Ancient genomic sequences have started to reveal the origin and the demographic impact of farmers from the Neolithic period spreading into Europe…The adoption of farming, stock breeding and sedentary societies during the Neolithic may have resulted in adaptive changes in genes associated with immunity and diet4. However, the limited data available from earlier hunter-gatherers preclude an understanding of the selective processes associated with this crucial transition to agriculture in recent human evolution. Here we sequence an approximately 7,000-year-old Mesolithic skeleton discovered at the La Braña-Arintero site in León, Spain, to retrieve a complete pre-agricultural European human genome. Analysis of this genome in the context of other ancient samples suggests the existence of a common ancient genomic signature across western and central Eurasia from the Upper Paleolithic to the Mesolithic. The La Braña individual carries ancestral alleles in several skin pigmentation genes, suggesting that the light skin of modern Europeans was not yet ubiquitous in Mesolithic times. Moreover, we provide evidence that a significant number of derived, putatively adaptive variants associated with pathogen resistance in modern Europeans were already present in this hunter-gatherer.
The headlines about this individual having dark skin are well founded, like the Luxembourg hunter-gatherer the sample has ancestral “non-European” copies of most of the major loci which are known to have large effect sizes (SLC24A5, which is now fixed in Europeans, SLC45A2, which is present at frequencies north of 80% in most of Europe, and KITLG, a lower frequency variant known to have a major impact on skin and hair). Additionally, this individual is related to the Ma’lta individual, just like the Swedish hunter-gatherers, but unlike the Luxembourg male (which did predate the Spanish samples by 1,000 years). Lots of functional stuff is in this paper too. Seems like immune adaptations aren’t just a function of agriculture.
One thing I want to note is that I’m not sure how much of the shift toward Finns of the Swedish and Spanish hunter-gatherers is due to Paleolithic European ancestry, vs. admixture with “eastern” elements. Since the Finns seem to have more recent East Asian ancestry excess paleo-Siberian in the Mesolithic samples may shift them in the same direction. The eastward since of the La Brana individuals is really obvious in the world wide PCA, they are farther toward East Asians than any other modern Europeans.