Fig. 3
Regional changes in the molecular clock rates of orthologous proteins in Eutherian and Metatherian genomes. The heatmaps with a human (a) or Monodelphis domestica (b) ranking order each integrate approximately 1.8 million pairwise comparisons of orthologous proteins departing from the core set of 15,727 mammalian proteins and 120 pairwise comparisons between 16 species. For each comparison, the %protein divergence (PD% = 100—%identical amino acids) was divided by the average protein divergence between the same two species. The resulting normalized %protein divergence (nPD%) represents k/kav, which is the molecular clock rate of the particular protein divided by the genome-wide average of the molecular clock constant. Sliding window analysis integrates the k/kav of the centered gene and its 100 neighbors (50 on each side). Details of the 120 comparisons (1–66 intra-Eutherian, 67–114 Eutherian-Metatherian, 115–120 intra-Metatherian). can be found in Additional File 2: Table S1. Most clear-cut landscapes with Eutherian and Metatherian signatures are seen with the intra-Eutherian and intra-Metatherian comparison