ABSTRACT
Classic evolutionary theory has focused mainly on the identifi cation of signatures of natural selection acting on single genes or molecules. This narrow view of the action of natural selection clashes with the idea that selection acts on individual organisms but not genes. In addition to this main limitation, a number of criticisms should prevent efforts to identify adaptive evolution in single genes, including that genes encode proteins that are part of large networks of interactions and which fold into complex protein structures involving precise atomic interactions between the amino acids. Therefore, proteins and amino acids rarely evolve in isolation but are part of complex networks of interactions. While most of this book, and indeed others, have devoted entire sections to methods that aim at identifying adaptive events acting on single genes and amino acids, the above
stated rationale leads to the conclusion that signatures derived from such methods are often simplistic. To shed light on the evolution of proteins, and indeed gene regulatory circuits, genes should be analyzed in the context of the biological network in which they are embedded. This is better understood if we take into account that each protein encoded by one or more genes contributes with a relative amount to the biological fi tness of an individual. This fi tness amount is not the result of selection acting on an individual gene but of the relative strength of the interaction of the function encoded by such gene with the remainder of the organismal molecular repertoire. This interaction embarks molecules into a co-adaptation process, in which molecules exercise reciprocal selection upon one another leading to a co-evolutionary dynamic. It follows then that, to understand how living systems work, it is important to discover the evolutionary dependencies among its components as these may point to their functional dependencies.
