Bayesian inference in phylogeny

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, Bob Mau in Madison, and Shuying Li in University of Iowa, the last two being PhD students at the time. The approach has become very popular since the release of the MrBayes software in 2001, and is now one of the most popular methods in molecular phylogenetics. Bayesian inference refers to a probabilistic method developed by Reverend Thomas Bayes based on Bayes' theorem. Published posthumously in 1763 it was the first expression of inverse probability and the basis of Bayesian inference. Independently, unaware of Bayes' work, Pierre-Simon Laplace developed Bayes' theorem in 1774. Bayesian inference or the inverse probability method was the standard approach in statistical thinking until the early 1900s before RA Fisher developed what's now known as the classical/frequentist/Fisherian inference. Computational difficulties and philosophical objections had prevented the widespread adoption of the Bayesian approach until the 1990s, when Markov Chain Monte Carlo (MCMC) algorithms revolutionized Bayesian computation. The Bayesian approach to phylogenetic reconstruction combines the prior probability of a tree P(A) with the likelihood of the data (B) to produce a posterior probability distribution on trees P(A|B). The posterior probability of a tree will be the probability that the tree is correct, given the prior, the data, and the correctness of the likelihood model. MCMC methods can be described in three steps: first using a stochastic mechanism a new state for the Markov chain is proposed. Secondly, the probability of this new state to be correct is calculated. Thirdly, a new random variable (0,1) is proposed.