Phylogenetic Reconstruction of Orthology, Paralogy, and Conserved Synteny for Dog and Human
Figure 5
dN/dS Cumulative Frequency Distribution for Orthologues, Paralogues, and Pseudogenes Predicted by PhyOP
Predicted pseudogenes exhibit median dN/dS ratios of 0.22 when compared with their orthologues, 0.55 with functional in-paralogues, and 0.65 with in-paralogues that are themselves also candidate pseudogenes. The 1:1 orthologues have a median dN/dS of 0.11. Assuming a constant mutation rate, the dN/dS after loss of function in pseudogenes should relax towards approximately 0.55 (the average of 1.00 for no selection and 0.11 for purifying selection) when compared with a functional homologue, and towards 1.00 when compared with a homologue which is also a pseudogene. The dN/dS distribution between in-paralogues (dashed lines) is greatly shifted upwards, suggesting that the changes in selective constraints for both functional and pseudogene paralogues tend to be much more recent than the dog–human divergence.