The Ancient Skull, a new window into human migrations, the Denisovan Meetings

Zoom in / These fossils have identified Denisovan DNA within the sediments.

Dongju Zhang, Dongju Zhang, Lanzhou University

Denisova occupies a very strange place in human history. Like Neanderthals, they are an early branch of the lineage that produced modern humans and later mixed with modern humans. But we had known about Neanderthals for about 150 years before we had any of their DNA sequences and identified a set of anatomical features that defined them. In contrast, we had no idea the Denisovans even existed until their DNA unexpectedly appeared in one tiny bit of a finger. And to this day, we haven’t identified enough remains to really say anything about what they looked like.

But over time, we obtained increasingly ancient DNA samples that provide a clearer picture of our interactions with this mysterious lineage. Now, there are two new reports describing the ancient DNA providing more details. One paper describes the modern human genome from Asia that dates back to a time closer to when hybridization should take place. It provides additional evidence of at least two instances of interbreeding, and helps elucidate how early populations moved across Asia. The second asserts that the Denisovans lived along the Tibetan plateau and may have adapted to higher elevations.

Mongolian skull

In 2006, mining in the Salkhit Valley in Mongolia revealed the crest of a skull that was clearly ancient. But, since it did not have any specific features, people argued about whether it could have been a Neanderthal or Standing man. However, the initial sequencing of the DNA indicates that it belongs to modern humans, with a carbon date being located around 34,000 years old.

This is actually a critical period in human history. At this time, there were distinct populations from East Asia and East Eurasia (or Siberia), with the latter being somewhat related to Western Eurasia. Their history is enormously complex. A 40,000-year-old skeleton from near Beijing is clearly the closest to contemporary East Asia, but is closely related to a skeleton found in Belgium (! ??!?). The 45,000-year-old Siberian skeleton does not appear to have any modern relatives, while a 24,000-year-old individual from the same region identified a population that mixed with East Asia to produce Ancestors of the Native Americans. But two other Siberian skeletons from roughly the same time period do not show this convergence and generally show Eurasia.

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If you are not confused after this, come back and read it again.

Given this mess, any other DNA from that era and region could be of help. So, researchers did what became standard procedure for handling DNA at this age. First they looked for sequences that matched human DNA to extract all of the human-like sequences. To eliminate contamination from modern humans, they then looked for signs of damage that are more common as DNA ages. Anything that was clearly human and damaged was used to assemble the genome.

The end result was about what to expect, given the age of the skull apex. Most of the differences in DNA matched those of modern humans, but there were a number of regions that matched Neanderthals and Denisovans. Modern human parts were closely matched to East Eurasians and Native Americans, confirming earlier results.

Lots of education

But it’s still as confusing as it used to be. “The [newly described] The Salkhit individual shares many alleles with Tianyuan [Beijing] As with the approximately 31,000-year-old Yana individuals from northeastern Siberia, “the researchers wrote,” however, the Tianyuan and Yana individuals share fewer alleles with each other than the Salkhet individual. In general, the researchers concluded that at some time after the populations of West and East Eurasia separated, and there was some interbreeding between East Eurasia and East Asia.

But of course, the newly described Siberian DNA has a marked similarity to the skeleton of Belgium, indicating that some Western Eurasian DNA is still being traced back to the breed.

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Other ancients

As far as Neanderthals go, the new Siberian skeleton is so typical of the modern Asian population, about 1.7 percent of its DNA comes from Neanderthals. Denisovan content is difficult to judge, but researchers have discovered 18 large extensions of DNA inherited from Denisovans. The size of these researchers led to the conclusion that interbreeding had lasted for nearly 10,000 years. This corresponds to the complete absence of Denisovan DNA in the 45,000-year-old Siberian skeleton. Existing Denisovan DNA is more consistent with the amount seen in later East Asian skeletons.

The interesting thing here is that the parts in the new Salkhit genome do not overlap with those in the genomes of modern people in Southeast Asia and the Pacific. The obvious conclusion from this is that modern humans mixed with Denisovans on at least two different occasions. This is something other findings have indicated, but modern East Asia has DNA from both events. The genome of Silchite provides a clear separation between them.

Meanwhile, a separate paper examines where the Denisovans lived – specifically in the Baixia Karst Cave on the edge of the Tibetan plateau. At more than 3,000 meters (nearly 11,000 feet) above sea level, this was a high-altitude environment, to which it was difficult to return during the last glacial period. However, a portion of the jawbone was found there. While it did not yield any DNA, the protein fragments indicated that the jaw it came from belonged to Denisovans.

DNA from dirt

Most of the ancient DNA samples are heavily contaminated with bacteria, with severe DNA damage and dispersion. As a result, researchers have developed various procedures to help them separate out human-like DNA and then identify the ancient DNA based on the pattern of accumulated damage. Gradually, it was realized that these same technologies could work even when pollution is higher and human sequences are more scarce: soil samples. So, while we were unable to get the DNA out of the jawbone, a team decided that there might be some residue in the environment that it came from.

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So, the team dug through the sediments on the floor of the cave, chronicling the different layers in order to make an estimated chronology. Most of the layers contain mammalian DNA, which was very old based on the damage. So, the researchers pulled human mitochondrial DNA and began sequencing it. It was clearly a Denisovan, with a slim chance of a fraction of modern human DNA.

In general, there are signs that Denisovans were occupied more than 100,000 years ago and until recently, about 30,000 years ago. This is a long history of occupancy, although we can’t tell if it’s steady, seasonal, or choppy. Regardless, 70,000 years is definitely enough time, the researchers suggest, to adapt to the high altitude. This turns out to be consistent with another genetic finding: that some genetic adaptations in Tibet are at high altitudes Inherited from Denisovan.

Science, 2020. DOI: 10.1126 / science. abc1166And the 10.1126 / science. abb6320 (About DOIs).

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