The beginning of agriculture and animal domestication, which began in the Near East before 11,000 years ago, had a tremendous impact on human lifestyle. Hunter-gatherers were replaced in many places by sedentary farmers, and there were large increases in population size that laid the foundation for larger towns and eventually complex societies. Archaeological evidence suggests that the transition to a farming lifestyle in central Europe occurred around 7,500 years ago, with the appearance of the Linearbandkeramik (LBK), a sedentary farming culture.
It has long been debated whether that change in subsistence strategy involved the mass migration of people from the Near East bringing innovative technologies and domestic animals to Europe or whether it was due to a transmission of cultural practices passed on from neighbouring populations. Recent genetic studies on ancient hunter-gatherers and early farmer remains have suggested a massive migration of people to Europe coinciding with the spread of farming. The size and distribution of the genetic components contributed to indigenous European hunter-gatherers, however, remain unclear.
An international consortium led by researchers from the University of Tübingen and Harvard Medical School analyzed ancient human genomes from a ~7,000-year-old early farmer from the LBK culture from Stuttgart in Southern Germany, a ~8,000-year-old hunter-gatherer from the Loschbour rock shelter in Luxembourg, and seven ~8,000-year-old hunter-gatherers from Motala in Sweden. In order to compare the ancient humans to present-day people, the team also generated genome-wide data from about 2,400 humans from almost 200 diverse worldwide contemporary populations.
Their surprising finding was that present-day Europeans trace their ancestry back to three and not just two ancestral groups: The first is indigenous hunter-gatherers; the second is Near Eastern farmers that migrated to Europe around 7,500 years ago; and a novel third is a more mysterious population that spanned North Eurasia and genetically connects Europeans and Native Americans. “We find a major surprise: Europeans are a mixture of three ancient populations, not two,” says David Reich from Harvard Medical School, one of the lead investigators of the new study. “We had previously found an ancient genetic link of present-day Europeans and Native Americans,” adds Nick Patterson from the Broad Institute in Boston. “To our surprise this component was not present in the ancient hunter-gatherer from Luxembourg, nor was it present in the first European farmers”.
“It seems clear now that the third group linking Europeans and Native Americans arrives in Central Europe after the early farmers,” explains Johannes Krause from the University of Tübingen and director of the Max Planck Institute for History and Sciences in Jena, Germany. “We are however not sure yet when the Northern Eurasian component enters central Europe”
Using the large dataset of present-day and ancient human data, the researchers were able to calculate the proportion of the ancestral components in present-day Europeans. “Nearly all Europeans have ancestry from all three ancestral groups,” says Iosif Lazaridis from Harvard Medical School. “Differences between them are due to the relative proportions of ancestry. Northern Europeans have more hunter-gatherer ancestry—up to about fifty percent in Lithuanians—and Southern Europeans have more farmer ancestry.”
However, he cautions: “Even the early farmers themselves had some hunter-gatherer ancestry: They were not unmixed descendants of the original Near Eastern migrants that brought farming to Europe.” How Europeans received their Northern Eurasian ancestry remains an open question: “The Northern Eurasian ancestry is proportionally the smallest component everywhere in Europe, never more than twenty per cent, but we find it in nearly every European group we’ve studied and also in populations from the Caucasus and Near East. A profound transformation must have taken place in West Eurasia after the Neolithic Revolution.”
The researchers also analyzed genes with known phenotypic association and show that some of the hunter-gatherers likely had blue eyes and darker skin, whereas the early farmers had lighter skin and brownish eyes. Both the hunter-gatherers as well as the early farmers displayed high copy numbers of amylase genes in their genomes, suggesting that both populations had already adapted to a starch-rich diet. However, none of the ancient humans was yet adapted to digest milk sugar into adulthood.
The researchers were also able to fit the genomic data of modern and ancient humans into a simplified genetic model to reconstruct the deep population history of modern humans outside Africa in the last 50,000 years. While the model suggests that present-day Europeans received contributions from at least three ancestral populations, it also suggests that Early Near Eastern farmers carried genetic material that falls outside the typical non-African variation.
