ABSTRACT
Department of Informational Statistics, Korea University, Sejong-city, South Korea
Faming Liang
Department of Statistics, Texas A&M University, College Station, Texas, USA
CONTENTS
7.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 129 7.2 Bayesian phylogeny inference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 130
7.2.1 Tree representation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 130 7.2.2 Evolutionary models . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 132 7.2.3 Bayesian approach . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 134
7.3 Monte Carlo methods for Bayesian phylogeny inference . . . . . . . . 135 7.3.1 Markov chain Monte Carlo algorithms . . . . . . . . . . . . . . . . . . 135
7.3.1.1 Rannala and Yang (1996) . . . . . . . . . . . . . . . . . . . . 136 7.3.1.2 Mau and Newton (1997) . . . . . . . . . . . . . . . . . . . . . 137 7.3.1.3 Mau et al. (1999) and Newton et al. (1999) . 139 7.3.1.4 Larget and Simon (1999) . . . . . . . . . . . . . . . . . . . . . 140 7.3.1.5 Li et al. (2000) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 142
7.3.2 Advanced MCMC algorithms . . . . . . . . . . . . . . . . . . . . . . . . . . . 144 7.3.2.1 Huelsenbeck and Ronquist (2001) . . . . . . . . . . . . 144 7.3.2.2 Feng et al. (2003) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 146 7.3.2.3 Altekar et al. (2004) . . . . . . . . . . . . . . . . . . . . . . . . . . 149 7.3.2.4 Stochastic approximation Monte Carlo . . . . . . 151 7.3.2.5 Sequential stochastic approximation Monte
Carlo . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 154 7.4 Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 162
The construction of phylogenetic trees is of interest in evolutionary studies. Phylogenetic inference is based on the analysis of hereditary molecular differences, mainly in DNA sequences, to gain information on the evolutionary
Algorithms, and
relationships of organisms. In general, the result of a molecular phylogenetic analysis can be expressed in a phylogenetic tree. Phylogenetic trees have been used for a long time to graphically represent evolutionary relationships among species and genes.
