ABSTRACT
Under the contemporary molecular view of the principle of descendent with modifi cation by Charles Darwin, new genes and functions originate by the modifi cation of ancestral ones, a process known as functional divergence. Both genetic and environmental factors infl uence the emergence of novel functions. In this chapter we will focus mainly on the methods that allow inferring functional divergence using protein-coding sequences. The underlying assumption when inferring functional divergence from sequences is that the more identical two protein sequences are the more similar their functions are. That is, the divergence 1 School of Genetics & Microbiology, Dept. of Genetics, University of
between any two sequences from a single common ancestral sequence is proportional to the divergence in the functions of the proteins they encode. While this assumption may hold true in general, the proportionality between sequence divergence and functional divergence remains debated.
