This makes inversions particularly prone to accumulating mutations involved in local adaptation.
Further, by analyzing the nucleosome position of two closely related yeast species, Tirosh et al. [ 27] indicated that the major contribution towards divergence of nucleosome positioning is through mutations in the local sequences (cis-effects).
For example, it can occur through mutations in the local repressor gene, in a global regulatory gene/transcriptional activator, in the promoter region of the efflux-pump gene or mutation in insertion elements located upstream of the efflux-pump gene [ 25].
Third, the duplication may represent a precursor enhancing the likelihood of the substitution of a beneficial mutation through an increase in the mutational target and in local mutation rates.
Conversely, models of background selection (i.e., the removal of weakly deleterious mutations) can result in local reductions of Ne (Charlesworth et al. 1993).
Allele distribution of the G388R mutation in our local breast cancer population showed 51.7% of patients with homozygous Gly/Gly alleles, 37.2% with heterozygous Gly/Arg alleles, and 11.1% with homozygous Arg/Arg alleles.
The tumor tissue used for isolation of mammospheres and DNA preparation was taken from the same 10 mm core biopsies (Additional file 1: Figure S2) but a mutation in a local clone present only in the tissue used for mammosphere isolation might be an explanation for this finding.
However, can this result be accounted for by a difference in local mutation bias, e.g., 3' UTR has a higher mutation rate?
To again take into account the effects of heterogeneity in local mutation rates, we normalized our estimates of nucleotide diversity by sequence divergence with D. simulans.
We estimated these rates as the length of the tree branch from the human-chimp ancestor to the human using a normalization approach to correct for differences in local mutation rates (Materials and Methods).
