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

[jimmy olsen]

The little mongrel village dogs that you see all over the crappier parts of Eurasia and probably make up a majority of the world's dog population are pretty mellow and timid from thousands of years of having rocks thrown at them.

That phenotype probably only became fixed due to selective pressures introduced by the transition from humans from nomadic hunter gathering to agricultural villages.

I imagine that the wolf dogs following hunters on the steppe looked an acted quite different.

[jimmy olsen]

Aryan invasion of India circa 2000 BC confirmed by ancient DNA.

http://www.thehindu.com/sci-tech/science/how-genetics-is-settling-the-aryan-migration-debate/article19090301.ece

Good map of that Y chromosome haplotype. Z93 is the one that expanded into India.

[The Brain]

Did they get the DNA from sticky pages in ancient texts?

[jimmy olsen]

Interesting, the Baltic and Ukraine, while impacted by migrants from the the Steppe, seem not to have been impacted by the Anatolian deluge that overran Central and Western Europe.

http://www.cell.com/current-biology/fulltext/S0960-9822(16)31542-1

[Grinning_Colossus]

Weird. I assumed that the Trypillia Culture was the work of Near Eastern farmers.

[Ed Anger]

Spellus got Anatoilan Deluge when was ridden by a Turk bareback.

[crazy canuck]

From August, but I think interesting confirmation that the Greeks are directly descended from the Bronze age cultures that inhabited the area.  And little support for the other theories that those peoples were entirely displaced - or that they came from Africa.

http://www.sciencemag.org/news/2017/08/greeks-really-do-have-near-mythical-origins-ancient-dna-reveals

...ancient DNA suggests that living Greeks are indeed the descendants of Mycenaeans, with only a small proportion of DNA from later migrations to Greece. And the Mycenaeans themselves were closely related to the earlier Minoans...

The ancient Mycenaeans and Minoans were most closely related to each other, and they both got three-quarters of their DNA from early farmers who lived in Greece and southwestern Anatolia, which is now part of Turkey, the team reports today in Nature. Both cultures additionally inherited DNA from people from the eastern Caucasus, near modern-day Iran, suggesting an early migration of people from the east after the early farmers settled there but before Mycenaeans split from Minoans.

The Mycenaeans did have an important difference: They had some DNA—4% to 16%—from northern ancestors who came from Eastern Europe or Siberia. This suggests that a second wave of people from the Eurasian steppe came to mainland Greece by way of Eastern Europe or Armenia, but didn't reach Crete, says Iosif Lazaridis, a population geneticist at Harvard University who co-led the study.

[jimmy olsen]

No Denisovan DNA? That's surprising given the relative proximity in time and space of the Altai Denisovans. Perhaps those Denisovans were a relict population on the edge of the human range.

http://www.sciencemag.org/news/2017/10/was-ancient-person-china-offspring-modern-humans-and-neandertals

Was this ancient person from China the offspring of modern humans and Neandertals?

By Ann GibbonsOct. 12, 2017 , 12:00 PM

When scientists excavated a 40,000-year-old skeleton in China in 2003, they thought they had discovered the offspring of a Neandertal and a modern human. But ancient DNA now reveals that the "Tianyuan Man" has only traces of Neandertal DNA and none detectable from another type of extinct human known as a Denisovan. Instead, he was a full-fledged member of our species, Homo sapiens, and a distant relative of people who today live in East Asia and South America. The work could help scientists retrace some of the earliest steps of human migration.

"The paper is very exciting because it is the first genome to fill a really big gap, both geographically and temporally, in East Asia," says paleogeneticist Pontus Skoglund of Harvard Medical School in Boston, who was not involved in the work.

The first modern humans arose in Africa about 300,000 years ago. By 60,000 years ago, a subset swept out of Africa and mated with Neandertals, perhaps in the Middle East. After that, they spread around the world—DNA from ancient humans in Europe, western Asia, and the Americas has revealed the identity of those early migrants and whether they were related to people living today, especially in Europe. But the trail grows cold in eastern Asia, where warmer climates have made it hard to get ancient DNA from fossils.

The new genome sheds some light on those missing years. In the first genome-wide study of an ancient East Asian, researchers led by Qiaomei Fu, a paleogeneticist at the Chinese Academy of Sciences in Beijing, extracted DNA from the thighbone of the Tianyuan Man—so named because he was found in Tianyuan Cave, 56 kilometers southwest of Beijing.

The team calculated that the Tianyuan Man inherited about as much Neandertal DNA—4% to 5%—as ancient Europeans and Asians of similar age. That's a bit higher than the 1.8% to 2.6% of Neandertal DNA in living Europeans and Asians. The Tianyuan Man did not have any detectable DNA from Denisovans, an elusive cousin of Neandertals known only from their DNA extracted from a few teeth and small bones from a Siberian cave and from traces of their DNA that can still be found in people in Melanesia—where they got it is a major mystery. 

