At Least 20% of Human DNA Is Neanderthal

[Buster's Uncle]

Modern humans more Neanderthal than once thought, studies suggest
Reuters
By Sharon Begley  1 hour ago



An exhibit shows the life of a neanderthal family in a cave in the new Neanderthal Museum in the northern town of Krapina February 25, 2010. REUTERS/Nikola Solic



NEW YORK (Reuters) - It's getting harder and harder to take umbrage if someone calls you a Neanderthal.

According to two studies published on Wednesday, DNA from these pre-modern humans may play a role in the appearance of hair and skin as well as the risk of certain diseases.

Although Neanderthals became extinct 28,000 years ago in Europe, as much as one-fifth of their DNA has survived in human genomes due to interbreeding tens of thousands of years ago, one of the studies found, although any one individual has only about 2 percent of caveman DNA.

"The 2 percent of your Neanderthal DNA might be different than my 2 percent of Neanderthal DNA, and it's found at different places in the genome," said geneticist Joshua Akey, who led one of the studies. Put it all together in a study of hundreds of people, and "you can recover a substantial proportion of the Neanderthal genome."

Both studies confirmed earlier findings that the genomes of east Asians harbor more Neanderthal DNA than those of Europeans. This could be 21 percent more, according to an analysis by Akey and Benjamin Vernot, published online in the journal Science.

Still, "more" is a relative term.

According to the paper by geneticists at Harvard Medical School, published in Nature, about 1.4 percent of the genomes of Han Chinese in Beijing and south China, as well as Japanese in Tokyo come from Neanderthals, compared to 1.1 percent of the genomes of Europeans.

Anthropologists expressed caution about the findings.

Fewer than half a dozen Neanderthal fossils have yielded genetic material, said Erik Trinkaus of Washington University in St. Louis, one of the world's leading experts on early humans. Using this small sample to infer how much Neanderthal DNA persists in today's genome is therefore questionable, he said.


INTERBREEDING

As expected, since Neanderthals never existed in Africa, Africans and those who trace their ancestry to that continent have almost no Neanderthal DNA, the Harvard team found.

Human ancestors began migrating out of humanity's natal continent as early as 1 million years ago, paleoanthropologists infer from fossil evidence, and between 500,000 and 200,000 years ago evolved into the robust, large-browed Homo neanderthalensis in Western Europe.

Ever since scientists extracted DNA from the remains of Neanderthals, they have known that people today carry snippets of cavemen genes, in the amounts of 2 percent to 3 percent.

That clinched the case that Neanderthals and modern humans interbred, probably 40,000 to 80,000 years ago, soon after the latter arrived in Europe from Africa. The new studies add details about how much DNA and of what kind we inherited.

"The story of early human evolution is captivating in itself, yet it also has far-reaching implications for understanding the organization of the modern human genome," Irene Eckstrand of the National Institutes of Health's National Institute of General Medical Sciences, which partially funded the research, said in a statement.

"Every piece of this story that we uncover tells us more about our ancestors' genetic contributions to modern human health and disease."


DISEASES

The Harvard team used a novel genetic algorithm to estimate the probability that a particular genetic variant arose from Neanderthals. Basically, they started with the genome of a 50,000-year-old Neanderthal, and determined whether pieces of it also appeared in some non-Africans but not in sub-Saharan Africans.

The algorithm identified remnants of Neanderthal DNA, called alleles, in genes associated with type 2 diabetes, Crohn's disease, lupus, biliary cirrhosis and smoking behavior.

"But we can't tell if the Neanderthal alleles are contributing to disease," said Harvard's Sriram Sankararaman, lead author of the paper in Nature.

Areas "with increased Neanderthal ancestry tend to be higher the farther away you go from genes," sitting, instead, in regions of the genome that do not actually produce the proteins, enzymes and other working molecules of the body.

Neanderthal DNA does sit within some genes, however, such as those for keratin, a fibrous protein that makes skin, hair and nails tough and can be beneficial in colder environments by providing thicker insulation.

The endurance of this Neanderthal DNA suggests that our caveman inheritance was adaptive, picked by natural selection to persist in our genome, generation after generation, because it conferred a survival advantage in individuals who carried it.


