Oldest ever human genome sequence may rewrite human history

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14 March 2016

https://www.newscientist.com/

What secrets lurk in the pit of bones?

Javier Trueba, Madrid Scientific Films

The oldest ever human nuclear DNA to be reconstructed and sequenced reveals Neanderthals in the making – and the need for a possible rewrite of our own origins.
The 430,000-year-old DNA comes from mysterious early human fossils found in Spain’s Sima de los Huesos, or “pit of bones”.
The fossils look like they come from ancestors of the Neanderthals, which evolved some 100,000 years later. But a 2013 study found that their mitochondrial DNA is more similar to that of Denisovans (see video, below), who also lived later and thousands of kilometres away, in southern Siberia.
So who were the Sima people – and how are they related to us?

To find out, a team led by Matthias Meyer at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, pieced together parts of the hominin’s nuclear DNA from samples taken from a tooth and a thigh bone.

One of the Sima de los Huesos skeletons

Javier Trueba, Madrid Scientific Films

The results suggest they are more closely related to ancestors of Neanderthals than those of Denisovans – meaning the two groups must have diverged by 430,000 years ago. This is much earlier than the geneticists had expected.
It also alters our own timeline. We know that Denisovans and Neanderthals shared a common ancestor that had split from our modern human lineage. In light of the new nuclear DNA evidence, Meyer’s team suggests this split might have happened as early as 765,000 years ago.
Previous DNA studies had dated this split to just 315,000 to 540,000 years ago, says Katerina Harvati-Papatheodorou at the University of Tubingen in Germany.
But a date of 765,000 years ago actually brings the DNA evidence more in line with some recent fossil interpretations that also suggest an older divergence between modern humans and the ancestor of the Neanderthals and Denisovans.
“I am very happy to see that ideas about the divergence based on ancient DNA and on anatomical studies of the fossil record seem to be converging,” says Aida Gómez-Robles at George Washington University in Washington DC, who was involved in the fossil research.

Tree redrawn?

But if such an ancient split is correct, we might have to redraw parts of our evolutionary tree.
Conventional thinking is that modern humans, Neanderthals and Denisovans all evolved from an ancient hominin called Homo heidelbergensis.
However, H. heidelbergensis didn’t evolve until 700,000 years ago – potentially 65,000 years after the split between modern humans and the Neanderthals and Denisovans.
Instead, another, obscure species called Homo antecessor might now be in the frame as our common ancestor.
This species first appeared more than a million years ago – and its face is very similar to that of modern humans, says Chris Stringer at the Natural History Museum in London.

Further puzzles

“Research must now refocus on fossils from 400,000 to 800,000 years ago to determine which ones might actually lie on the respective ancestral lineages of Neanderthals, Denisovans and modern humans,” he says.
Another puzzle remains. The study confirmed a previous finding that the mitochondrial DNA of the Sima hominin is more similar to Denisovans than to Neanderthals – but no one knows why.
Perhaps there was another unidentified lineage of hominins in Eurasia that interbred with the ancestors of both – but not with the particular group of hominins that evolved into the Neanderthals.
Or, Meyer says, perhaps such mitochondrial DNA was typical of early Neanderthals and Denisovans, and it was only later that Neanderthals acquired different mitochondrial DNA from an African population of “proto-Homo sapiens“.
Journal reference: Nature, DOI: 10.1038/nature17405
Find out more about the oldest human genome dug up in Spain’s pit of bones:

 

Neanderthal diet: Only 20 percent vegetarian

Researchers have long debated the precise diet of early humans, but the latest study is the first to nail down precise percentages.

By Brooks Hays   |   March 14, 2016 at 12:33 PM

Fossil analysis suggests Neanderthals ate a diet of
80 percent meat. Photo by OrdinaryJoe/Shutterstock

