Often the factor that has been used to mitigate the discrepancy has been the implied mutation rate of Y-DNA, but room for manipulation of that calibrating factor has declined as direct measurements of mutation rates have accumulated with a declining margin of error.
But, a preprint by David Hamilton at biorXiv has found another culprit that fits data points from the emerging pool of ancient Y-DNA. The subtle issue is that conventional estimates of TMCRA include only clades that we see, and doesn't make allowance for the fact that many other clades developed in parallel and died off before being observed. Considering this factor generically lowers the TMCRA observed:
Our method for ``Time to most recent common ancestor'' TMRCA of genetic trees for the first time deals with natural selection by apriori mathematics and not as a random factor. Bioprocesses such as ``kin selection'' generate a few overrepresented ``singular lineages'' while almost all other lineages terminate. This non-uniform branching gives greatly exaggerated TMRCA with current methods. Thus we introduce an inhomogenous stochastic process which will detect singular lineages by asymmetries, whose ``reduction'' then gives true TMRCA. Reduction implies younger TMRCA, with smaller errors. This gives a new phylogenetic method for computing mutation rates, with results similar to ``pedigree'' (meiosis) data. Despite these low rates, reduction implies younger TMRCA, with smaller errors.
We establish accuracy by a comparison across a wide range of time, indeed this is only y-clock giving consistent results for 500-15,000 ybp. In particular we show that the dominant European y-haplotypes R1a1a & R1b1a2, expand from c3700BC, not reaching Anatolia before c3300BC. This contradicts current clocks dating R1b1a2 to either the Neolithic Near East or Paleo-Europe. However our dates match R1a1a & R1b1a2 found in Yamnaya cemetaries of c3300BC . . . together proving R1a1a & R1b1a2 originates in the Russian Steppes.This methodological advance undermines one of the last genetic evidence arguments for a Neolithic/Anatolian hypothesis of Indo-European linguistic origins in favor of a Copper Age/Bronze Age Steppe hypothesis.