Biological sequence analysis is founded on solid evolutionary principles (see Chapter 2). Similarities and divergence among related biological sequences revealed by sequence alignment often have to be rationalized and visualized in the context of phylogenetic trees. Thus, molecular phylogenetics is a fundamental aspect of bioinformatics. In this chapter, we focus on phylogenetic tree construction. Before discussing the methods of phylogenetic tree construction, some fundamental concepts and background terminology used in molecular phylogenetics need to be described. This is followed by discussion of the initial steps involved in phylogenetic tree construction.

MOLECULAR EVOLUTION AND MOLECULAR PHYLOGENETICS

To begin the phylogenetics discussion, we need to understand the basic question, “What is evolution?” Evolution can be defined in various ways under different contexts. In the biological context, evolution can be defined as the development of a biological form from other preexisting forms or its origin to the current existing form through natural selections and modifications. The driving force behind evolution is natural selection in which “unfit” forms are eliminated through changes of environmental conditions or sexual selection so that only the fittest are selected. The underlying mechanism of evolution is genetic mutations that occur spontaneously. The mutations on the genetic material provide the biological diversity within a population; hence, the variability of individuals within the population to survive successfully in a given environment. Genetic diversity thus provides the source of raw material for the natural selection to act on.