Mezmaiskaya Cave offered shelter to Neanderthals for tens of thousands of years. The cave, located near Russia's border with Georgia, preserved Neanderthal remains so well that researchers have now been able to extract genetic information from two different individuals who lived approximately 20,000 years apart. And it's just one of the sites that's featured in a new collection of Neanderthal genomes: two from caves in Belgium, one from France, one from Croatia, and one from Mezmaiskaya.

As scientists publish more Neanderthal genomes, they’re able to start sketching more details of the long-ago drama and danger these people experienced. The new genomes are all from 39,000 to 47,000 years ago—late in the history of the population. The new data helps us piece together new details on Neanderthal population groups, their movements across Europe, and when they’re most likely to have bred with humans.

Replacement

The researchers, led by Mateja Hajdinjak at the Max Planck Institute for Evolutionary Anthropology, extracted tiny amounts of bone or tooth powder—sometimes as little as 9mg—and used a chemical process to remove modern genetic contamination. They also checked for the telltale signs of degradation found in ancient DNA.

They compared the data from the new sequences to previously published data from other ancient individuals, including a range of Neanderthals and a Denisovan, as well as samples from our own species. (The researchers found that their new sample from Vindija Cave in Croatia actually came from the same individual as a previously sequenced sample from the same cave.)

When they looked at existing data from Mezmaiskaya 1 (the individual who had died in Mezmaiskaya Cave around 70,000 years ago), they found hints of an ancient population replacement. Rather than finding that Mezmaiskaya 1 and Mezmaiskaya 2 were closely related to each other and more distantly related to the Western European Neanderthals, they found that Mezmaiskaya 2 seemed to be a Western European transplant, more closely related to the Croatian, Belgian, and French Neanderthals than to geographically closer Mezmaiskaya 1.

The finding implies that the population of Neanderthals in the Caucasus may have been wiped out at some point and replaced by an influx of Neanderthals from another region. The two events might not have been directly related, as that time window coincides precisely with “pronounced climatic fluctuations” in the region.

The authors write that “extreme cold periods in northern Europe may have triggered the local extinction of Neanderthal populations.” Following this extinction, they suggest, the area may have been re-colonized by Neanderthals from elsewhere. It’s also possible that the turnover worked the other way around—that Western European Neanderthals, including the individuals from Croatia, Belgium, and France, stem from a population that spread out from the Caucasus.

Interbreeding

The comparisons also allowed the researchers to look for genetic flow between Neanderthals and our own species. Surprisingly, even though these Neanderthals were around when we had already moved into Europe, there were “no indications of recent gene flow from early modern humans to late Neanderthals,” the authors write. The data also suggested that Neanderthal gene flow into humans came from a group of Neanderthals that branched off from these individuals' ancestral group between 70,000 and 150,000 years ago..

“It’s an amazing paper,” said Anders Eriksson in a phone call with Ars. He studies ancient genomes at King's College London, and wasn't involved in this work. “This really opens up the possibility of starting to do proper population genetics on Neanderthals.” He pointed to the researchers’ success at extracting and decontaminating the samples as particularly exciting: “I can see this opening up avenues for getting a lot more ancient DNA.”

The new information about Neanderthal populations and when they mixed with modern humans fits into our growing picture of the evidence, Eriksson said. The new data “fills in a lot of detail where we only really had a couple of data points,” he enthused. By comparing each new genome to the data we already have, we can slowly start to color in the sketch of ancient Neanderthal history—“so you can really start putting together a picture of the population that you had in Europe.”

Nature, 2018. DOI: doi:10.1038/nature26151 (About DOIs).

Note: this story was updated to correct the details of Neanderthal gene flow into humans.