I took chrY SNP data from the 1000Genomes Project, with the goal of estimating the age of the root of the Y chromosome phylogeny. I used the mutation rate of 3x10^-8 mutations/nucleotide/generation of Xue et al. (2009), and a generation length of 25 years.
I decided to use a rather unconventional model-free approach, not building a phylogeny, but simply observing the distribution of pairwise TMRCA between all 526 Y chromosomes. A histogram thereof can be seen below:
Cruciani et al. (2011) which was based on a 200kb region of the MSY.
In any case, a re-rooting of the Y chromosome phylogeny is apparently in the works, so we're bound to know much more in the near future; we are long overdue for a systematic revision of node split times using the SNP counting method.
It is also imperative that African outliers in Eurasia be better studied to determine whether they have shallow or deep divergences with their African cousins. Much will depend on this, since the argument for recent Out-of-Africa crucially depends on Eurasia harboring a subset of African variation, a proposition which relies on the dismissal of apparently African outliers in Eurasia as recent migrants rather than relics.
UPDATE (July 30): I have now updated my age estimate using a newer cleaner version of the 1000 Genomes chrY data.