It has been shown that Neanderthals contributed genetically to modern humans outside Africa 47,000–65,000 years ago. Here we analyse the genomes of a Neanderthal and a Denisovan from the Altai Mountains in Siberia together with the sequences of chromosome 21 of two Neanderthals from Spain and Croatia. We find that a population that diverged early from other modern humans in Africa contributed genetically to the ancestors of Neanderthals from the Altai Mountains roughly 100,000 years ago. By contrast, we do not detect such a genetic contribution in the Denisovan or the two European Neanderthals. We conclude that in addition to later interbreeding events, the ancestors of Neanderthals from the Altai Mountains and early modern humans met and interbred, possibly in the Near East, many thousands of years earlier than previously thought.
"It's been known for several years, following the first sequencing of the Neanderthal genome in 2010, that Neanderthals and humans must have interbred," says Professor Adam Siepel, a co-team leader and Cold Spring Harbor Laboratory (CSHL) quantitative biologist. "But the data so far refers to an event dating to around 47,000-65,000 years ago, around the time that human populations emigrated from Africa. The event we found appears considerably older than that event."
In addition to Siepel, who is Chair of CSHL's Simons Center for Quantitative Biology, the team included several members of the Max Plank Institute for Evolutionary Anthropology, including Martin Kuhlwilm, Svante Pääbo, Matthias Meyer and co-team leader Sergi Castellano. Kuhlwilm was co-first author of the new paper with Ilan Gronau, a former member of Siepel's Lab who is now at the Herzliya Interdisciplinary Center, Israel. Melissa Hubisz, a Ph.D. student with Siepel at Cornell University, also made major contributions to the work. The full international research team included 15 additional co-authors.
"One very interesting thing about our finding is that it shows a signal of breeding in the 'opposite' direction from that already known," Siepel notes. "That is, we show human DNA in a Neanderthal genome, rather than Neanderthal DNA in human genomes." This finding, the result of several kinds of advanced computer modeling algorithms comparing complete genomes of hundreds of contemporary humans with complete and partial genomes of four archaic humans, has implications for our knowledge of human migration patterns.
Figure 2: Distinguishing between two scenarios of introgression into archaic humans
People living today who are of European, Eurasian and Asian descent have well-identified Neanderthal-derived segments in their genome. These fragments are traces of interbreeding that followed the "out of Africa" human migration dating to about 60,000 years ago. They imply that children born of Neanderthal-modern human pairings outside of Africa were raised among the modern humans and ultimately bred with other humans, explaining how bits of Neanderthal DNA remain in human genomes.
Figure 3: Refined demography of archaic and modern humans.
The team's evidence of "gene flow" from descendants of modern humans into the Neanderthal genome applies to one specific Neanderthal, whose remains were found some years ago in a cave in southwestern Siberia, in the Altai Mountains, near the Russia-Mongolia border. The modern human ancestor who contributed genes to this particular Neanderthal individual - called the "Altai Neanderthal," and known from a tiny toe bone fragment - must have migrated out of Africa long before the migration that led Africans into Europe and Asia 60,000 years ago, the scientists say.
Figure 4: Homozygous segments on chromosome 21.
In contrast, the two Neanderthals from European caves that were sequenced for this study -- one from Croatia, another from Spain -- both lack DNA derived from ancestors of modern humans. The team also included in their analysis DNA from another archaic human relative, a Denisovan individual, whose remains were found in the same cave in the Altai Mountains. Denisovans, like Neanderthals, are members of the human line that eventually became extinct. Both of these archaic human cousins lived in the same cave, although at different times in the past.
Around 100,000 years ago, most H. sapiens were still in Africa and the first interbreeding event between H. sapiens and the Neanderthals could have taken place in East Africa or the Arabian Peninsula. Mitochondrial Eve (L), the matrilineal most recent common ancestor, lived in East Africa approximately 100,000–200,000 years ago, when anatomically modern humans were developing as a population distinct from other human sub-species. Its descendant haplogroup L3 arose in Eastern Africa 104,000 years ago and the L3 people gradually spread to the Arabian Peninsula as the first group of H. sapiens who ventured out of Africa. Therefore, there is a possibility that it was the L3 people who interbred with the Neanderthals in the Arabian Peninsula. Haplogrpup L3 further split into N and M and all European mtDNA haplogroups descended from Haplogroup N and most Asian haplogroups are the descendants of Haplogrpup M, which explains why Asians and Europeans are up to 5% Neanderthal. It's also known that the Cro-Magnons in Europe and the Jomon, the indigenous people of Japan, belonged to Haplogroup N, which did not come into existence until 71,000 years ago.
