|La Braña 1 without makeup|
The late Epipaleolithic forager from NW Iberia (previously discussed here) had the patrilineal haplogroup C6, found so far only very rarely among modern Europeans (Scozzari 2012). This, I must say, I know by the moment only from secondary sources (Eurogenes, Dienekes and a personal communication) because I have not been able yet to put my hands on the relevant paper and this key detail is not mentioned in the abstract.
→ freely available supplementary materials.
Ancient genomic sequences have started to reveal the origin and the demographic impact of farmers from the Neolithic period spreading into Europe1, 2, 3. 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.
There have been some rush to conclusions on the pigmentation of this and another Western European hunter-gatherer based only on genetics. I think that some of the conclusions are most likely incorrect, at least to some extent, because they are based on a SNP which only weights ~15% on skin coloration.
Judging on the figures (freely accessible, it seems), La Braña 1 carried two pigmentation alleles of gene SLC45A2 now rare among Europeans (but common elsewhere, i.e. the ancestral variant):
- rs16891982, which affects hair color (7x chances of black hair among Europeans)
- rs1426654, which affects skin pigmentation to some degree (correlated with skin color in Indians, irrelevant among modern Europeans because of fixation, weights only ~15% in Cape Verdeans’ skin coloration).
Notice that while you can find online reconstructions that give La Braña 1 a very dark coloration, this is not necessarily the case at all but rather an oversimplistic interpretation based only on one allele, allele that is not just dominant in West Asians and Europeans but also, for example, among Gujaratis, who are quite dark for European standards.
It seems correct anyhow that this allele was only brought to Europe with Neolithic farmers (Stuttgart had it) but its alleged effect on pigmentation seems very much exaggerated.
|Fig. 4 from Beleza 2013 highlights that no single gene is decisive in skin pigmentation.|
- rs2745098 (PTX4)
- rs11755393 (UHRF1BP1, related to lupus)
- rs10421769 (GPATCH1)
|Extended Data Figure 5: Pairwise outgroup f3 statistics.
a, Sardinian versus Karitiana. b, Sardinian versus Han.
c, La Braña 1 versus Mal’ta. d, Sardinian versus Mal’ta.
e, La Braña 1 versus Karitiana. The solid line represents y = x.
Update: I already got the paper (thanks again to the donor), I’ll see to update as need be once I have time to read it. Minor urgent edits above in red (and slashed out text).
Update (Jan 29): The supplementary data is freely available (LINK) but I could not find it earlier. Almost all the information is in it, including a long list, much longer than mentioned above, of the SNPs found in La Braña 1, compared to various modern population frequencies. I don’t have time right now to dwell on it but I guess from a first read that I will have to amend some comments made on the issue of pigmentation above.
Regarding the Y-DNA haplogroup, it is important to notice that its adscription withing haplogroup C seems very clear but its assignation to C6-V20 is more dubious because of the low quality of the genome. Only the V20 marker could be assigned, so the authors themselves are in doubt and wonder if it could alternatively be C* or C5, both with a South Asian affinity.
In this sense I think it is worth noticing that the reference Y-DNA site ISOGG has recently revised the phylogeny of macro-haplogroup C and that they have already renamed C6-V20 as C1a2, making it a relative of the minor Japanese lineage earlier known as C1 (now renamed to C1a1), similarly South Asian C5-M356 has been renamed to C1b. So C1 is now perceived as a lineage that spans all Eurasia with an arguable South Asian centrality.
Another (Papuan?) lineage once known as “C6” has long vanished from the phylogeny because of lack of plural samples, I understand.