A big surprise is that the Tianyuan Man shares DNA with one ancient European—a 35,000-year-old modern human from Goyet Caves in Belgium. But he doesn't share it with other ancient humans who lived at roughly the same time in Romania and Siberia—or with living Europeans. But the Tianyuan Man is most closely related to living people in east Asia—including in China, Japan, and the Koreas—and in Southeast Asia, including Papua New Guinea and Australia.

All of this suggests that the Tianyuan Man was not a direct ancestor, but rather a distant cousin, of a founding population in Asia that gave rise to present-day Asians, Fu's team reports today in Current Biology. It also shows that these ancient "populations moved around a lot and intermixed," says paleoanthropologist Erik Trinkaus of Washington University in St. Louis in Missouri, who is not a co-author.

And some left offspring whereas others did not. "I find it interesting that ... some of the early modern colonizers of Eurasia were successful while others were not," says co-author Svante Pääbo, a paleogeneticist at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany.

The Tianyuan Man also was a distant relative of Native Americans living today in the Amazon of South America, such as the Karitiana and Surui peoples of Brazil and the Chane people of northern Argentina and southern Bolivia. They inherited about 9% to 15% of their DNA from an ancestral population in Asia that also gave rise to the Tianyuan Man. But he is not an ancestor to ancient or living Native Americans in North America, which suggests there were two different source populations in Asia for Native Americans.

This is welcome news to Skoglund, who found in a separate study in 2015 that the Karitiana and Surui peoples are closely related to indigenous Australians, New Guineans, and Andaman Islanders. At the time, he predicted that they came from the same "ghost" source population in Asia, which was separate from another Asian population that gave rise to Native Americans in North America. "It's fascinating that a prediction of a 'ghost population' based on modern-day populations alone can be confirmed in this way," he says.

[The Minsky Moment]

From August, but I think interesting confirmation that the Greeks are directly descended from the Bronze age cultures that inhabited the area.  And little support for the other theories that those peoples were entirely displaced - or that they came from Africa.

Anything else would be pretty surprising.  Bronze Age Greece would have had a population near or even over 1 million.  Even assuming significant losses in the collapse, it would take very large migrations to make a big dent in the ethnic composition in the area.  The logistical challenges of moving large numbers of people long distances with pre-modern technology can't be overstated.

[crazy canuck]

From August, but I think interesting confirmation that the Greeks are directly descended from the Bronze age cultures that inhabited the area.  And little support for the other theories that those peoples were entirely displaced - or that they came from Africa.

Anything else would be pretty surprising.  Bronze Age Greece would have had a population near or even over 1 million.  Even assuming significant losses in the collapse, it would take very large migrations to make a big dent in the ethnic composition in the area.  The logistical challenges of moving large numbers of people long distances with pre-modern technology can't be overstated.

I agree.  But this is with the benefit of the knowledge gained over the last decade or so.  It was not so long ago that large migration theories were proposed.  This confirms what is now, as you say, unsurprising.

[grumbler]

From August, but I think interesting confirmation that the Greeks are directly descended from the Bronze age cultures that inhabited the area.  And little support for the other theories that those peoples were entirely displaced - or that they came from Africa.

Anything else would be pretty surprising.  Bronze Age Greece would have had a population near or even over 1 million.  Even assuming significant losses in the collapse, it would take very large migrations to make a big dent in the ethnic composition in the area.  The logistical challenges of moving large numbers of people long distances with pre-modern technology can't be overstated.

Until modern DNA sampling techniques were developed, this is pretty much in line with what was believed to be true in Italy after the fall of the Roman Empire, as well:  a dying-out of the existing, largely urban population and its replacement by a barbarian invader population.  We've known for some time now that that isn't what happened, and that Italy's modern population is overwhelmingly descended from its ancient population. 

That being also true for Greece isn't surprising.

However, the shift in England away from a primarily Celtic to a primarily Norse and German population shows that such invasions can happen when the technology is there.

[The Minsky Moment]

However, the shift in England away from a primarily Celtic to a primarily Norse and German population shows that such invasions can happen when the technology is there.

My recollection from the Blood if the Isles book is that the Neolithic substrate is still by far the ethnic component in England. Anglo-Saxon and Danish ancestry ranged from 10-25% across England depending on region.  Again the cultural impact differs from the genetic.

20 odd percent is still a lot.  With Britain, migration could have a more significant impact because it happened over centuries and because migrants came in by sea, which in pre-modern technology is an easier way of moving relatively large groups of people.

[Valmy]

Supposedly the Angles moved over almost entirely but that is probably hard to prove DNA-wise.

[The Minsky Moment]

East Anglia IIRC has the highest concentration of "Germanic" DNA markers so something to the idea of high levels of Angle migration.  It's a patrilineal lineage though.  It doesn't seem to have been a full-scale population movement.

[Razgovory]

I'm very skeptical of these type of DNA studies.  firstly because it's hard to get a good population survey from people who have been dead for thousands of years and second because I don't fully understand what is is being measured when they compare Haplogroups.  I'm never comfortable using evidence I don't understand.