Bayesian inference in phylogeny

Bayesian inference in phylogeny
ClassificationEvolutionary biology
SubclassificationMolecular phylogenetics
Optimally search criteriaBayesian inference

Bayesian inference of phylogeny combines the information in the prior and in the data likelihood to create the so-called posterior probability of trees, which is the probability that the tree is correct given the data, the prior and the likelihood model. Bayesian inference was introduced into molecular phylogenetics in the 1990s by three independent groups: Bruce Rannala and Ziheng Yang in Berkeley,[1][2] Bob Mau in Madison,[3] and Shuying Li in University of Iowa,[4] the last two being PhD students at the time. The approach has become very popular since the release of the MrBayes software in 2001,[5] and is now one of the most popular methods in molecular phylogenetics.

  1. ^ Rannala, Bruce; Yang, Ziheng (September 1996). "Probability distribution of molecular evolutionary trees: A new method of phylogenetic inference". Journal of Molecular Evolution. 43 (3): 304–311. Bibcode:1996JMolE..43..304R. doi:10.1007/BF02338839. PMID 8703097. S2CID 8269826.
  2. ^ Yang, Z.; Rannala, B. (1 July 1997). "Bayesian phylogenetic inference using DNA sequences: a Markov Chain Monte Carlo Method". Molecular Biology and Evolution. 14 (7): 717–724. doi:10.1093/oxfordjournals.molbev.a025811. PMID 9214744.
  3. ^ Mau, Bob; Newton, Michael A.; Larget, Bret (March 1999). "Bayesian Phylogenetic Inference via Markov Chain Monte Carlo Methods". Biometrics. 55 (1): 1–12. doi:10.1111/j.0006-341x.1999.00001.x. JSTOR 2533889. PMID 11318142. S2CID 932887.
  4. ^ Li, Shuying; Pearl, Dennis K.; Doss, Hani (June 2000). "Phylogenetic Tree Construction Using Markov Chain Monte Carlo". Journal of the American Statistical Association. 95 (450): 493–508. doi:10.1080/01621459.2000.10474227. JSTOR 2669394. S2CID 122459537.
  5. ^ Huelsenbeck, J. P.; Ronquist, F. (1 August 2001). "MRBAYES: Bayesian inference of phylogenetic trees". Bioinformatics. 17 (8): 754–755. doi:10.1093/bioinformatics/17.8.754. PMID 11524383.