The new research, published in Nature, provides the first genetic evidence that some Homo sapiens left the African continent at least 100,000 years ago, tens of thousands of years earlier than widely assumed. The smoking-gun proof came not from human fossils but a single Neanderthal whose remains were found in a cave in the Altai Mountains of southern Siberia, near the Russian-Mongolian border.
Embedded in the genome of the ancient caveman — in chromosome 21, to be precise — were traces of human DNA. This is the earliest known case of inter-species sex between Homo sapiens and Neanderthals. More significantly, it also pushes back the departure of our forebear from the cradle of humanity by some 35,000 years, the researchers said.
“It is the first genetic evidence of modern humans outside Africa,” Sergi Castellano, a scientist at the Max Planck Institute for Evolutionary Anthropology and co-leader of the study, told AFP.
The findings are bolstered by the discovery, announced last October, of human teeth in southern China dating back 80,000 to 120,000 years, though there is no reason to think the two groups were linked, the researchers said. In both cases, they speculate, it is likely that these early migrations from East Africa moved across the Arabian Peninsula.
From there, some may have gone north towards central Asia and Siberia, in one case, and across the Middle East towards east Asia, in the other. The new study also concluded, however, that the humans who interbred with the Altai Neanderthals are not from the same stock that populated Europe and Asia some 65,000 years ago (i.e. haplogroups N, M).
European Neanderthals lacked DNA derived from modern humans because they lived long before the emergence of H. sapiens in Africa that occurred 200,000 years ago. The Neanderthal fossils in Spain date back 430,000 years, more than 200,000 years older than Mitochondrial Eve (L), while the Altai Neanderthals lived around 50,000 years ago and interbred with modern humans. The Denisovans are known to be even more archaic than the Neanderthals and they possibly interbred with an unidentified species such as Homo erectus or Java Man.
They are often depicted as big, brutish and not terribly bright, but Neanderthals may have actually been sophisticated chemists who harnessed the power of explosive materials in rocks. Scientists claim to have uncovered evidence that the extinct species of early human used powdered manganese dioxide to help them light fires 50,000 years ago.
Blocks of the dark material have been found at sites inhabited by Neanderthals in south west France and was thought to have been used to produce a powder to decorate their bodies. In a series of experiments the researchers found powdered manganese dioxide, which is powerful oxidant, reduces the temperature that wood ignites at, making it much easier to start a fire.
They found it even made green wood, which is usually much harder to light, easier to ignite. The findings may help to settle the long-running debate about whether Neanderthals were capable of lighting fires. While there is evidence that they used fire and may even have cooked with it, some anthropologists have suggested they were only able to do this by taking advantage of natural fires.
'Starting a fire using sparks from flint without a metal striker is not as easy as it may seem but manganese dioxide has a significant beneficial effect.' Manganese dioxide blocks were discovered at a site in Pech-de-l'Aze in the Dordogne in south west France that was inhabited by Neanderthals 50,000 years ago. The blocks occur naturally in the limestone formations where the Neanderthals made their home. But some of the blocks found at the site were covered in scratches which suggests they may have been scraped to produce a powder.
A unique assemblage of 28 hominin individuals, found in Sima de los Huesos in the Sierra de Atapuerca in Spain, has recently been dated to approximately 430,000 years ago1. An interesting question is how these Middle Pleistocene hominins were related to those who lived in the Late Pleistocene epoch, in particular to Neanderthals in western Eurasia and to Denisovans, a sister group of Neanderthals so far known only from southern Siberia. While the Sima de los Huesos hominins share some derived morphological features with Neanderthals, the mitochondrial genome retrieved from one individual from Sima de los Huesos is more closely related to the mitochondrial DNA of Denisovans than to that of Neanderthals2. However, since the mitochondrial DNA does not reveal the full picture of relationships among populations, we have investigated DNA preservation in several individuals found at Sima de los Huesos. Here we recover nuclear DNA sequences from two specimens, which show that the Sima de los Huesos hominins were related to Neanderthals rather than to Denisovans, indicating that the population divergence between Neanderthals and Denisovans predates 430,000 years ago. A mitochondrial DNA recovered from one of the specimens shares the previously described relationship to Denisovan mitochondrial DNAs, suggesting, among other possibilities, that the mitochondrial DNA gene pool of Neanderthals turned over later in their history.
