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DNA reveals mysteries of ancient humans

Who were the Denisovans? Who were the steppe invaders? Who were the ghost ancestors of Africa?
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The neat and tidy answer to who we are is Homo sapiens, and, more specifically, Homo sapiens sapiens. But the real answer is not that neat, and not that tidy.

Evidence points to H. sapiens evolving from archaic humans such as H. heidelbergensis, H. rhodensiensis, or H. antecessor. Those ancestors lived between 1.2 million and 300,000 years ago and migrated out of Africa. They gradually replaced H. erectus and other now-extinct archaic humans such as the Neanderthals and the Denisovans.

It’s that “gradual replacement” which has spawned numerous questions and led to a reckoning about the development of our species. DNA studies of ancient extinct humans are revealing a complicated picture which suggests some human species inter-mated and others mysteriously showed up, then vanished.

Beginning around 2005, genomic sequencing found evidence of Neanderthal DNA in modern humans, and we now know that the DNA of humans alive today is 1-4% Neanderthal.

“This admixture was created roughly 200,000 years ago when the first humans moving out of Africa mated with Neanderthals in Europe, and that the exchange went both ways, with some human-Neanderthal offspring later returning to Africa," according to a study published in Cell.

In 2013, the oldest-known DNA, dating back some 400,000 years, offered new details on the Denisovans, who ranged from what is now southeast Asia to Siberia. Those details included evidence that modern humans interbred with both groups, and subsequent studies, for example, showed that 4-6% of the DNA of modern residents of the islands of New Guinea and Bougainville is shared with the Denisovans.

That 400,000-year-old DNA came from a thigh bone found in a cave in northern Spain.

"This is the oldest human genetic material that has been sequenced so far," Matthias Meyer, a molecular biologist at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, told Live Science. "This is really a breakthrough — we'd never have thought it possible two years ago that we could study the genetics of human fossils of this age." Until now, the previous oldest human DNA known came from a 100,000-year-old Neanderthal from a cave in Belgium.

Meyer and his team reconstructed a nearly complete genome of the bone’s mitochondria, and since fossils found in the cave resembled Neanderthals, he expected the mitochondrial DNA to be Neanderthal.

“Surprisingly, the mitochondrial DNA reveals this fossil shared a common ancestor not with Neanderthals, but with Denisovans, splitting from them about 700,000 years ago,” the Live Science article stated. “This is odd, since research currently suggests the Denisovans lived in eastern Asia, not in western Europe, where this fossil was uncovered.”

What were Denisovans doing in Europe? How could they and the Neanderthals diverge genetically even as their ranges overlapped? Did this represent a new branch of human evolution?

A 2016 article in Nature offered more tantalizing clues and allowed researchers to gain a fuller picture of how different species of humans interbred. As summarized in a different Nature article, there was breeding between early modern humans and Neanderthals, humans and Neanderthals, humans and Denisovans, Neanderthals and Denisovans, and Denisovans and a “ghost” population of hominins.

It’s that last headline which is the most mysterious. Evidence of that early human ancestor, who apparently hailed from Asia, paints a picture where humans of different species lived together.

“What it begins to suggest is that we’re looking at a Lord of the Rings-type world — that there were many hominid populations,” Mark Thomas, an evolutionary geneticist at University College London, told Nature. One theory posited that they were related to H. heidelbergensis.

But that’s not the only mystery human discovered through an analysis of ancient DNA. A 2019 study of 8,000 years of genetics in the Iberian Peninsula—i.e., Spain and Portugal—hinted at a single mysterious migration more than 4,500 years ago. That migration was from the steppes of Russia, near the Black and Caspian seas, and from about 2,500 B.C. the DNA of Iberians was overtaken by it.

The finding backed up what is called the “Steppe hypothesis”—that a group of mostly males on horseback carrying bronze weapons swept into Europe from the east. Separate studies have hinted that those men may be linked to today’s Basque, who speak a non-Indo-European language and carry genetic markers closely related to those from the steppes.

While Neanderthal DNA is relatively easy to obtain, the same is not true for DNA from Denisovans—and is definitely not true for many of the mystery humans who scientists think once existed, such as the Basal Eurasians, whose DNA are found in modern Europeans but who show no evidence of interbreeding with Neanderthals. Did something happen, environmentally or culturally, to isolate this branch of humans? And what about DNA traces found in groups like the Baka hunter-gatherers of Cameroon and the Hadza and Sandawe of Tanzania, both of which appear to have DNA from another hominin species. Because this DNA is only found in a small group of humans today it suggests this ghost species bred with H. sapiens and lived alongside them until very recently—perhaps within the past 30,000 years.

“We have no physical record of these ancient hominins—no bones, no tools, no archaeological remains whatsoever,” writes New Scientist. “Yet the genetic code that they left within fossils of other hominins, and in living humans too, is offering profound and unprecedented insights into how our species came to be, and what the world was like at the time.”

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