Introduction to Statistical Phylogenetics

摘要: The objective of molecular phylogenetics is to reconstruct the evolutionary relationships among different species or strains from biological sequence alignments and present them in an appropriate, usually tree-structured, graph. Besides being fundamental importance itself — aiming estimate, for instance, ancestry human race infer whole tree life has recently become heightened interest epidemiology, where it promises provide increased insight into emergence evolution infectious diseases, forensic science. Evolution driven by stochastic forces that act on genomes, essentially tries discern significant similarities between diverged sequences amidst a chaos random mutation natural selection. Faced with noisy data resulting intrinsically processes, most powerful methods make use probability theory. This chapter first discusses shortcomings older non-probabilistic clustering parsimony then describes more recent probabilistic approach. Based explicit mathematical model nucleotide substitution terms homogeneous Markov chain, phylogenetic can be interpreted as Bayesian network. interpretation allows application inference introduced Chapters 1 2. Two particular optimization algorithms have been implemented widely used software packages will described. question statistical significance results, contrasts two estimation: frequentist approach bootstrapping versus method chain Monte Carlo.