  One of the basic questions of phylogenomics is how gene function evolves,
whether among species or inside gene families. In this chapter, we provide a
brief overview of the problems associated with defining gene function in a
manner which allows comparisons which are both large scale and evolutionarily
relevant. The main source of functional data, despite its limitations, is
transcriptomics. Functional data provides information on evolutionary
mechanisms primarily by showing which functional classes of genes evolve under
stronger or weaker purifying or adaptive selection, and on which classes of
mutations (e.g., substitutions or duplications). However, the example of the
"ortholog conjecture" shows that we are still not at a point where we can
confidently study phylogenomically the evolution of gene function at a precise
scale.
