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Supercomputing and other Methods reveal surprising European ancestors

Submitted by coldrum on Friday, 09 January 2015  Page Views: 2085

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What if you researched your family's genealogy, and a mysterious stranger turned out to be an ancestor? That's the surprising feeling had by a team of scientists who peered back into Europe's murky prehistoric past thousands of years ago. With sophisticated genetic tools, supercomputing simulations and modeling, they traced the origins of modern Europeans to three distinct populations.

The international research team published their September 2014 results in the journal Nature. XSEDE, the Extreme Science and Engineering Discovery Environment, provided the computational resources used in the study. It's a single virtual system that scientists use to interactively share computing resources, data and expertise. Genomic analysis code ran on Stampede, the nearly 10 petaflop Dell/Intel Linux supercomputer at the Texas Advanced Computing Center (TACC). The research was funded in part by the National Cancer Institute of the National Institutes of Health.

"The main finding was that modern Europeans seem to be a mixture of three different ancestral populations," said study co-author Joshua Schraiber, a National Science Foundation Postdoctoral fellow at the University of Washington. Schraiber said these results surprised him because the prevailing view among scientists held that only two distinct groups mixed between 7,000 and 8,000 years ago in Europe, as humans first started to adopt agriculture.

Hunter-gatherers with olive skin and mainly blue-eyes first expanded upon the continent about 12,000 years ago, moving north with the retreat of glaciers at the end of the last Ice Age. Later, early European farmers from the Near East migrated west and mixed with the hunter-gatherers. Genetic evidence revealed these farmers had light-colored skin and brown eyes. The third mystery group that emerged from the data is ancient northern Eurasians.

"People from the Siberia area is how I conceptualize it. We don't know too much anthropologically about who these people are. But the genetic evidence is relatively strong, because we do have ancient DNA from an individual that's very closely related to that population, too," Schraiber said. That individual is a three-year-old-boy whose remains were found near Lake Baikal in Siberia at a site called Mal'ta. Scientists determined his arm bone to be 24,000 years old. They then sequenced his genome, making it the second oldest one yet sequenced of a modern human.

Interestingly enough, in late 2013 scientists used the Mal'ta genome to find that about one-third of Native American ancestry originated through gene flow from these ancient North Eurasians. "I think there was a little bit of luck in this," Schraiber said, referring to the Mal'ta genome. "We knew the models weren't fitting. But we didn't know what was wrong. Luckily, this new ancient DNA had come out." What scientists did was take the genomes from these ancient humans and compare them to those from 2,345 modern-day Europeans. "I used the POPRES data set, which had been used before to ask similar questions just looking at modern Europeans," Schraiber said. "And then I used a piece of software called Beagle, which was written by Brian Browning and Sharon Browning at the University of Washington, which computationally detects these regions of identity by descent." The heavy demand on CPU time and RAM caused a bottleneck in the analysis. "Having access to the Stampede supercomputer at TACC was essential for me because at some point I was using a hundred gigabytes of RAM to do something. It took days, even spreading it across multiple processors. It takes a lot of effort to do this identity by descent detection," Schraiber said.

Working on the hunch that the Mal'ta genome might fill in some missing blanks that the modeling pointed out, Schraiber saw a lot more identity by descent between the ancient individuals and modern individuals than he expected. "It made us happy in a lot of ways to find that these are people who share ancestors with modern Europeans."

Schraiber looks to East Asia and Africa as the next hot spots to study human history as scientists push forward to discover and analyze new sources of ancient DNA. "Using archeological evidence tells you a lot. Modern DNA tells you a lot. But it's by combining the two and getting ancient DNA, which is anthropological evidence and genetic evidence at the same time, you're able to unravel these things. You're able to find complexity that you just didn't know was there before," he said.

See archaeologynewsnetwork.blogspot.co.uk/2014/

Note: DNA number crunching shows origins of modern Europeans in three distinct populations: Ice Age Hunter Gatherers, Near East Farmers, Siberians.
Contributor Bio for coldrum: Based in Milkyway, contributing since 2002. Favourite site: Avebury.

