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Genomic diversity: Did farmers and hunters mate with one another in prehistory?

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What was it like living in Sweden 7,000 years ago or 5,000 years in the past? Interested in demographic history of prehistoric peoples and their DNA? Genomic diversity and admixture differs for Stone-Age Scandinavian foragers and farmers, says a new study. An osteologist specializes in the archaeology and archaeogenetics of skeletons found in caves, at archeology sites, and anywhere else skeletons are found and studied by scientists for clues on how people lived in the past.

Stone-Age hunter-gatherers had much lower genetic diversity than farmers. This suggests that Stone-Age foraging groups were in low numbers compared to farmers, according to the study, "Genomic Diversity and Admixture Differs for Stone-Age Scandinavian Foragers and Farmers," published online April 24, 2014 in Science. More food can feed more children.

An international team led by researchers at Uppsala University and Stockholm University reports a breakthrough on understanding the demographic history of Stone-Age humans. A genomic analysis of eleven Stone-Age human remains from Scandinavia revealed that expanding Stone-age farmers assimilated local hunter-gatherers and that the hunter-gatherers were historically in lower numbers than the farmers.

The transition between a hunting-gathering lifestyle and a farming lifestyle has been debated for a century

As scientists learned to work with DNA from ancient human material, a complete new way to learn about the people in that period opened up. But even so, prehistoric population structure associated with the transition to an agricultural lifestyle in Europe remains poorly understood.

"For many of the most interesting questions, DNA-information from people today just doesn't cut it, the best way to learn about ancient history is to analyze direct data—despite the challenges", says Dr. Pontus Skoglund of Uppsala University, now at Harvard University, and one of the lead authors of the study, according to the April 24, 2014 news release, "Genomic diversity and admixture differs for Stone-Age Scandinavian foragers and farmers."

"We have generated genomic data from the largest number of ancient individuals" says Dr. Helena Malmström, according to the news release. Malmström is with Uppsala University and one of the lead authors. "The eleven Stone-Age human remains were between 5,000 and 7,000 years old and associated with hunter-gatherer or farmer life-styles" says Helena Malmström. Anders Götherström, who led the Stockholm University team, is satisfied with the amount of DNA that they could retrieve. "Not only were we able to generate DNA from several individuals, but we did get a lot of it. In some cases we got the equivalent of draft genomes. A population genomic study on this level with a material of this age has never been done before as far as I know."

DNA retrieved from the stone-age hunters to examine much of their genome comparing farmers to hunter-gatherers

The material used in the study is from mainland Scandinavia as well as from the Baltic island Gotland, and it includes information about hunter-gatherers from various time periods as well as early farmers. Professor Mattias Jakobsson, who led the Uppsala University team, is intrigued by the results. "Stone-Age hunter-gatherers had much lower genetic diversity than farmers. This suggests that Stone-Age foraging groups were in low numbers compared to farmers", says Mattias Jakobsson.

Jan Storå at Stockholm University shares Mattias' fascination. "The low variation in the hunter gatherers may be related to oscillating living conditions likely affecting the population sizes of hunter-gatherers. One of the additional exciting results is the association of the Mesolithic individual to both the roughly contemporaneous individual from Spain but also the association to the Neolithic hunter-gatherers."

Hunter-gatherers and farmers were genetically distinct, but the farmers had admixture from the hunter-gatherers -- yet the hunter-gatherers from the Baltic Sea area showed no admixture with the farmers

The study confirms that Stone-Age hunter-gatherers and farmers were genetically distinct and that migration spread farming practices across Europe, but the team was able to go even further by demonstrating that the Neolithic farmers had substantial admixture from hunter-gatherers. Surprisingly, the hunter-gatherers from the Baltic Sea displayed no evidence of introgression from farmers.

"We see clear evidence that people from hunter-gatherer groups were incorporated into farming groups as they expanded across Europe", says Pontus Skoglund, according to the news release. "This might be clues towards something that happened also when agriculture spread in other parts of the world."

Assymmetric gene flow shows farmers admixed with hunter-gatherers

"The asymmetric gene-flow shows that the farming groups assimilated hunter-gatherer groups, at least partly", says Mattias Jakobsson. "When we compare Scandinavian to central European farming groups that lived at about the same time, we see greater levels of hunter-gatherer gene-flow into the Scandinavian farming groups."

This study is part of the recently initiated "Atlas project" - a large-scale genomic investigation of ancient human remains in Scandinavia led by Stockholm and Uppsala Universities and funded by the Swedish Foundation for Humanities and Social Sciences and the Swedish Research Council. The present study brings the first results from the project. "We have only begun to scratch the surface of the knowledge that this project may bring us in the future" says Anders Götherström, according to the news release. You can check out an Atlas Map of admixture from different geographic areas of the world online here.

Another noteworthy study by different researchers shows that much further back in time than 7,000 years ago, Neanderthals and Cro-Magnons didn't coincide in what today is Spain and Portugal, according to the April 14, 2014 news release, "Neanderthals and Cro-magnons did not coincide on the Iberian Peninsula." Or you can check out news of another study that raises questions on how and when livestock were domesticated, "More questions than answers as mystery of domestication deepens."

The meeting between a Neanderthal and one of the first humans, which we used to picture in our minds, did not happen on the Iberian Peninsula. That is the conclusion reached by an international team of researchers after redoing the dating of the remains in three caves located on the route through the Pyrenees of the first beings of our species.

