DNA Sequencing Megathread! Neanderthals, Denisovans and other ancient DNA!

[Razgovory]

And what are the limits to these tests?

[jimmy olsen]

And what are the limits to these tests?

That's the best thing about it, the technology is getting better and better at an enormous rate. 10 years ago you could only manage to recover and analyze mtDNA and now they can sequence the entire nuclear genome of a Neanderthal as well as they could that of a living person.

[Razgovory]

And what are the limits to these tests?

That's the best thing about it, the technology is getting better and better at an enormous rate. 10 years ago you could only manage to recover and analyze mtDNA and now they can sequence the entire nuclear genome of a Neanderthal as well as they could that of a living person.

You didn't answer my question, what are the limits with this test?

[jimmy olsen]

And what are the limits to these tests?

That's the best thing about it, the technology is getting better and better at an enormous rate. 10 years ago you could only manage to recover and analyze mtDNA and now they can sequence the entire nuclear genome of a Neanderthal as well as they could that of a living person.

You didn't answer my question, what are the limits with this test?

I'm not sure what you mean.

Do you mean how far they can go back and successfully sequence something?  The record so far is 700,000 years (done on a horse).

[dps]

And what are the limits to these tests?

That's the best thing about it, the technology is getting better and better at an enormous rate. 10 years ago you could only manage to recover and analyze mtDNA and now they can sequence the entire nuclear genome of a Neanderthal as well as they could that of a living person.

You didn't answer my question, what are the limits with this test?

I'm not sure what you mean.

Do you mean how far they can go back and successfully sequence something?  The record so far is 700,000 years (done on a horse).

I'd think that if you wanted to go back in time, you'd need a time machine, not a horse.

[The Brain]

What are the litmus with this test?

[jimmy olsen]

This is only the tip of the iceberg, I can't wait to see what the rest of their genes do!

http://www.bbc.com/news/science-environment-28127785

Tibetan altitude gene inherited 'from extinct species'
By Paul Rincon Science editor, BBC News website
Tibetans

A gene that allows present-day people to cope with life at high altitude was inherited from an extinct species of human, Nature journal has reported.

The variant of the EPAS-1 gene, which affects blood oxygen, is common in Tibetans - many of whom live at altitudes of 4,000m all year round.

But the DNA sequence matches one found in the extinct Denisovan people.

Many of us carry DNA from extinct humans who interbred with our ancestors as the latter expanded out of Africa.

Both the Neanderthals - who emerged around 400,000 years ago and lived in Europe and western Asia until 35,000 years ago - and the enigmatic Denisovans contributed DNA to present-day people.

The Denisovans are known only from DNA extracted from the finger bone of a girl unearthed at a cave in central Siberia. This 40,000-50,000-year-old bone fragment, as well as a rather large tooth from another individual, are all that is known of this species.

The tiny "pinky" bone yielded an entire genome sequence, allowing scientists to compare it to the DNA of modern people in order to better understand the legacy of ancient interbreeding.

Now, researchers have linked an unusual variant of the EPAS1 gene, which is involved in regulating the body's production of haemoglobin - the molecule that carries oxygen in the blood - to the Denisovans. When the body is exposed to the low oxygen levels encountered at high elevations, EPAS1 tells other genes in the body to become active, stimulating a response that includes the production of extra red blood cells.

The unusual variant common among Tibetans probably spread through natural selection after their ancestors moved onto the high-altitude plateau in Asia several thousand years ago.

"We have very clear evidence that this version of the gene came from Denisovans," said principal author co-author Rasmus Nielsen, from the University of California, Berkeley.

He told BBC News: "If you and I go up to high altitude, we'll immediately have various negative physiological effects. We'll be out of breath, we might suffer from altitude sickness.

"After a little while, we'll try to compensate for this by producing more red blood cells. But because we're not adapted to the high altitude environment, our response would be maladaptive - we would produce too many red blood cells.

"The blood becomes too thick and raises our blood pressure, placing us at risk of stroke and pre-eclampsia (in pregnant women)."

But Tibetans are protected against these risks by producing fewer red blood cells at high altitude. This keeps their blood from thickening.

The Tibetan variant of EPAS1 was discovered by Prof Nielsen's team in 2010. But the researchers couldn't explain why it was so different from the DNA sequences found in all other humans today, so they looked to more ancient genome sequences for an answer.

"We compared it to Neanderthals, but we couldn't find a match. Then we compared it to Denisovans and to our surprise there was an almost exact match," he explained.

He says the interbreeding event with Denisovans probably happened very long ago.

"After the Denisovan DNA came into modern humans, it lingered in different Asian populations at low frequencies for a long time," Prof Nielsen said.

"Then, when the ancestors of Tibetans moved to high altitudes, it favoured this genetic variant which then spread to the point where most Tibetans carry it today."

He says it remains unclear whether the Denisovans were also adapted to life at high altitudes. Denisova Cave lies at an elevation of 760m - not particularly high. But it is close to the Altai Mountains which rise above 3,000m.

Prof Nielsen said it was a "clear and direct" example of humans adapting to new environments through genes acquired via interbreeding with other human species.

Previous research has shown that ancient humans introduced genes that may help us cope with viruses outside Africa.

And a study of Eurasian populations showed that Neanderthal DNA is over-represented in parts of the genome involved in making skin, hair and nails - hinting, perhaps, at something advantageous that allowed Homo sapiens to adapt to conditions in Eurasia.

[Siege]

I refuse to read long posts without highlights.