SPEECH

The Harvard team analyzed the genomes of 1,004 people to estimate which populations got more or fewer Neanderthal DNA. Confirming a 2013 study, they found more in the genomes of east Asians than in Europeans.

But they also dug deeper.

Puerto Ricans and Spaniards have the least Neanderthal DNA, 1.05 percent and 1.07 percent respectively. That is curious because Neanderthals made their last stand on the Iberian peninsula, finally dying out there 28,000 years ago.

Across all populations, Neanderthal DNA is conspicuously low in regions of the X chromosome and in testes-specific genes. The paucity of Neanderthal genes among those active in the testes suggests that interbreeding wasn't a resounding success: It produced viable children, but the males were infertile.

Although as much as 20 percent of Neanderthal DNA persists in modern genomes, according to the Washington scientists, vast regions of the latter are Neanderthal deserts. Among them is a region of chromosome 7 that includes a gene called FOXP2.

"FOXP2 has previously been implicated in speech and language and may be an example of a gene that influences a uniquely human trait, which is why we find no Neanderthal sequences in these regions," said Akey.


http://news.yahoo.com/modern-humans-more-neanderthal-once-thought-studies-suggest-191322659.html

[Buster's Uncle]

Fossils of Neanderthal DNA clump in human genome
Associated Press
By SETH BORENSTEIN  1 hour ago



FILE - This Jan. 8, 2003 file photo shows a reconstructed Neanderthal skeleton, right, and a modern human version of a skeleton, left, on display at the Museum of Natural History in New York. Next time you call someone a Neanderthal, better look in a mirror. Much of the genes that help determine most people’s skin and hair are much more Neanderthal than not, according to two new studies that look at the DNA fossils hidden in the modern human genome. Scientists isolated the parts of the non-African modern human genetic blueprint that still contain Neanderthal remnants. Barely more than 1 percent comes from 50,000 years ago when modern humans leaving Africa mated with the soon-to-be-extinct Neanderthals. (AP Photo/Frank Franklin II, File)



WASHINGTON (AP) — Next time you call someone a Neanderthal, better look in a mirror. Many of the genes that help determine most people's skin and hair are more Neanderthal than not, according to two new studies that look at the DNA fossils hidden in the modern human genome.

About 50,000 years ago, modern day humans migrated out of Africa north to Europe and East Asia and met up with furrow-browed Neanderthals that had been in the colder climates for more than 100,000 years. Some of the two species mated. And then the Neanderthals died off as a species — except for what's left inside of us.

Scientists isolated the parts of the modern human genetic blueprint that still contain Neanderthal remnants. Overall, it's barely more than 1 percent, said two studies released Wednesday in the journals Nature and Science.

However, in some places, such as the DNA related to the skin, the genetic instructions are as much as 70 percent Neanderthal and in other places there's virtually nothing from the species that's often portrayed as brutish cavemen.

The difference between where Neanderthal DNA is plentiful and where it's absent may help scientists understand what in our genome "makes humans human," said University of Washington genome scientist Joshua Akey, lead author of the paper in Science.

The studies mostly examined the genomes of people whose ancestors left Africa at some point. People whose ancestors have all stayed in Africa have almost no Neanderthal DNA because there was little interbreeding.

Harvard researcher Sriram Sankararaman, the lead author of the Nature study, said the place where Neanderthal DNA seemed to have the most influence in the modern human genome has to do with skin and hair. Akey said those instructions are as much as 70 percent Neanderthal.

"We're more Neanderthal than not in those genes," Akey said.

However, Sankararaman cautions that scientists don't yet know just what the Neanderthal DNA dictates in our skin and hair.



