When I discussed yesterday the new A00 Y-DNA lineage, you may have found strange that I was accepting the rather extreme age estimates when I am usually very critical of "molecular clock" age estimates.
The reason is that my main criticism is against the way too common such estimates (for Y-DNA) based on a handful of STR markers, which do not seem but a pointer and not the real stuff. The real stuff is in the SNPs instead but the problem is that, right now, we know only a few of the many that must be lurking in the actual Y chromosomes that all men carry in their cells. As the exact amount of SNPs in any given lineage is unknown, there is no way of counting them and, that way, establishing the relative chronology of the Y-DNA phylogeny.
However this will change soon if is not already doing so, because full chromosome sequencing is every day cheaper and that is what has allowed, for example the 1000 Genomes Project. A few weeks ago, an open access paper by A. Van Geylesteen et al., emphasized this immediate future in which our knowledge of the Y-DNA tree will almost literally explode.
But the fact is that there is at least one person who has been already working in the open with that perspective in mind. Terry D. Robb, at his site mostly dedicated to haplogroup I1, published some months ago a (partial) Y-DNA tree of Humankind (update 10 or this PDF) that calculates haplogroup relative ages based on nucleotide differences between the Y-chromosome sequences of the 1000 Genomes Project.
It is still not rocket science but it is getting quite close. A problem may be that some haplogroups are too thinly represented (actually only R1b, O3 and E1b have large enough samples to be fairly safe about them internally) but while this may be a problem for coalescence ages (because maybe key sublineages are not represented), it should not be at all for divergence ones, i.e. the node where they separate from their closest relatives. So we cannot be certain that the apparent coalescent relative age of, for example, haplogroup D (n=17) is correct but we can be quite certain that the relative age of its divergence from its "brother" E at the DE node is good.
The other and main problem is calibration. And this is the only (albeit important) aspect where I disagree with Robb's method. He insists on scholastically using academic references from only the population genetics literature (which systematically produces too recent "ages") and ignores archaeological references altogether. Therefore I have taken his graph and modified that part as follows:
|click to expand|
As you can see, I calibrated by equating age(CF) = 80,000 years ago. This is based on Petraglia 2007 and other materials that establish that there was modern human presence in South Asia since c. 80,000 BP, before and after the Toba ash layer (74 Ka BP). A minor doubt would be if that date would better correspond with Y-DNA F (which in my calibration above shows up right after the Toba event) but that would have made all ages even older (not really a problem for me but I rather like better this calibration).
The result is somewhat shocking because it pushes the age of A0 to c. 265,000 years ago, making it effectively pre-Sapiens. Relatedly, it would push the age of A00 (assuming everything else in the Méndez paper is correct) to c. 450,000 years ago. But after the initial surprise... why not? After all most of us have Neanderthal admixture and they must have diverged a million year ago or earlier. And some peoples even have minor Homo erectus admixture most likely, diverging some 1.8 Ma years ago probably.
So, well, these are my reasons and this tree by Terry D. Robb, with my own chronology as above, is probably the best and most realistic estimate around of Y-DNA haplogroup ages.