I recently came across an interesting phenomenon that I understand may have been documented on a now defunct genetic genealogy forum.
A1b1: Seven at One Blow
The Walk Through the Y project established that one of the ancestors of the A1b1 haplogroup who lived after the most recent common ancestor with A1b overwrote a segment of the Y chromosome with a segment of the X chromosome.
A segment of length 13 happened to contain six mismatches, places where the X chromosome had a different allele than the ancestral Y chromosome. These were then assigned names L424 to L429.
The 29 base pairs before this segment and the 13 base pairs following this segment happen to match the ancestral Y chromosome exactly.
After the next 14 identical base pairs, A1b1 also has the X chromosome allele C instead of the ancestral A (L430), indicating that this entire range of 14 identical base pairs was also ‘silently’ overwritten, the only evidence of the overwrite being that the 15th base pair again matches the homologous segment of the X chromosome rather than the ancestral allele of the Y chromosome.
A1b1’s ancestor inherited seven at one blow – seven SNPs that actually derive from a single event.
Interestingly, J2b-Y33795 underwent nearly the same phenomenon.
J2b-Y33795: Six at One Blow
J2b-Y33795 is the only other subclade sharing L424-L429 with A1b1.
Lightning did not strike six times independently in these two very distantly related lineages.
Instead, they both relied on the same mechanism to repair this segment of the Y chromosome.
The results of the repair are not completely identical. J2b-Y33795 did not overwrite 15,484,143 with the allele from the X chromosome like A1b1 did.
That is why J2b-Y33795 is just Six at One Blow.
Implications for Haplogroup TMRCA Estimation
Ideally, a model that estimates haplogroup TMRCAs should not count these six or seven SNPs as independently occurring mutations, because it appears that all SNPs were acquired at once.