FILE - This Oct. 1996 file photo shows a replica of a Neanderthal man at the Neanderthal museum in Mettmann, western Germany. Next time you call someone a Neanderthal, better look in a mirror. Much of the genes that help determine most people’s skin and hair are much more Neanderthal than not, according to two new studies that look at the DNA fossils hidden in the modern human genome. Scientists isolated the parts of the non-African modern human genetic blueprint that still contain Neanderthal remnants. Barely more than 1 percent comes from 50,000 years ago when modern humans leaving Africa mated with the soon-to-be-extinct Neanderthals. (AP Photo/Heinz Ducklau, File)


Sarah Tishkoff, a professor of genetics and biology at the University of Pennsylvania who was not part of either study, theorized that the Neanderthal DNA probably helped the darker humans out of Africa cope with the cooler less bright north. Living in the cooler Europe means less ultraviolet light and less vitamin D from the sun. Darker skin blocks more of those needed rays, so lighter skin is more advantageous in the north and it seems that humans adopted that Neanderthal adaptation, she said.

Another area where we have more Neanderthal DNA is parts of genetic codes that have to do with certain immune system functions, Sankararaman said. Again, scientists can't say more than that these Neanderthal genes seem connected to certain diseases, such as type 2 diabetes and Crohn's disease and lupus, but they are there.

Tiskhoff and Akey said one of the most interesting parts in comparing human and Neanderthal genomes is where we don't see any caveman influence. That, Tiskhoff said, is "what makes us uniquely human" and those regions of genetic code "you just can't mess with."

One of those areas has been heavily connected to genes that determine speech and communication and there's nothing Neanderthal there, Akey said. This fits with theories that lack of communication skills hurt Neanderthal and speech ability was a distinctly human advantage, he said.

And the study in Nature found something that may help explain why the brutish and virile cavemen haven't influenced humans much: They may have made babies, but the male hybrids of Neanderthals and humans weren't very fertile. Scientists figured that out because the genes associated with the testicles in humans and the X chromosome were unusually empty of Neanderthal influence.

While Neanderthal males themselves were likely good at breeding, their half-human sons weren't and "they must have been disappointed in their sons," said Nature co-author Svante Paabo of the Max Planck Institute in Germany.

The Nature paper found that people of more East Asian descent had slightly more Neanderthal than Europeans, indicating that there may have been a second wave of interbreeding in Asia, researchers said.

Three outside scientists praised the two studies, which used different techniques to reach similar conclusions. And those conclusions were so close to each other and standard evolution theory that it all fits together in a scary way for scientists used to findings that surprise, said New York University anthropology professor Todd Disotell.

Disotell recently had his genome tested by a private company and found he's got more Neanderthal DNA than most people, about 2.9 percent: "I'm quite proud of that."


http://news.yahoo.com/fossils-neanderthal-dna-clump-human-genome-180148237.html

[Buster's Uncle]

At Least 20% of Human DNA Is Neanderthal
LiveScience.com
By Charles Q. Choi, LiveScience Contributor  3 hours ago



A girl goes nose-to-nose with a Neanderthal statue in Germany. Ancient DNA research is increasingly revealing the genetic links between modern humans and our extinct ancestors, including Neanderthals and the mysterious Denisovans.



At least one-fifth of the Neanderthal genome may lurk within modern humans, influencing the skin, hair and diseases people have today, researchers say.

Although modern humans are the only surviving human lineage, other groups of early humans used to live on Earth. The closest extinct relatives of modern humans were the Neanderthals, who lived in Europe and Asia until they went extinct about 40,000 years ago. The ancestors of modern humans diverged from those of Neanderthals between 550,000 and 765,000 years ago.

Recent findings revealed that Neanderthals interbred with ancestors of modern humans when modern humans began spreading out of Africa perhaps about 40,000 to 80,000 years ago, although some research suggests the migration began earlier. About 1.5 to 2.1 percent of the DNA of anyone outside Africa is Neanderthal in origin.

However, scientists reasoned that the Neanderthal DNA found in one person might not be the same Neanderthal DNA of someone else.

"If you are 2 percent Neanderthal and I'm 2 percent Neanderthal, we might not have the same Neanderthal DNA between us," said study lead author Benjamin Vernot, a population geneticist at the University of Washington in Seattle. "We might have inherited different portions of the Neanderthal genome.

This logic suggested a significant portion of the Neanderthal genome might survive within the genomes of present-day humans. Past calculations suggested that anywhere from 35 to 70 percent of the Neanderthal genome could exist in modern people.



