Molecular Phylogenetic Analysis
Phylogenetic analysis, in the strictest sense, is the process of testing hypotheses about the descent of species from a common ancestor. This chapter provides an overview of a task essential to all: obtaining a working hypothesis of the evolutionary relationships among a group of organisms, summarized as a phylogenetic tree. Molecular phylogenetic analysis became more powerful and more accessible with the advent of rapid, inexpensive DNA sequencing, eventually leading to a major revision in the understanding of the evolutionary relationships among all living organisms. In order to provide a statistically robust representation of the phylogeny, a phylogenetic marker needs to have a sufficient number of independently evolving positions so that at least several changes differentiate the most closely related taxa of interest. After a phylogenetic marker has been selected, one must obtain sequence data. The core of automated alignment algorithms is optimization of a scoring function. Points are added for identities and similarities at each position, points are subtracted for mismatches, and many points are subtracted for gaps. The chapter emphasizes the use of aligned sequence databases in preference to de novo alignment not only for the savings in time and effort but also for the higher quality. It discusses maximum parsimony and maximum likelihood, the most widely implemented character based methods, as well as Bayesian phylogenetic inference, a relatively new method rapidly growing in popularity. Although it may be possible to identify an optimal topology, the reader is cautioned that an optimal tree does not guarantee the true phylogeny.