[jimmy olsen]

There's highlights

[Siege]

There's highlights

Some of yours do, and I thank you for it.
But all these other faggots suck at posting long posts.
And you suck too some times.

[The Brain]

I refuse to read long posts that don't come with a free mug.

[Ideologue]

I refuse to read posts.

[The Brain]

I've written more posts than I've read.

[jimmy olsen]

Seems odd that the farmers from the Near East had variants for ligher skin. Why would that have been advantageous for them? Sexual selection at work, I guess. 

http://news.sciencemag.org/archaeology/2015/04/how-europeans-evolved-white-skin

How Europeans evolved white skin
By Ann Gibbons  2 April 2015 5:00 pm 14 Comments

ST. LOUIS, MISSOURI—Most of us think of Europe as the ancestral home of white people. But a new study shows that pale skin, as well as other traits such as tallness and the ability to digest milk as adults, arrived in most of the continent relatively recently. The work, presented here last week at the 84th annual meeting of the American Association of Physical Anthropologists, offers dramatic evidence of recent evolution in Europe and shows that most modern Europeans don't look much like those of 8000 years ago.

The origins of Europeans have come into sharp focus in the past year as researchers have sequenced the genomes of ancient populations, rather than only a few individuals. By comparing key parts of the DNA across the genomes of 83 ancient individuals from archaeological sites throughout Europe, the international team of researchers reported earlier this year that Europeans today are a mix of the blending of at least three ancient populations of hunter-gatherers and farmers who moved into Europe in separate migrations over the past 8000 years. The study revealed that a massive migration of Yamnaya herders from the steppes north of the Black Sea may have brought Indo-European languages to Europe about 4500 years ago.

Now, a new study from the same team drills down further into that remarkable data to search for genes that were under strong natural selection—including traits so favorable that they spread rapidly throughout Europe in the past 8000 years. By comparing the ancient European genomes with those of recent ones from the 1000 Genomes Project, population geneticist Iain Mathieson, a postdoc in the Harvard University lab of population geneticist David Reich, found five genes associated with changes in diet and skin pigmentation that underwent strong natural selection.

First, the scientists confirmed an earlier report that the hunter-gatherers in Europe could not digest the sugars in milk 8000 years ago, according to a poster. They also noted an interesting twist: The first farmers also couldn't digest milk. The farmers who came from the Near East about 7800 years ago and the Yamnaya pastoralists who came from the steppes 4800 years ago lacked the version of the LCT gene that allows adults to digest sugars in milk. It wasn't until about 4300 years ago that lactose tolerance swept through Europe.

When it comes to skin color, the team found a patchwork of evolution in different places, and three separate genes that produce light skin, telling a complex story for how European's skin evolved to be much lighter during the past 8000 years. The modern humans who came out of Africa to originally settle Europe about 40,000 years are presumed to have had dark skin, which is advantageous in sunny latitudes. And the new data confirm that about 8500 years ago, early hunter-gatherers in Spain, Luxembourg, and Hungary also had darker skin: They lacked versions of two genes—SLC24A5 and SLC45A2—that lead to depigmentation and, therefore, pale skin in Europeans today.

But in the far north—where low light levels would favor pale skin—the team found a different picture in hunter-gatherers: Seven people from the 7700-year-old Motala archaeological site in southern Sweden had both light skin gene variants, SLC24A5 and SLC45A2. They also had a third gene, HERC2/OCA2, which causes blue eyes and may also contribute to light skin and blond hair. Thus ancient hunter-gatherers of the far north were already pale and blue-eyed, but those of central and southern Europe had darker skin.

Then, the first farmers from the Near East arrived in Europe; they carried both genes for light skin. As they interbred with the indigenous hunter-gatherers, one of their light-skin genes swept through Europe, so that central and southern Europeans also began to have lighter skin. The other gene variant, SLC45A2, was at low levels until about 5800 years ago when it swept up to high frequency.

The team also tracked complex traits, such as height, which are the result of the interaction of many genes. They found that selection strongly favored several gene variants for tallness in northern and central Europeans, starting 8000 years ago, with a boost coming from the Yamnaya migration, starting 4800 years ago. The Yamnaya have the greatest genetic potential for being tall of any of the populations, which is consistent with measurements of their ancient skeletons. In contrast, selection favored shorter people in Italy and Spain starting 8000 years ago, according to the paper now posted on the bioRxiv preprint server. Spaniards, in particular, shrank in stature 6000 years ago, perhaps as a result of adapting to colder temperatures and a poor diet.

Surprisingly, the team found no immune genes under intense selection, which is counter to hypotheses that diseases would have increased after the development of agriculture.

The paper doesn't specify why these genes might have been under such strong selection. But the likely explanation for the pigmentation genes is to maximize vitamin D synthesis, said paleoanthropologist Nina Jablonski of Pennsylvania State University (Penn State), University Park, as she looked at the poster's results at the meeting. People living in northern latitudes often don't get enough UV to synthesize vitamin D in their skin so natural selection has favored two genetic solutions to that problem—evolving pale skin that absorbs UV more efficiently or favoring lactose tolerance to be able to digest the sugars and vitamin D naturally found in milk. "What we thought was a fairly simple picture of the emergence of depigmented skin in Europe is an exciting patchwork of selection as populations disperse into northern latitudes," Jablonski says. "This data is fun because it shows how much recent evolution has taken place."

Anthropological geneticist George Perry, also of Penn State, notes that the work reveals how an individual's genetic potential is shaped by their diet and adaptation to their habitat. "We're getting a much more detailed picture now of how selection works."

[derspiess]

DNA is a social construct.