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"Supercomputing and other Methods reveal surprising European ancestors" | Login/Create an Account | 2 News and Comments
  
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Europe Was a Melting Pot From the Start, Ancient DNA from Kostenki Russia Reveals by bat400 on Friday, 09 January 2015
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Genetic analysis of a 37,000-year-old human bone from Russia suggests widespread intermingling during Paleolithic times.

Modern Europeans have genetic ties that bind them together much further back in time than once thought, scientists report after analyzing a prehistoric Russian man's DNA.

Scraps of DNA harvested from a tiny fragment of the man's 37,000-year-old leg bone show that, genetically speaking, he was remarkably similar to people living in Europe today.

The man's genes include signature traces of DNA long thought to have been part of separate movements into Europe, says Eske Willerslev, a geneticist at the University of Copenhagen and co-author of a study published Thursday in the journal Science.

The findings suggests that Europe's past wasn't marked by waves of migration when people met, clashed, and mingled; rather, people arrived in a single event or as a continuous flow over millennia.

The leg bone belongs to a hunter-gatherer found at a Russian site called Kostenki, not far from the city of Voronezh. Excavated in 1954, the Kostenki bone is one of the oldest specimens of a modern human found in Europe.

"One of the surprising things is that if you go 37,000 years back in time, you find all the major genetic components that are present in modern Europeans," Willerslev says.

Archaeologists and geneticists have long debated who the ancestors of modern Europeans are—and how, and when, they arrived. It's typically been a tale of migration and invasion, of people moving into Europe in waves that left distinct genetic signatures behind.

First, the thinking goes, there were groups of hunter-gatherers, moving from Africa into Europe beginning about 40,000 years ago. Much later, a separate group of farmers and herders from the Middle East made their way north, eventually out-competing the hunter-gatherer locals and forming the basis for the European genome we see today.

The introduction of agriculture by this second wave of people—the so-called Neolithic Revolution—was such a pivotal moment in prehistory that it can be seen in both artifacts and genes.

What other geneticists have identified as separate hunter-gatherer and farmer genes are all present in the Kostenki find. "You wouldn't predict if you go back to one of our earliest individuals, all the components of modern Europeans were already there," Willerslev says.

Genes once thought to have arrived with the first farmers, for instance, now seem to have been around much earlier. "Until now, it seemed clear this was something that came into Europe during the Neolithic," says Pontus Skoglund, a geneticist at Harvard Medical School. "It's an extremely interesting suggestion that they have."

The complex mixture of DNA in such an old specimen, Willerslev says, suggests that Stone Age Europe was a lively place. Instead of separate groups colliding and occasionally mingling, Willerslev argues there was a single, genetically similar population sprawling across the continent, from Russia to the Middle East to northern Europe.

"Rather than separate populations moving into each others' areas and having sex with each other," he says, "there was a single 'meta-population' having sex—or exchanging genes—in a complex and heterogeneous way."

While the results challenge our understanding of Europe's past, they seem to confirm what geneticists have said more broadly about human migration out of Africa.

Looking at the genes of modern people around the world, researchers see three major movements out of Africa: first a group that wound up in what is now Australia and the Pacific Islands, then a population that settled in East Asia, and finally western Eurasians, or Europeans.

And indeed, the Kostenki man's DNA shows that he was unrelated to East Asians or Australo-Melanesians, suggesting that the populations diverged more than 37,000 years ago.

The new find complicates a picture of Europe's deep past that geneticists thought was becoming clearer. "We all thought you could sequence these bones and come up with a simple story. This paper really shows things are not as simple as people thought they were," Willerslev says. "Europe has always been a melting pot."

Thanks to coldrum for the link: See
news.nationalgeographic.com
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Re: Supercomputing beyond genealogy reveals surprising European ancestors by bat400 on Friday, 09 January 2015
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See also, other DNA studies:

DNA and the Origins of Europeans
Central European Early Neolithic Farmers DNA Reveals Near Eastern Affinity
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