“The finding of an ancient lineage that is present in Europeans and Near Easterners but not elsewhere in Eurasia was a major surprise of our study. It will be exciting to carry out further ancient DNA work to understand the archaeological cultures associated with the arrival of this ancestry,” says David Reich. “We are only starting to understand the complex genetic relationship of our ancestors,” adds Johannes Krause. “Only more genetic data from ancient human remains will allow us to disentagle our pre-historic past”.
The arms race is between mobile DNA sequences known as “retrotransposons” (a.k.a. “jumping genes”) and the genes that have evolved to control them. The UC Santa Cruz researchers have, for the first time, identified genes in humans that make repressor proteins to shut down specific jumping genes. The researchers also traced the rapid evolution of the repressor genes in the primate lineage.
Their findings, published September 28 in Nature, show that over evolutionary time, primate genomes have undergone repeated episodes in which mutations in jumping genes allowed them to escape repression, which drove the evolution of new repressor genes, and so on. Furthermore, their findings suggest that repressor genes that originally evolved to shut down jumping genes have since come to play other regulatory roles in the genome.
“We have basically the same 20,000 protein-coding genes as a frog, yet our genome is much more complicated, with more layers of gene regulation. This study helps explain how that came about,” said Sofie Salama, a research associate at the UC Santa Cruz Genomics Institute who led the study.
Retrotransposons are thought to be remnants of ancient viruses that infected early animals and inserted their genes into the genome long before humans evolved. Now they can only replicate themselves within the genome. Depending on where a new copy gets inserted into the genome, a jumping event can disrupt normal genes and cause disease. Often the effect is neutral, simply adding to the overall size of the genome. Very rarely the effect might be advantageous, because the added DNA can itself be a source of new regulatory elements that enhance gene expression. But the high probability of deleterious effects means natural selection favors the evolution of mechanisms to prevent jumping events.
Scientists estimate that jumping genes or “transposable elements” account for at least 50 percent of the human genome, and retrotransposons are by far the most common type.
“There have been successive waves of retrotransposon activity in primate evolution, when a transposable element changed to become expressed and replicated itself throughout the genome until something turned it off,” Salama said. “We’ve discovered a major mechanism by which the genome is able to shut down these mobile DNA elements.”
The repressors identified in the new study belong to a large family of proteins known as “KRAB zinc finger proteins.” These are DNA-binding proteins that repress gene activity, and they constitute the largest family of gene-regulating proteins in mammals. The human genome has over 400 genes for KRAB zinc finger proteins, and about 170 of them have emerged since primates diverged from other mammals.
According to Salama, her team’s findings support the idea that expansion of this family of repressor genes occurred in response to waves of retrotransposon activity. Because repression of a jumping gene also affects genes located near it on the chromosome, the researchers suspect that these repressors have been co-opted for other gene-regulatory functions, and that those other functions have persisted and evolved long after the jumping genes the repressors originally turned off have degraded due to the accumulation of random mutations.
“The way this type of repressor works, part of it binds to a specific DNA sequence and part of it binds other proteins to recruit a whole complex of proteins that creates a repressive landscape in the genome. This affects other nearby genes, so now you have a potential new layer of regulation available for further evolution,” Salama said.
KRAB zinc finger proteins are the subject of intensive research as scientists try to sort out their many regulatory roles within the genome. The idea that they are involved in repression of jumping genes is not new–previous studies by other researchers have shown that these proteins silence jumping genes in mouse embryonic stem cells. But until now, no one had been able to demonstrate that the same thing occurs in human cells.
The UC Santa Cruz team developed a novel assay to test whether a particular KRAB zinc finger protein could shut down certain jumping genes. The first authors of the paper, postdoctoral researcher Frank Jacobs and graduate student David Greenberg, came up with the strategy of testing primate retrotransposons in non-primate cells by using mouse embryonic stem cells that contain a single human chromosome. In the environment of a mouse cell, jumping genes that were repressed in primate cells became active. Greenberg then developed an assay for testing individual zinc finger proteins for their ability to turn off a primate jumping gene in the mouse cell environment.