Figure 1: Percentage of derived alleles shared between the SH specimen and the human, Neanderthal and Denisovan genomes.
Matthias Meyer has just published the results of what may be the world’s most wasteful genome-sequencing project. In decoding just 0.1% of the genome of the oldest DNA ever recovered from an ancient human, the molecular biologist at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, threw out enough raw data to map the modern human genome dozens of times over.
Figure 2: Sharing of derived alleles with the Altai Neanderthal.
But the excess was necessary, because the DNA in the 430,000-year-old bones was degraded and contaminated. Meyer’s feat of recovery has revealed that the remains, from a cavern in northern Spain, represent early Neanderthals — and has pushed back estimates of the time at which the ancient predecessors of humans must have split from those of Neanderthals (M. Meyer et al. Nature dx.doi.org/10.1038/nature17405; 2016).
Extended Data Figure 1: Sharing of derived alleles at diagnostic positions separating the hominin groups in the mitochondrial tree.
The analysis addresses confusion over which species the remains belong to. A report published in 2013 sequenced a femur’s mitochondrial genome — which is made up of DNA from the cell’s energy-producing structures that is more abundant in cells than is nuclear DNA. It suggested that at least one individual identified from the remains was more closely related to a group called Denisovans — known from remains found thousands of kilometres away in Siberia — than it was to European Neanderthals (M. Meyer et al. Nature 505, 403–406; 2014).
The Sima hominin skulls have the beginnings of a prominent brow ridge, as well as other traits typical of Neanderthals. But other features, and uncertainties around their age — some studies put them at 600,000 years old, others closer to 400,000 — convinced many researchers that they might instead belong to an older species known as Homo heidelbergensis. Confusion peaked when Meyer, his colleague Svante Pääbo and their team revealed the mitochondrial connection to the Denisovans. But they hoped that retrieving the skeletons’ nuclear DNA — which represents many more lines of ancestry than does mitochondrial DNA, which is inherited solely from the maternal line — would clear things up.
The team’s latest mitochondrial sequences, meanwhile, again confirm the puzzling link between the Sima hominins and the Denisovans. Meyer suggests that the ancestors of the two groups carried mitochondrial DNA that is reflected in both — but which is not present in later Neanderthals. This elimination could have happened by chance, but Meyer now favours the hypothesis that an as yet unknown species from Africa migrated to Eurasia and bred with Neanderthals, replacing the mitochondrial DNA lineages. (Supporting this idea, stone-tool technologies spread from Africa to Eurasia around half a million years ago, and again 250,000 years ago).
Based on skeletal evidence, the 28 individuals buried in the 13m-deep cave shaft have been variously interpreted as belonging to a human species called Homo heidelbergensis or as proto-Neanderthals - that is, on their way to evolving the classic physical characteristics of the Neanderthals. But in 2013, a team reported their analysis of mitochondrial DNA (mtDNA) retrieved from remains at the archaeological site - known as Sima de los Huesos in Spanish. This type of genetic material is inherited only via the maternal line. They concluded that the mtDNA was more closely related to that found in the enigmatic Denisovans, a population of ancient humans who inhabited Asia more than 50,000 years ago, than to that found in Neanderthals.
The Denisovan link was a surprise, especially given the Neanderthal-like characteristics of the bones. But the latest genetic results reveal that the Pit of Bones people were indeed closely related to the Neanderthals. "Sima de los Huesos is currently the only non-permafrost site that allows us to study DNA sequences from the Middle Pleistocene, the time period preceding 125,000 years ago," says Matthias Meyer of the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany.
Analysis of the mitochondrial DNA from one individual supported a relationship to Denisovans - consistent with the previous study. This leads the scientists to speculate that mitochondrial DNA types seen in later, "classical" Neanderthals may have arrived in a migration from Africa, replacing those present in the Pit of Bones people.
Prof Chris Stringer, from London's Natural History Museum, who was not involved with the latest study, said the results shed new light on how our own species (Homo sapiens) and Neanderthals diverged from a common ancestor. "There has been continuing debate about how deep in time the Neanderthal-sapiens split was, with estimates ranging from about 800,000 years to 300,000 years," he explained.
"I have recently favoured a split time of about 400,000, and have argued for many years that the widespread species H. heidelbergensis at about 500,000 was probably their last common ancestor." He added: "When new genetic data are used to recalibrate divergence times, these now suggest older split times both between the Neanderthals and Denisovans (approximately 450,000 years) and their lineage and ours (approximately 650,000 years)."
