In two previous post I expressed my doubts about the reliablity of the "mtDNA clock" for measuring the age of mankind. Today I will point out another problem I noticed with the assumptions behind the mtDNA clock.
The ignored mutations
The different mtDNA haplogroups are assumed as branching in pairs upon a mutation that changes the sequence. Such as a change of a base "C" for a "T" in position "x" along the mtDNA.
Those individuals carrying this mutation (the "C") will pass it down matrilineally and they will form part of a "new" haplogroup (hg) (which we will call "Z") and those with the original sequence (the "T") will do the same and form another haplogroup (which we will cally "Y").
So when we compare individuals of each haplogroup we will immediately notice that there is a "C" instead of a "T" in position "x". And that is the key to tell hg Z apart from hg Y.
However if, long ago, all individuals of hg Z (that is, those carrying the "C" mutation) died without issue or only had sons (so their mtDNA was not passed on) or their daughters did not bear children, then there would be no living humans belonging to hg Z nowadays.
We would have an extinct haplogroup.
So if we looked at the sequence of those belonging to hg Y, who managed to survive until today, we would never imagine that, long ago, the base "T" at position "x" had mutated to "C" and originated a new haplogroup, now long gone, the extingt hg Z.
These mutations which cannot be recognized are what I term "ignored mutations".
The clock and the ignored mutations
The image below show several "hypothetical" haplogroups that branched off from the basal RSRS proposed by Behar et al. (the image is adapted from their paper ).
The original mutation points are marked with a green square, each originated a branch (which also had their own mutations along the sub-branches, all of which became extinct).
The branches are colored red and blue. And as we can see all individuals belonging to them ceased to pass their mtDNA along to their children long ago in Africa, before hg L3, split into M and N. Exactly how long ago is the issue which cannot be defined.
This does not mean the lineages of the individuals themselves became extinct. They may have only had sons, so the mtDNA stopped there but their nuclear genome kept on and is still among us.
The mtDNA "clock" can only take into account the mutations that we can see, comparing extant populations between themselves and noting the differences in their sequences.
But as I said at the beginning if a mtDNA branch disappears without trace, then, how can the mutations be recognized?
The only way would be to unearth the fossil remains of one of the individuals belonging to one of those haplogroups and noticing that yes, at position "x", the base "T" had changed to a "C". And that they split (the green squares in the image above) from the known haplogroups.
For this reason, the current mtDNA clock may be underestimating the quantity of mutations, which if they occurred at a regular rate as accepted by most mainline scientsts (a notion I disagree with), would mean that humans are much older than currently accepted.
 Doron M Behar, A “Copernican” Reassessment of the Human Mitochondrial DNA Tree from its Root. The American Journal of Human Genetics, Volume 90
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