Parsimony and phylogenetics in the genomic age

Parsimony analysis (Ockham's razor) as a general method of inference has a long history, from the arguments of Copernicus against Ptolemy's heliocentric solar system, through Sir Farncis Crick's reasoning for a single origin of the genetic code. Today, parsimony analysis in the systematic and evolutionary context stands as a method of phylogenetic inference from morphological or molecular observations. Parsimony and likelihood - a fequentist phylogenetic method - are equivalent under certain settings, but not in others. Likelihood methods model evolutionary processes and calculate the probability of data given that model. In the current genomic era, not only nucleotide substitutional differences are of interest, but also gene order, insertion-deletion history, inversion information, and estimation of horizontal gene transfer. Parsimony analysis, with its simple minimization of changes over all observations, has power in hierarchically summarizing such complex data. This chapter introduces this capacity through a general introduction to parsimony analysis and thoughts on its use for large-scale data sets.