Robustness of compound Dirichlet priors for Bayesian inference of branch lengths

Systematic Biology
Chi ZhangZiheng Yang

Abstract

We modified the phylogenetic program MrBayes 3.1.2 to incorporate the compound Dirichlet priors for branch lengths proposed recently by Rannala, Zhu, and Yang (2012. Tail paradox, partial identifiability and influential priors in Bayesian branch length inference. Mol. Biol. Evol. 29:325-335.) as a solution to the problem of branch-length overestimation in Bayesian phylogenetic inference. The compound Dirichlet prior specifies a fairly diffuse prior on the tree length (the sum of branch lengths) and uses a Dirichlet distribution to partition the tree length into branch lengths. Six problematic data sets originally analyzed by Brown, Hedtke, Lemmon, and Lemmon (2010. When trees grow too long: investigating the causes of highly inaccurate Bayesian branch-length estimates. Syst. Biol. 59:145-161) are reanalyzed using the modified version of MrBayes to investigate properties of Bayesian branch-length estimation using the new priors. While the default exponential priors for branch lengths produced extremely long trees, the compound Dirichlet priors produced posterior estimates that are much closer to the maximum likelihood estimates. Furthermore, the posterior tree lengths were quite robust to changes in the parameter values in the c...Continue Reading

References

Jul 1, 1994·Journal of Molecular Evolution·Z Yang
Aug 13, 2003·Bioinformatics·Fredrik Ronquist, John P Huelsenbeck
Oct 8, 2003·Systematic Biology·Vladimir MininJack Sullivan
Jul 14, 2005·Systematic Biology·Ziheng Yang, Bruce Rannala
May 10, 2007·Molecular Biology and Evolution·Ziheng Yang
Jul 31, 2007·Systematic Biology·Jeremy M Brown, Alan R Lemmon
Feb 13, 2008·Evolution; International Journal of Organic Evolution·Shannon M HedtkeDavid M Hillis
May 9, 2008·Molecular Phylogenetics and Evolution·Tony GambleAndrew M Simons
Sep 6, 2011·Molecular Biology and Evolution·Bruce RannalaZiheng Yang

❮ Previous
Next ❯

Citations

Jan 18, 2015·Systematic Biology·Bradley J NelsonJeremy M Brown
Feb 26, 2016·Molecular Ecology·Anthony J Barley, Robert C Thomson
Jul 28, 2016·Molecular Phylogenetics and Evolution·Fredrick J LarabeeAndrew V Suarez
Sep 11, 2019·Systematic Biology·Mathieu FourmentVladimir N Minin
Mar 30, 2012·Nature Reviews. Genetics·Ziheng Yang, Bruce Rannala
May 4, 2017·Current Protocols in Bioinformatics·Sebastian HöhnaTracy A Heath

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

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

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.

Microbicide

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.