TUBINGEN, Germany, March 14 (UPI) -- Neanderthals were apparently too busy hunting and scavenging to pay much attention to Michael Pollan's dietary advice: eat mostly plants.
New isotopic analysis suggests prehistoric humans ate mostly meat. As detailed in a new study published in the journal Quaternary International, the Neanderthal diet consisted of 80 percent meat, 20 percent vegetables.
Researchers in Germany measured isotope concentrations of collagen in Neanderthal fossils and compared them to the isotopic signatures of animal bones found nearby. In doing so, scientists were able to compare and contrast the diets of early humans and their mammalian neighbors, including mammoths, horses, reindeer, bison, hyenas, bears, lions and others.
"Previously, it was assumed that the Neanderthals utilized the same food sources as their animal neighbors," lead researcher Herve Bocherens, a professor at the University of Tubingen's Senckenberg Center for Human Evolution and Palaeoenvironment, said in a news release.
"However, our results show that all predators occupy a very specific niche, preferring smaller prey as a rule, such as reindeer, wild horses or steppe bison, while the Neanderthals primarily specialized on the large plant-eaters such as mammoths and woolly rhinoceroses," Bocherens explained.
All of the Neanderthal and animal bones, dated between 45,000 and 40,000 years old, were collected from two excavation sites in Belgium.
Researchers have long debated the precise diet of early humans, but the latest study is the first to nail down precise percentages.
Bocherens and his colleagues are hopeful their research will shed light on the Neanderthals' extinction some 40,000 years ago.
"We are accumulating more and more evidence that diet was not a decisive factor in why the Neanderthals had to make room for modern humans," he said.

Humans Interbred With Hominins on Multiple Occasions, Study Finds

Carl Zimmer

MATTER MARCH 17, 2016

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Photo

Skulls of the Neanderthal man. Credit European Pressphoto Agency

The ancestors of modern humans interbred with Neanderthals and another extinct line of humans known as the Denisovans at least four times in the course of prehistory, according to an analysis of global genomes published on Thursday in the journal Science.

The interbreeding may have given modern humans genes that bolstered immunity to pathogens, the authors concluded.

“This is yet another genetic nail in the coffin of our over-simplistic models of human evolution,” said Carles Lalueza-Fox, a research scientist at the Institute of Evolutionary Biology in Barcelona who was not involved in the study.

The new study expands on a series of findings in recent years showing that the ancestors of modern humans once shared the planet with a surprising number of near relatives — lineages like the Neanderthals and Denisovans that became extinct tens of thousands of years ago.

Before disappearing, however, they interbred with our forebears on at least several occasions, and today we carry DNA from these encounters.

The first clues to ancient interbreeding surfaced in 2010, when scientists discovered that some modern humans — mostly Europeans — carry DNA that matches material recovered from Neanderthal fossils.

Later studies showed that the forebears of modern humans first encountered Neanderthals after expanding out of Africa more than 50,000 years ago.

But the Neanderthals were not the only extinct humans that our own ancestors found. A finger bone discovered in a Siberian cave, called Denisova, yielded DNA from yet another group of humans.

Research later indicated that all three groups — modern humans, Neanderthals and Denisovans — shared a common ancestor who lived roughly 600,000 years ago. And, perhaps no surprise, some ancestors of modern humans also interbred with Denisovans.

Some of their DNA has survived in people in Melanesia, a region of the Pacific that includes New Guinea and the islands around it.

Those initial discoveries left major questions unanswered, such as how often our ancestors interbred with Neanderthals and Denisovans. Scientists have developed new ways to study the DNA of living people to tackle these mysteries.

Joshua M. Akey, a geneticist at the University of Washington, and his colleagues analyzed a database of 1,488 genomes from people around the world. The scientists added 35 genomes from people in New Britain and other Melanesian islands in an effort to learn more about Denisovans in particular.

The researchers found that all the non-Africans in their study had Neanderthal DNA, while the Africans had very little or none. That finding supported previous studies.

But when Dr. Akey and his colleagues compared DNA from modern Europeans, East Asians and Melanesians, they found that each population carried its own distinctive mix of Neanderthal genes.

The best explanation for these patterns, the scientists concluded, was that the ancestors of modern humans acquired Neanderthal DNA on three occasions.

The first encounter happened when the common ancestor of all non-Africans interbred with Neanderthals.

The second occurred among the ancestors of East Asians and Europeans, after the ancestors of Melanesians split off. Later, the ancestors of East Asians — but not Europeans — interbred a third time with Neanderthals.

Earlier studies had hinted at the possibility that the forebears of modern humans had multiple encounters with Neanderthals, but until now hard data was lacking.

“A lot of people have been arguing for that, but now they’re really providing the evidence for it,” said Rasmus Nielsen, a geneticist at the University of California, Berkeley, who was not involved in the new study.