The toe bone of a Neanderthal woman was uncovered in the Denisova Cave (shown here) in southern Siberia, the same place where the first signs of the Denisovans, a relatively newfound human lineage, were found.


Hidden Neanderthal genes

To find out just how much of the Neanderthal genome might hide within modern humans, Vernot and his colleague Joshua Akey analyzed the genomes of 379 European and 286 East Asian individuals. This involved identifying the DNA that didn't look modern human, and determining when that DNA was introduced into the genome.

To see if any DNA in these genomes was not characteristic of modern humans, the researchers focused on the mutations within it. After lineages split as the ancestors of modern humans and Neanderthals did, the more time these groups diverge, the more likely they will accumulate different mutations that set these lineages apart. Therefore, the scientists concentrated on sections of people's DNA whose mutations looked significantly different from their counterparts in other people, suggesting this DNA came from a very divergent lineage.

To find out when this DNA was introduced, the researchers focused on the length of various sections of DNA. When people have offspring, the chromosomes (packets that hold the cells' DNA) that get passed down are broken, mixed and reattached beforehand, meaning each child is a blend of their parents. With every generation, DNA gets broken into shorter and shorter fragments. By studying the length of a DNA section, the investigators could deduce approximately when it made its way into the modern human genome. [Unraveling the Human Genome: 6 Molecular Milestones]

The scientists focused on DNA that was not characteristic of modern humans and that apparently entered modern-human genomes about 50,000 years ago, when ancestors of modern humans are suspected to have mated with Neanderthals. They also compared this DNA with that found in Neanderthal fossils to confirm that it looked Neanderthal.



Researchers have completed the first high-quality sequence of a Neanderthal genome, using a sample from the toe bone of a Neanderthal woman.


The researchers discovered that about 20 percent of the Neanderthal genome could be found in modern humans. Although the majority of genes inherited from Neanderthals apparently do not do anything remarkably different from their modern-human counterparts, "some of the genes are beneficial," said Vernot, who, along with Akey, detailed these findings online Jan. 29 in the journal Science.

For instance, they found "evidence that both Europeans and East Asians have inherited genes having something to do with the skin," Vernot told LiveScience. "That makes sense — skin is an important organ, protecting against pathogens, protecting against ultraviolet light."

An independent team involving evolutionary geneticist David Reich at Harvard Medical School and his colleagues found mutations inherited from Neanderthals were most often in genes related to keratin, a component of skin and hair. These genetic changes may have helped modern humans adapt to chillier environments outside Africa.

"It's always really nice to get independent confirmation of your findings," Vernot said.


Lots of mating?

Both research groups also found that some regions of the modern-human genome are devoid of Neanderthal DNA, including areas involving the testes and the X chromosome. This suggests certain Neanderthal mutations were incompatible with modern humans and were removed during evolution, perhaps because they reduced fertility, both research teams said. Reich's group also identified Neanderthal-linked gene variants associated with the risk of diseases such as lupus, Type 2 diabetes and Crohn's disease (a chronic inflammatory bowel disease).

Although 20 percent might sound like a lot of mingling happened between Neanderthals and the ancestors of modern humans, it could have resulted from as few as 300 mating events, Vernot said.

The research team's computer simulations of modern-human intermingling with Neanderthals suggest about 40 percent of the Neanderthal genome may actually survive within modern human genomes. "We just identified 20 percent is all," Vernot said.

To identify the other 20 percent or so of Neanderthal genome hidden within modern humans, the scientists estimate they would need about 1,000 individuals from any given modern-human population — for instance, Europeans — to find nearly all the Neanderthal DNA present there.

However, identifying Neanderthal DNA will be challenging. "Because we're so similar to Neanderthals, there could be many, many regions that are virtually identical, with no differences that we can tell apart," Vernot said.

The method the scientists used to identify Neanderthal DNA could also be used to discover the DNA of previously unknown relatives with whom the ancestors of modern humans may also have interbred. This strategy could even work without DNA from fossils of such previously unknown human lineages as a reference point, although having such fossil DNA would make this research significantly more accurate, Vernot said.


http://news.yahoo.com/least-20-human-dna-neanderthal-190217345.html