Positive Darwinian selection: Does the comparative method rule?

To detect positive Darwinian selection it is thought essential to compare two sequences. Despite its defects, the comparative method rules. However, genes evolving rapidly under positive selection conflict more with internal forces (the genome phenotype) than genes evolving slowly under negative selection. In particular, there is conflict with stem-loop potential. The conflict between protein-encoding potential (primary information) and stem-loop potential (secondary information) permits detection of positive selection in a single sequence. The degree to which secondary information is compromised provides a measure of the speed of transmission of primary information. Thus, the sovereignty of the comparative method is challenged not only by its own defects, but also by the availability of a single-sequence method. However, while of limited utility for positive selection, the comparative method casts new light on Darwin's great question - the origin of species. Comparison of rates of synonymous and non-synonymous mutation suggests that branching into new species begins with synonymous mutations.