Supek, F. & Lehner, B. Differential DNA mismatch repair underlies mutation rate variation across the human genome.
Ségurel, L., Wyman, M. J. & Przeworski, M. Determinants of mutation rate variation in the human germline.
For Goodman, the recognition of mutation rate variation in cytochrome c was a preliminary motivation for further study of the causes of variation.
It is easy to speculate that the major driving force behind the mutation rate variation patterns described in this paper, including the positive correlation with G+C content and the increasing trends towards centromeres, is possibly associated with methylation.
As the divergence between D. melanogaster and D. simulans does not follow this pattern, the drop in variability cannot be explained by mutation rate variation, but is attributed to selection [27], [28].
One way to eliminate biases caused by mutation rate variation is to compare the ratio of fixed substitutions to polymorphisms using a Chi square test within the framework of the McDonald-Kreitman (MK) test [17] because mutation biases are expected to affect substitutions and polymorphisms equally.
Because processes operating at the DNA level, such as local mutation rate variation [9], should affect both dS and dN [10: p. 65] while natural selection on the protein should affects dN but not dS, and because protein-level selection is expected to vary across amino acid sites or protein domains, we expect dN to be more variable than dS [see also 3].
Divergent patterns of Ed provide evidence for horizontal transfer and mutation rate variation between genes (40).
The exact pattern of mutation rate variation in rice is unknown.
Most previous studies of mutation rate variation have focused on mammals.
Given mutation rate variation, the most appropriate metric is polymorphism normalized by divergence.
