Research into hundreds of genomes spanning 50,000 years of human history indicates that early modern humans and Neanderthals interbred in a relatively narrow time window, shedding light on the interactions between the ancient groups and distinguishing all modern humans from those who left Africa earlier.
One paper published today in Nature describes the oldest modern human genomes, which constrain the timing of Neanderthal mixing with Homo sapiens, and another paper published in Science describes insights about Neanderthal and human interactions based on genomes from modern and ancient humans.
There were at least two genetically distinct groups of early modern humans, whose skeletal remains were found in sites in Bulgaria and Czechia. The latter group—represented by the skull of an individual dubbed Zlatý kůň—is one of the earliest modern human populations in Europe. Zlatý kůň’s genome indicates that her population only mixed once with Neanderthals, while the Bulgarian group may have mixed with our nearest human cousins twice.
The team in Nature also found that Zlatý kůň was related to two of the individuals that lived near Ranis, Germany, between 41,000 and 49,500 years ago. The team does not think the Ranis population, which had about 3% Neanderthal ancestry, has any modern-day descendants. Based on the genetic analysis, the Neanderthal DNA seems to have been introduced to the Ranis population’s DNA about 80 generations prior.
“We know that Ranis and Zlatý kůň individuals also overlapped in time with Neanderthals in Europe, but they only carry Neanderthal ancestry that is also common to all people outside of Africa today,” said Arev Sümer, a researcher at the Max Planck Institute for Evolutionary Anthropology and lead author of the Nature paper, at a press conference held earlier this week. “This contrasts with early modern human genomes that are previously published from Europe, such as the ones from Bulgaria and Romania.”
The Ranis site was originally excavated in the 1930s and revisited in a second round of excavations between 2016 and 2022. “The material that was excavated was at the time [the 1930s] mostly seen as fauna,” Johannes Krause, a geneticist at the Max Planck Institute for Evolutionary Anthropology, told Gizmodo during the press conference. And by the time the excavation in the mid-1930s finished, World World II had begun. The splintered bone was boxed up and sat in a museum in central Germany for nearly a century, until a team from the Planck institute revisited the site and found some bone fragments in a freshly dug pit.
Hélène Rougier, a researcher at California State University, Northridge, and co-author of the Science paper, sifted through over 100 boxes containing tens of thousands of bone fragments, confirming the site in Germany belonged to one of the earliest groups of modern humans in Europe.
“What was really fantastic is that it turned out we have the same individual in the old excavation as the new excavation,” Krause said. “Four of the fragments were actually from the same person, and that person is from the pit and spread out in the old excavation.”
“Why that person ended up spread out over several square meters—we can only imagine what happened there 45,000 years ago,” Krause added. “Kind of don’t even want to think about what would’ve caused such a spread-out human. ”
A particularly neat finding from the Nature paper: The remains of early modern humans older than 50,000 years outside Africa represent entirely distinct non-African populations from those alive today. In other words, the remains of a roughly 50,000-year-old early modern human found outside Africa would not belong to an ancestor of modern humans.
All humans are a little bit Neanderthal. Though they don’t walk the Earth as a distinct species, Neanderthals were closely enough related to Homo sapiens that the two groups interbred and slowly hybridized. In some parts of East Asia, the proportion of Neanderthal DNA in human genomes is up to 24% higher than in other parts of the world. Even genes related to the shape of tall noses can be traced back to our nearest human cousins.
The Zlatý Kůň skull. Photo: Petr VelemínskýThe Science study investigated more than 300 genomes from the last 50,000 years of human evolution. 59 genomes belong to ancient individuals who lived between 2,200 and 45,000 years ago. The research indicated that humans inherited Neanderthal genes related to skin color, immune response, and metabolism.
The team sought to understand the timing and duration of the Neanderthal admixture, and the findings indicated that the Neanderthal gene flow occurred during an interbreeding event between 43,500 years ago and 50,500 years ago. Krause said that the effective early modern human population size was about 5,000 individuals, and over a relatively rapid time period—maybe several centuries—about 200 Neanderthals mixed into that population.
“Understanding this timing is really important because it has implications for the timing of the Out of Africa migration,” said Priya Moorjani, a molecular biologist at UC Berkeley and senior author of the Science paper, in the press conference. “Our analysis shows the Out-of-Africa migration must have completed by 43,500 years ago and earlier waves may have been from individuals that have not contributed to living, non-African individuals.”
The relative recency of Neanderthals mixing with humans brings to mind the roughly 45,000-year-old fossil Neanderthal named Thorin, whose genome was analyzed earlier this year. Thorin’s remains were found in France, and indicated that the individual was genetically distinct from other groups in the area by about 50,000 years.
About 39,500 years ago, the situation in Eurasia was further complicated by the Campanian Ignimbrite eruption, which spread ash from Italy to Russia. “You have the extinction of those early human groups and of course Neanderthals, and the first people who are genetically connected to Europeans are buried in the ash—so after the volcano,” Krause said. “It’s quite an interesting coincidence, but it could be the explanation. Of course it remains a hypothesis for the moment.”
Neanderthals disappear from the fossil record around 39,000 years ago—shortly after the interbreeding events pointed to by the Science and Nature papers. The ancient human group was subsumed by our own and they live on (in a sense) through their DNA.
“These are not really two species, they’re two groups,” Moorjani said. “The differences that we imagine to be quite big between these groups were actually quite small, genetically. We were far more similar than we were different.”
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