Fig. 4

Strong conservation of regional effects in the molecular clock rate in Eutherian and Metatherian landscape signatures. The data set of Fig. 2 was further integrated by calculating the mean sliding window values of 66 intra-Eutherian (red) and nPD% is shown while in blue the average of the 6 intra-Metatherian (blue) comparisons, using the human (a) or Monodelphis domestica (b) genome order. Clear-cut subtelomeric increments above the genome-wide averages (dashed lines) can be observed with discriminative intra-Eutherian and intra-Metatherian maximal values (e.g., the right telomere of human chromosome 14 or Monodelphis domestica chromosome 8). Distribution of the window-averaged nPD% is fundamentally different when genes were in random order (grey) as compared to the order of the human genome (red, c) or Monodelphis domestica genome (blue, d). When using a threshold based on mean + 3SD of the random distribution we found 1,833 eutherian windows and 1504 Metatherian windows with window-averaged nPD% exceeding these thresholds. e These two gene sets show minimal overlap, providing further evidence for a Eutherian and Metatherian signature of regional effects in the molecular clock rate. That subtelomeric regions with high window-averaged nPD% remain subtelomeric despite changes in karyotypes is suggested by a Circos plot (f) that connect in two Eutherian species (pig and human) concordant subtelomeric regions with high window-averaged nPD% (green lines) as opposed to few discordant subtelomeric regions with high window-averaged nPD% in one species only (black lines). In contrast human subtelomeric regions with high window-averaged nPD% are predominantly non-subtelomeric in the Monodelphis domestica genome (black lines g). Similarly, Monodelphis domestica subtelomeric regions with high window-averaged nPD% are predominantly non-subtelomeric in the human genome (black lines h)