Genetic analysis of ancient skeletons is bringing pictures of our ancestors to light in vivid colours. What is particularly astounding to me is the mobility of our ancestors – and their genes – already in the pleistocene.
Less than 350 generations for the light skin gene to have spread all over Europe seems to be a very short time. But that is what is concluded from the genetic analysis of two hunter-gatherer skeletons discovered in a cave in the mountains of north-west Spain in 2006.
The lead author, Dr Carles Lalueza-Fox, said: “One explanation is that the lighter skin colour evolved much later than was previously assumed.” …
The cool, dark conditions meant the remains (called La Brana 1 and 2) were remarkably well preserved. Scientists were able to extract DNA from a tooth of one of the ancient men and sequence his genome.
The team found that the early European was most closely genetically related to people in Sweden and Finland. But while his eyes were blue, his genes reveal that his hair was black or brown and his skin was dark. “This was a result that was unexpected,” said Dr Lalueza-Fox.
Scientists had thought the first Europeans became fair soon after they left Africa and moved to the continent about 45,000 years ago. “It has been assumed that it is something that happens in response to going from Africa to higher latitudes where the UV radiation is very low and you need to synthesise vitamin D in your skin. Your skin becomes lighter quite soon,” explained Dr Lalueza-Fox.
“It is obvious that this is not the case, because this guy has been in Europe for 40,000 years and he still has dark skin.” …..
The hunter-gatherer’s genome also gave the team an insight into how humans had changed as they moved from foraging to farming.
The early European would have subsisted on a diet of mainly protein, and his DNA reveals that he was lactose-intolerant and unable to digest starch. These are traits that came after agriculture was adopted and people changed what they ate.Commenting on the research, David Reich, from Harvard Medical School in the US, said: “The significance of this paper is that it reports the oldest European genome sequence reported to date – the first European genome sequence that predates the appearance of agriculture.
“The dark skin is a very interesting finding, as light skin is nearly universal across Europe today. These results suggest that the light skin seen across Europe today is a development of the last at least 7,000 years.”
With all that qualification, it does seem that these La Brana individuals have genetic affinities with populations as far afield as Central Siberia, and the New World (via these Siberians). Additionally, like the other ancient European hunter-gatherers it exhibits signs of reduced genetic diversity compared to modern populations. What are we to think of this? In the broad view this is really not that surprising. 400,000 year old Iberian hominins seem to have had affinities to populations which were later found in Siberia. The Neandertals, from the Altai to Spain, seem to be surprisingly similarly and genetically homogeneous. Eurasian wolves have also gone through a population bottleneck during the Pleistocene. What this suggests to me is that the Palearctic ecozone has been characterized by a high degree of population mobility, and, extinction. Ancient DNA is sampled from northern locations due to likelihood of preservation, but these regions are also on the settlement frontier, and it wouldn’t be surprising to me that the populations are going to be characterized by low effective population sizes because they’re expanding rapidly from small founding groups.
Finally, this has some implications for our model of population assimilation and replacement. It seems that modern Europeans are a synthesis of disparate strands which have co-mingled over the past 10,000 years. One element, the majority element in the north and east, are hunter-gatherers which descend from the early West Eurasian settlers of the northwest. These were the Ice Age inhabitants of Europe. Likely they had long had connections across the latitudes of the Palearctic zone. One thing that we are seeing with the pigmentation genes is that these Western European hunter-gatherers werevery different from modern Europeans. If about ~50% of the ancestry of Western Europe derives from these populations, then we’re confronted with the possibility that several of these loci have experienced nearly complete selective sweeps after an admixture event. This is not impossible, but, another option is presented us when we consider that the far north has long been a conveyor belt of peoples: that eastern cousins of the Western hunter-gatherers, or at least their genes assimilated into another population, brought whole-genome affinities into modern Europeans similar to these ancient individuals, but also were already changed in their phenotype. The paper’s supplements reports that the Y chromosome of the La Brana seem to be ancient branch of haplogroup C, which is dominant in Eastern Eurasia. A possible connection to the Mal’ta people? Perhaps. But it is important to note that very low frequencies of this haplogroup still exist in Southern Europe. So the hunter-gatherers are likely not gone in toto. But combined with the mtDNA evidence of massive changes, this may point to later Bronze Age demographic shifts, being masked by the wide scope of genetic homogeneity in Eurasia.
Dienekes comments: The new study La Brana 1 identifies it as ancestral in the SLC24A5 locus in which virtually all Europeans are derived. This comes in the heels of the Loschbour preprint which identified that sample from Luxembourg as also being ancestral. Taken together, it’s now clear that hunter-gatherers from Mesolithic Western Europe were brown.
Curiously, it now seems that both Europe and India were (in part) inhabited by brown people and became lighter by a process of admixture + selection. The process went “all the way” in Europe, but a cline of pigmentation was sustained in India.
The other finding (not mentioned in the abstract) is that La Brana 1 belonged to Y-haplogroup C6! This is a low-frequency European clade of haplogroup C. So now, we have evidence that haplogroup C is not eastern Eurasian (as the presence of its subclades in Australia, India, East Asia, and the Americas might suggest), but a pan-Eurasian entity. It remains to be seen whether this C-in-Europe can be pushed further back in time, but finding it in Mesolithic Iberia reduces the chance that it’s some random eastern Eurasian who made it to the outskirts of Europe recently.
Finally, La Brana 1 has derived alleles at loci associated with pathogen resistance. This might be important, because a common hypothesis is that Europeans developed this type of resistance during the Neolithic as they started interacting with the pathogens of domesticated species and started living in less-hygienic higher-density settlements
Nature (2014) doi:10.1038/nature12960
Abstract: 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.