Neanderthals and Cro-magnons did not coincide on the Iberian Peninsula

Until now, the carbon 14 technique, a radioactive isotope which gradually disappears with the passing of time, has been used to date prehistoric remains. When about 40,000 years, in other words approximately the period corresponding to the arrival of the first humans in Europe, have elapsed, the portion that remains is so small that it can become easily contaminated and cause the dates to appear more recent. It was from 2005 onwards that a new technique began to be used; it is the one used to purify the collagen in DNA tests. Using this method, the portion of the original organic material is obtained and all the subsequent contamination is removed.

And by using this technique, scientists have been arriving at the same conclusions at key sites across Europe: "We can see that the arrival of our species in Europe took place 8,000 years earlier than what had been thought and we can see the earliest datings of our species and the most recent Neanderthal ones, in which, in a specific regional framework, there is no overlapping," explained Alvaro Arrizabalaga, according to the April 14, 2014 news release, "Neanderthals and Cro-magnons did not coincide on the Iberian Peninsula." Arrizabalaga is a professor of the department of Geography, Prehistory and Archaeology, and one of the UPV/EHU researchers alongside María-José Iriarte and Aritza Villaluenga.

The three caves chosen for the recently published research are located in Girona (L'Arbreda), Gipuzkoa (Labeko Koba) and Asturias (La Viña). In other words, at the westernmost and easternmost tips of the Pyrenees. And it was where the flow of populations and animals between the peninsula and continent took place.

"L'Arbreda is on the eastern pass; Labeko Koba, in the Deba valley. It's located on the entry corridor through the Western Pyrenees (Arrizabalaga and Iriarte excavated it in a hurry in 1988 before it was destroyed by the building of the Arrasate-Mondragon bypass) and La Viña is of value as a paradigm, since it provides a magnificent sequence of the Upper Palaeolithic, in other words, of the technical and cultural behavior of the Cro-magnons during the last glaciation," pointed out Arrizabalaga, according to the April 14, 2014 news release, "Neanderthals and Cro-magnons did not coincide on the Iberian Peninsula."

The selecting of the remains was very strict allowing only tools made of bones or, in the absence of them, bones bearing clear traces of human activity, as a general rule with butchery marks, in other words, cuts in the areas of the tendons so that the muscle could be removed. "The Labeko Koba curve is the most consistent of the three, which in turn are the most consistent on the Iberian Peninsula," explained Arrizabalaga according to the news release. Eighteen remains were dated at Labeko Koba and the results are totally convergent with respect to their stratigraphic position, in other words, those that appeared at the lowest depths are the oldest ones.

The main conclusion – that the scene of the meeting between a Neanderthal and a Cro-magnon does not seem to have taken place on the Iberian Peninsula– is the same conclusion as the one that has been gradually reached over the last three years by different research groups when studying key settlements in Great Britain, Italy, Germany and France

"For 25 years we had been saying that Neanderthals and early humans lived together for 8,000-10,000 years. Today, we think that in Europe there was a gap between one species and the other and, therefore, there was no hybridation, which did in fact take place in areas of the Middle East," explained Arrizabalaga, according to the news release. The UPV/EHU professor is also the co-author of a piece of research published in 2012 that puts back the datings of the Neanderthals.

"We did the dating again in accordance with the ultrafiltration treatment that eliminates rejuvenating contamination, remains of the Mousterian, the material culture belonging to the Neanderthals from sites in the south of the Peninsula. Very recent dates had been obtained in them –up to 29,000 years– but the new datings go back to 44,000 years older than the first dates that can be attributed to the Cro-Magnons," explained the UPV/EHU professor, according to the news release.

Some studies say Neanderthals and Homo Sapiens met and admixed in the Middle East around 50,000 to 60,000 years ago and in parts of Central Asia before the Homo Sapiens reached Europe or ventured further East in Asia. And there also were other types in Asia, not just Neanderthals, for example Denisovans. It's still unknown how many other varieties of people were around in those times in addition to Densiovans and Neanderthals or where the borders for Neanderthals stop and the Denisovan borders start.

Denisovans genome sequenced

You have the Denisovans who eventually migrated to the southeastern parts of Asia and mixed again with Homo Sapiens as well as the Neanderthals, since no one knows where the border for Neanderthals end in Central Asia and where Denisovans area starts in the Altai and further east.

You may wish to see an excellent YouTube video, "Archaic Genomics - Svante Pääbo" on this topic of Neanderthals, Denisovans, and their prehistoric admixture with Homo Sapiens. Svante Pääbo sequenced the genome of Neanderthals and Denovisans, including recent research into FOXP2, the language gene. You also may wish to see the October 12, 2012 study, published in Science, "A high-coverage genome sequence from an archaic Denisovan Individual." (Pääbo S, et al.)

Denisovans are extinct relatives of Neanderthals

In the study, the quality of this genome allows a direct estimation of Denisovan heterozygosity indicating that genetic diversity in these archaic hominins was extremely low. Looks like some relatives from the same family may have admixed with one another, with Neanderthals, and with Homo Sapiens.

The study also allows tentative dating of the specimen on the basis of "missing evolution" in its genome, detailed measurements of Denisovan and Neanderthal admixture into present-day human populations, and the generation of a near-complete catalog of genetic changes that swept to high frequency in modern humans since their divergence from Denisovans.

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