Unusually strong positive selection over the past 5,000 years, rather than population replacement or even admixture, is responsible for the high frequencies of light skin, hair and eyes among present-day Eastern Europeans, according to a new paper by Wilde et al. at PNAS.
The authors were able to infer pigmentation traits from ancient DNA for 63 Eneolithic and Bronze Age samples, mostly from Kurgan mounds from the Pontic-Caspian steppe of Ukraine and surrounds. The results suggest that the ancient individuals were overall much darker than present-day Ukrainians, who, nevertheless, appear to be their direct descendants based on mitochondrial DNA (mtDNA) sequences. Quoting the paper:
To this end we compared the 60 mtDNA HVR1 sequences obtained from our ancient sample to 246 homologous modern sequences (29–31) from the same geographic region and found low genetic differentiation (FST = 0.00551; P = 0.0663) (32). Coalescent simulations based on the mtDNA data, accommodating uncertainty in the ancient sample age, failed to reject population continuity under a wide range of assumed ancestral population size combinations (Fig. 1).Well, either this is indeed a remarkable finding, or something's not quite right. I think it's the latter.
Conversely, continuity between early central European farmers and modern Europeans has been rejected in a previous study (33). However, the Eneolithic and Bronze Age sequences presented here are ∼500–2,000 y younger than the early Neolithic and belong to lineages identified both in early farmers and late hunter–gatherers from central Europe (33).
In sum, a combination of selective pressures associated with living in northern latitudes, the adoption of an agriculturalist diet, and assortative mating may sufficiently explain the observed change from a darker phenotype during the Eneolithic/Early Bronze age to a generally lighter one in modern Eastern Europeans, although other selective factors cannot be discounted. The selection coefficients inferred directly from serially sampled data at these pigmentation loci range from 2 to 10% and are among the strongest signals of recent selection in humans.
The argument for genetic continuity from the Eneolithic/Bronze Age to the present on the Pontic-Caspian steppe based on mtDNA sequences is actually very weak. The results could simply mean that the ancient samples shared deep maternal ancestry with modern Ukrainians and most other Europeans.
Indeed, we know for a fact that much of the Pontic-Caspian steppe was occupied by Turkic groups of Asian origin from the early Middle Ages until only a couple of hundred years ago. They were eventually cleared out by Tsarist Russia, and mainly replaced by East Slavic settlers from just northwest of the steppe. This process might not be easy to see by comparing low resolution mtDNA data, even between European populations separated by 5,000 years, but it's likely to be obvious when looking at full mtDNA genomes, high-density genome-wide data, and/or Y-chromosome haplogroups.
Surprisingly, the article doesn't mention Keyser et al. 2009, a very important study which showed that a sample of Kurgan nomads from Bronze and Iron Age South Siberia had frequencies of light hair and eyes comparable to those of present-day Northern and Eastern Europeans (see here). Also worth noting is that the most common Y-chromosome haplogroup among these individuals was R1a, which is today the most frequent haplogroup in Eastern Europe, including Ukraine.
What this suggests to me is that the Kurgan cultural horizon was not genetically homogeneous. I suspect that Kurgan groups closer to the Balkans carried significantly higher levels of Near Eastern Neolithic farmer ancestry, and were thus much darker than those in the more temperate northerly regions. However, it seems that at some point, the Neolithic farmer DNA was diluted enough by continuous movements of light pigmented groups from the north and east, possibly made up mostly of males, that there was a major shift in pigmentation traits from Near Eastern-like to North European-like across most of Eastern Europe. This scenario actually fits very nicely with the latest on the genetic origins of Europeans (see here).
We won't know what really happened until we see at least a few complete ancient genomes from Eastern Europe. But for now, I'd have to suspend my disbelief to accept that present-day Eastern Europeans are, by and large, descendants of these exceedingly brunet prehistoric people of the Pontic-Caspian steppe.
Wilde et al., Direct evidence for positive selection of skin, hair, and eye pigmentation in Europeans during the last 5,000 y, PNAS, Published online before print on March 10, 2014, DO:I10.1073/pnas.1316513111
PCA of ancient European mtDNA