A new paper argues that the SE-NW gradient of genetic variation in modern Europeans is consistent with a large Paleolithic contribution of the European gene pool if modern Europeans are principally descended from people who spent the last Ice Age in the Iberian refugium.
In my opinion, the question cannot be solved on the basis of modern populations alone: clines do not carry dates, and can be formed by accretion of different events operating under the constraints of a given geography. Ancient DNA has already begun to inform our view of the past: we now have data from Mesolithic Iberians, the presumable denizens of a pre-farming refugium, and they do not appear closely related to modern Iberians. Moreover, Europe as a whole shows discontinuity between Neolithic and Mesolithic populations, and even between Neolithic and modern ones.
If humans expanded from Iberia in postglacial times, and modern Europeans are largely descended from them, then it is strange that the gene pool of Mesolithic Europeans is so restricted: why didn't the Out-of-Iberians create a modern European-like mtDNA and Y chromosome gene pool in the thousands of years intervening between deglaciation and the available DNA samples?
Arguably, the ancient DNA record of Europe (except in the case of mtDNA) is still in its infancy and there may be more surprises to come. But, the way things look like right now, Paleolithic genetic continuity does not seem warranted. As more ancient samples accumulate from different regions and different periods, we will see how clines of variation in modern populations were formed. But, if history of the field is any guide, we're probably in for a few strange surprises.
Mol Biol Evol (2012) doi: 10.1093/molbev/mss203
Influence of admixture and Paleolithic range contractions on current European diversity gradients
Miguel Arenas et al.
Cavalli-Sforza and colleagues (1963) initiated the representation of genetic relationships among human populations with principal component analysis (PCA).Their study revealed the presence of a southeast–northwest (SE-NW) gradient of genetic variation in current European populations, which was interpreted as the result of the demic diffusion of early Neolithic farmers during their expansion from the Near East. However, this interpretation has been questioned, as PCA gradients can occur even when there is no expansion, and because the first PC axis is often orthogonal to the expansion axis. Here, we revisit PCA patterns obtained under realistic scenarios of the settlement of Europe, focusing on the effects of various levels of admixture between Paleolithic and Neolithic populations, and of range contractions during the Last Glacial Maximum (LGM). Using extensive simulations, we find that the first PC (PC1) gradients are orthogonal to the expansion axis, but only when the expansion is recent (Neolithic). More ancient (Paleolithic) expansions alter the orientation of the PC1 gradient due to a spatial homogenization of genetic diversity over time, and to the exact location of LGM refugia from which re-expansions proceeded. Overall we find that PC1 gradients consistently follow a SE-NW orientation if there is a large Paleolithic contribution to the current European gene pool, and if the main refuge area during the last ice age was in the Iberian Peninsula. Our study suggests that a SE-NW PC1 gradient is compatible with little genetic impact of Neolithic populations on the current European gene pool, and that range contractions have affected observed genetic patterns.