Figure 5. Effect of evolutionary filter on binding sites used in model.

The average CC over all 37 CRMs of the DirectInt model (without cooperative DNA-binding) is shown. The x-axis indicates the number of species in which conservation of a binding site was required for it to be included in the model's input. The red curve corresponds to the case where the conservation filter does not allow turnover, i.e., the sites used in the model must be fully conserved across all species considered. The blue curve represents a conservation filter that allows turnover, i.e., where a site may undergo lineage-specific changes. Thus for “number of species” = 6, a site used in the model may be conserved in six or fewer species, as long as the conservation is deemed significant by the procedure described in Text S1.