“We did all our tests in mouse cells because they lack all of the primate zinc finger proteins, so when you put primate retrotransposons into a mouse cell they’re all active,” Salama explained.
The results demonstrated that two human proteins called ZNF91 and ZNF93 bind and repress two major classes of retrotransposons (known as SVA and L1PA) that are currently or recently active in primates. Assistant research scientist Benedict Paten directed graduate student Ngan Nguyen in a painstaking analysis of primate genomes, including the reconstruction of ancestral genomes, which showed that ZNF91 underwent structural changes 8 to 12 million years ago that enabled it to repress SVA elements.
Experiments with ZNF 93, which shuts down L1PA retrotransposons, provided a striking illustration of the arms race between jumping genes and repressors. The researchers found that, while it is good at shutting down many L1PA elements, there is one subset of a recently evolved lineage of L1PA that has lost a short section of DNA that includes the ZNF93 binding site. Without the binding site, these jumping genes evade repression by ZNF93. Interestingly, when the researchers put the missing sequence back into one of these genes and put it in a mouse cell without ZNF93, they found that it was better at jumping. So even though the sequence helps with jumping activity, losing it gives the jumping gene an advantage in primates by allowing it to escape repression by ZNF93.
“That’s kind of the icing on the cake for aficionados of molecular evolution, because it demonstrates that this is a never-ending race,” Salama said. “KRAB zinc finger proteins are a rare class of proteins that is rapidly expanding and evolving in mammalian genomes, which makes sense because the transposable elements are themselves continually evolving to escape repression.”
Corresponding author David Haussler, professor of biomolecular engineering and director of the UC Santa Cruz Genomics Institute, said the study involved close collaboration between his group’s “wet lab,” directed by Salama, and the “dry lab” where researchers under Paten’s direction used the computational tools of genome bioinformatics to reconstruct the evolutionary history of primate genomes. Haussler, a Howard Hughes Medical Institute investigator who has used his background in computer science to do pioneering work in genomics, said he established the wet lab to enable just this kind of collaboration.
“Both parts were integral to this study, and there was a lot of back and forth between them. This paper shows how important it is to integrate computational and experimental approaches to fundamental scientific problems, such as how and why we continuously evolve to be more complex,” Haussler said.
Researchers from Royal Holloway, University of London, together with an international team from across the United States and Europe, have found evidence which challenges the belief that a type of technology known as Levallois – where the flakes and blades of stones were used to make useful products such as hunting weapons – was invented in Africa and then spread to other continents as the human population expanded.
They discovered at an archaeological site in Armenia that these types of tools already existed there between 325,000 and 335,000 years ago, suggesting that local populations developed them out of a more basic type of technology, known as biface, which was also found at the site.
Dr Simon Blockley and Dr Alison MacLeod, from the Department of Geography at Royal Holloway, analysed volcanic material that preserved the archaeological site in the village of Nor Geghi, in the Kotayk Province of Armenia. By employing innovative procedures developed at Royal Holloway, they extracted suitable material to help date the Levallois tools.
“The discovery of thousands of stone artefacts preserved at this unique site provides a major new insight into how Stone Age tools developed during a period of profound human behavioural and biological change”, said Dr Blockley. “The people who lived there 325,000 years ago were much more innovative than previously thought, using a combination of two different technologies to make tools that were extremely important for the mobile hunter-gatherers of the time.
“Our findings challenge the theory held by many archaeologists that Levallois technology was invented in Africa and spread to Eurasia as the human population expanded. Due to our ability to accurately date the site in Armenia, we now have the first clear evidence that this significant development in human innovation occurred independently within different populations.”
Archaeologists argue that Levallois technology was a more innovative way of crafting tools, as the flakes produced during the shaping of the stone were not treated as waste but were made at predetermined shapes and sizes and used to make products that were small and easy to carry. With the more primitive biface technology, a mass of stone was shaped through the removal of flakes from two surfaces in order to produce bigger tools such as a hand axes.
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