Figure 2

p-values obtained for monophyletic evolution hit region detection (a) Positive selection - Variable hit region inside conserved context. Quartile distribution of p-values obtained for the function . Abscissa represents scaling factor of the conserved context in which the variable hit region resides. Values close to 0 represent conservation (maximum discrimination), while values close to 1 represent variability (identical to context). Variable hit region is always maintained at a scaling factor of 1. Ordinate represents p-values in log-scale. Horizontal dashed line represents the significance threshold of 0.05. (b) Lineage specific selection - Heterogeneous hit region inside neutral context. Quartile distribution of p-values obtained for the function . Abscissa represents the difference in scaling factors among the two lineages present in the hit region. Values close to 0 represent homogeneous evolutionnary speed (similar to the neutral context in which it resides), while values close to 1 represent divergence among these lineages. Context is always maintained at a scaling factor of 0.5, simulating neutral evolution. Horizontal dashed line represents the significance threshold of 0.05. In the case of lineage specific selection, the value of the Q′-tγpe functions corresponding to 1 on the abscissa scale cannot be computed because it involves a sub-tree with 0 edge lengths.