Phylogenetic reconstruction.

APHYLOGENETIC TREE IS THE ONLY figure in On the Origin of Species, evidence of the central importance of such trees to evolutionary biology. As discussed in Chapter 5, a phylogenetic tree is a graphical representation of the evolutionary relationships among entities that share a common ancestor. Those entities can be species, genes, genomes, or any other operational taxonomic unit (OTU). More specifically, a phylogenetic tree, with its pattern of branching, represents the descent from a common ancestor into distinct lineages. It is critical to understand that the branching patterns and branch lengths that make up a phylogenetic tree can rarely be observed directly, but rather they must be inferred from other information. The principle underlying phylogenetic inference is quite simple: Analysis of the similarities and differences among biological entities can be used to infer the evolutionary history of those entities. However, in practice, taking the end points of evolution and inferring their history is not straightforward. The goal of this chapter is to discuss both the principles and methods used in phylogenetic inference as well as some of the complications. In the first section, we discuss the process of selecting and gathering appropriate datasets for subsequent analysis. In the next section, we explain three widely used methods of phylogenetic inference: parsimony, distance, and likelihood methods. This is followed by a discussion of how these methods can be evaluated objectively and how the reliability and accuracy of the resulting inferences are assessed. We then raise several problematic issues that must be considered when using any phylogenetic method. Finally, we consider the fruits of phylogenetic reconstruction—how they can shed light on past evolutionary events, such as gene duplications and lateral gene transfers, as well as how they can be used for other purposes, such as predicting gene function and resolving RNA secondary structures.