To further resolve whether high levels of variation in centromeres result from the action of gene conversion or spontaneous mutation, I investigated the mutation spectrum in centromere sequences.
However, sequence analysis showed that all of these cases appear to comprise short-tract gene conversions or mutations of KIR2DP1 or KIR2DS1.
This may be either due to partial gene conversion or back mutation.
Alternatively, an Alu element can be defined as belonging to a subfamily if it is reasonable to assume that at the moment of integration, the sequence corresponded to that of the subfamily source gene, which may have since undergone gene conversion or back mutation such that it might show diagnostic changes.
Also CpT (32, 3.9%) and CpA (33, 3.7%) dinucleotides seem to get occasionally methylated, while 14 methylcytosines followed by another cytosine represent only 2.3% of all CpC positions and might be, therefore, artifacts of incomplete bisulfite conversion or PCR mutations [25].
Numerous Y-SNPs with unknown mutation conversion or phylogenetic position were identified in the test samples.
This fluctuation assay measures the fraction of cells that no longer express structurally intact sIgM, and thus scores mutation events resulting from gene conversion, point mutation, insertion or deletion [12], [20], [21].
In contrast to microsatellites, DNA recombination-like processes that involve unequal crossover or gene conversion display mutation mechanisms in the larger minisatellite sequences (3).
Such elements may have been generated by back mutation, gene conversion, or more likely a mixture of these two processes.
