Seven multiplets had mutations separated by 15 spacing regions.
Half the doublets have mutations separated by 9 bp or less (the "half-life of mutation spacing"; see Terminology in Materials and Methods).
Sanger sequencing of mutant plaques shows that the proportion of plaques with more than one mutation (synonymous or non-synonymous) can be as high as 11%%, and the proportion of plaques with mutations separated by hundreds of nucleotides is around 3%% [ 6].
Similarly, using the same criterion to distinguish clustered mutations in both datasets (≥5 linked mutations separated from their neighbour by <8.5 kb), 274 of the 1064 mutations observed in AID* wild type transformants are found within clusters compared to 28 of the 2088 mutations in the AID* ung1Δ transformants (Supplementary file 1B).
For example, our platform was less sensitive for minority variants in which two mutations are separated by less than six bases, and we were unable to detect variants with neighboring mutations (Figure S9 and data not shown).
For Western blot analyses, albumin depleted plasma samples (SwellGel Blue Albumin Removal Kit, Pierce, Rockford, IL) and protein samples extracted from cerebellar brain homogenates of FTLD patients with and without GRN mutations, were separated by SDS PAGE using pre-cast 4 20% Tris Glycine gels (Invitrogen, Carlsbad, CA) and transferred to nitrocellulose membranes.
Eventually, through multiple generations and recombination events, the marker and the mutation are separated by a recombination event in some individuals.
In general, the interplay of multiple mutations cannot be ruled out as nonadditive energetic effects have been observed for mutations at positions separated by more than 9 Å [ 44].
The two southern haplotypes are distinguished by 5 mutations with 13 mutations separating southern and northern haplotype groups (Fig. 2B).
Similar selection might result in mutation-based speciation if subpopulations accumulate a different series of mutations, which is subsequently separated by ecological speciation (Schluter and Conte 2009).
Notably, a small class of fz alleles show only a cell-autonomous defect in cuticle polarity and do not show the nonautonomous effects, leading to the conclusion that fz has two activities that can be separated by mutation, functioning both in the transmission and in the reception/interpretation of planar polarity signals (Adler et al. 1987; Vinson and Adler 1987).
