jul 15, 2003·Systematic Biology·Michael P CummingsKatarina Winka
Feb 18, 2004·Systematic Biology·Johan A A NylanderJosé Luis Nieves-Aldrey
Mar 23, 2004·Molecular Biology and Evolution·John P HuelsenbeckMichael E Alfaro
Jun 19, 2004·Systematic Biology·Alan R Lemmon, Emily C Moriarty
Oct 27, 2004·Systematic Biology·Chung-Ping LinThomas K Wood
Oct 27, 2004·Systematic Biology·Todd A CastoeChristopher L Parkinson
Jul 1, 1985·Evolution; International Journal of Organic Evolution·Joseph Felsenstein
Jul 1, 1988·Evolution; International Journal of Organic Evolution·Kåre Bremer

❮ Previous
Next ❯


Aug 21, 2009·Journal of Molecular Evolution·Darin R RokytaHolly A Wichman
Aug 29, 2009·Molecular Biology and Evolution·Dawn M SimonSteven Zimmerly
Oct 12, 2010·Molecular Biology and Evolution·Nicolas Lartillot, Raphaël Poujol
Aug 30, 2011·Molecular Biology and Evolution·Sudhir KumarKoichiro Tamura
Jan 26, 2007·Biology Letters·Beata UjvariThomas Madsen
Oct 15, 2008·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Ziheng Yang
Oct 15, 2008·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Kasper MunchRasmus Nielsen
Sep 10, 2009·Annual Review of Entomology·Birgit C Schlick-SteinerRoss H Crozier
Dec 8, 2009·Annual Review of Entomology·Fredrik Ronquist, Andrew R Deans
Feb 16, 2011·BMC Evolutionary Biology·Bettina E SchirrmeisterHomayoun C Bagheri
Nov 13, 2007·BMC Evolutionary Biology·Alexei J Drummond, Andrew Rambaut
Mar 23, 2007·BMC Evolutionary Biology·Maria S Poptsova, J Peter Gogarten
Jan 27, 2009·BMC Evolutionary Biology·Ye XiongGuang Yang
Jun 15, 2007·PloS One·Johannes Bergsten, Kelly B Miller
Mar 10, 2009·PloS One·Eileen KnorrBoran Altincicek
Dec 17, 2009·PloS One·Bryan Kolaczkowski, Joseph W Thornton
Nov 10, 2013·PloS One·Pengjun XuKongming Wu

❮ Previous
Next ❯

Related Concepts

Trending Feeds


Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.


Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.


Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.