The presumed shallow time depth of the human Y-chromosome phylogeny is one of the main arguments of the recent Out-of-Africa theory. One of the major things I found while working on my Y-STR series is that point estimates from Y-STR variation are associated with huge confidence intervals, because of uncertainty about factors such as generation length, population history, mutation rates, even if the mutation model behaves "perfectly" in symmetrical stepwise fashion.
Trouble is, the deeper we go in time, the more uncertain we are about the behavior of our models. That is why I have generally avoided providing any age estimates for events prior to the Neolithic.
Nonetheless, it is interesting to see the state of the art in this area, because claims about the shallow time depth of the human Y-chromosome phylogeny are always flying around, but, if you follow the citation labyrinth, you will soon realize that the whole edifice is erected on sand.
Fortunately, I was recently reminded of a thoughtful post by Tim Janzen on the GENEALOGY-DNA-L from 2009 which is probably the "best thing" when it comes to Y-chromosome age estimation for deep clades of the phylogeny.
The most basal clade in the phylogeny is haplogroup A which is found in Africa. By comparing A chromosomes with those of the BT clade (everyone else), we can arrive at an estimate of Y-chromosome Adam. And, since BT clade contains much structure itself, we can compare A chromosomes with different subclades within BT, e.g., E or J or T.
This is essentially what Tim did: he compared a group of haplogroup A chromosomes with all the major clades of the BT group. Different age estimates produced by this method are not independent, because different haplogroups share more recent common ancestors: for example A vs I and A vs J both contain a common line of patrilineal descent (from the BT founder to the IJ founder). In any case, the different age estimates should all give approximately the same figure, as they are estimating the same quantity: if they do not, this is evidence about the inability of Y-STRs to provide good age estimates.
Tim went a step further, and he did his comparisons on different sets of markers: slow-evolving ones to fast-evolving ones. Again, age estimates with fast vs. slow-evolving markers should give similar age estimates. If they do not, then this means that an age estimate is a product not only of the true age of a lineage, but also of the particular mix of fast- and slow-evolving markers that one uses.
In short: age estimates by comparing haplogroup A with several other haplogroups and by using different sets of markers should be roughly similar. But, that is hardly what happened.
Below is Tim's table of age estimates in years. I have added an extra row and extra column: this contains the standard deviation of each column/row divided by the average (in %), and is useful to quantify how varied the age estimates are across different BT haplogroups and across different marker sets.
The standard deviation of the age estimates across haplogroups is reasonably small, but large enough to render any archaeological correlations useless. The real trouble is in the standard deviation of the age estimates across marker sets: they are higher than 100%!
What this means is that age estimates are largely a function of whether one uses slow- or fast- mutating markers.
Age estimates vary overall between 6,530 years and 535,755! It is obvious that fast/medium mutating markers provide unbelievably small age estimates (most of them are less than 20 thousand years). However, if we limit the analysis to slow mutating markers, most age estimates are in excess of 300,000 years!
In short, you can arrive at any age estimate you want, by choosing a particular mix of slow and fast mutating markers.
It could be argued that using all markers (50 markers column) would provide a better estimate, and, indeed, that estimate is in the order of 40-80ky, which is close to what is usually reported for human Y-chromosomes.
But that is equivalent to having a number of different clocks, some of which tell you that 3 seconds have transpired, and some which tell you that it's been a whole minute. The rational thing to do is not to take an average, but to throw the clocks in the garbage, or figure out what's wrong with them.
At present I am aware of no research that quantifies the depth of the human Y-chromosome phylogeny with anything bearing a semblance of accuracy. The 1000 genomes project has the potential to do this using using relatively well-behaved point mutations rather than Y-STRs, but, in the initial publication no actual age estimates were given, and the samples used to produce Supplementary Figure 7 lacked the most basal part of the tree (both clade A and the next most basal clade B).
UPDATE (Jan 2, 2011):
In a post in GENEALOGY-DNA-L, I show that by using slow- vs. fast-evolving markers using the Ballantyne et al. mutation rates and the tested haplogroup A and haplogroup C 67-marker haplotypes from the respective FTDNA projects, you can arrive at age estimates between 10-219ky.
This has confirmed to my mind that Tim Janzen's numbers about the dependence of age estimates on marker mutation rates are basically correct, and that age estimates about Y-chromosome Adam using Y-STRs are basically useless.
Let's hope that the 1000 Genomes Project will produce the data in the coming year that will allow us to make a better estimate, in terms of number of SNPs between A and non-A chromosomes presented as e.g., (i) a fraction of number of SNPs between human and chimpanzee, or (ii) by dividing with father-son Y-SNP mutation rates; the latter is already estimated but should become better fixed by looking at the father-son pairs included in 1000 genomes project