What a 55,000-year-old fetus reveals about the decline of Neanderthals

Between 1968 and 1970, a dozen tiny ancient human bones were found in the Sesselfelsgrotte rock shelter above a village in southern Germany. They went unnoticed in a museum collection for decades until the 1990s, when scientists re-examined them. The bones—which included femur and fibula fragments, a skull cap, and a few ribs—were not fully formed. Measuring only a few centimeters each, they were smaller than those of even the smallest child.  

Then, in 2006, a scientist in Germany formally announced the identity of the bones: they belonged to a Neanderthal fetus that was just about to be born some 55,000 years ago.

"The skeletal remains of very young Neanderthal children, pre-birth or after birth, they're really, really rare," says National Geographic Explorer Alvise Barbieri, an archaeologist and geoscientist at Portugal's University of the Algarve. "I think only one other has been studied, from France."

Now, Barbieri and his colleagues have extracted ancient DNA from the Neanderthal fetus and sequenced its mitochondrial genome. Their analysis determined that the fetus belonged to an older branch of the Neanderthal family tree, rather than the final lineage that dominated Europe and then went extinct about 40,000 years ago. The rare fetal DNA gave the researchers a clearer picture of the older branch, allowing them to pinpoint a severe population crash that shrank Neanderthal genetic diversity tens of thousands of years before they vanished.

They published their findings Monday in the journal Proceedings of the National Academy of Sciences.

In addition to the mitochondrial genome from the fetus, the team sequenced nine other mitochondrial genomes from Neanderthal remains found across Europe, at sites in Belgium, France, Germany, and Serbia. The researchers analyzed 10 new Neanderthal mitochondrial genomes alongside 49 previously known ones and determined that the earlier Neanderthal lineage—represented by the fetus—was distinct from the final Neanderthal lineage.

That finding enabled the researchers to estimate that Neanderthals suffered a "genetic bottleneck," or population crash that wiped out much of their genetic diversity, about 65,000 years ago. The new study provides the best estimate yet for the date of this genetic bottleneck.

The researchers think this happened around the time when the vast ice sheets of Ice Age Europe had pushed the Neanderthals back to the relatively ice-free region of south-western France—a safe haven that scientists call a "glacial refugium."

The study suggests that after the ice sheets receded and the Neanderthal population rebounded and spread again throughout Europe, the Neanderthals were very genetically similar. Ultimately, the Neanderthals underwent a final population collapse between 45,000 and 42,000 years ago, shortly before their extinction (though some interbred with Homo sapiens). The researchers think their final demise may have been due to climatic changes that shrank their hunting and foraging territory.

Joshua Akey, a geneticist from Princeton University who was not involved in the study, says it was striking how genetically similar late Neanderthals seem to have been.

"The rapid decline in population size,” says Akey, “suggests that Neanderthals were already experiencing demographic stress before their final disappearance."

Neanderthal population bottleneck

The new study is among the first to propose a date for the genetic bottleneck suffered by Neanderthals, although scientists have long suggested that such a bottleneck must have existed. Thanks to the mitochondrial genome of the fetus and other Neanderthals, however, the researchers now think they can pin down when it happened.

While noting that the exact time is still open to debate, "I think the general concept is well-supported," says paleoanthropologist John Hawks of Wisconsin-Madison, who was not involved in the study. "Later European Neanderthals emerged in part from a small founder population that lived sometime after 65,000 years ago."

Charikleia Karageorgiou, a geneticist at SUNY Buffalo who was not involved in the study, says the finding that the final Neanderthal lineage had only limited genetic diversity is "extremely interesting."

Only by sequencing the genomes of many more individuals could scientists better understand what had happened to the Neanderthals, she says: "That, to my mind, is a very exciting frontier in the field right now."

Analyzing a Neanderthal fetus

Extracting useful DNA from 55,000-year-old bones is always difficult, but Barbieri and his colleagues faced additional problems extracting it from a fetus. To start, scientists often find ancient DNA, or “aDNA,” in tooth samples, where it is protected by layers of enamel. But fetuses have no teeth, and these remains didn't have an entire jaw. The petrous bones of the inner ear are usually reservoirs of ancient DNA, but here they were never found.

Barbieri emphasizes that only a fraction of a percent of the bone samples from the fetus yielded usable ancient DNA for analysis. The amount was so small that only mitochondrial DNA—the subset of genes found in the cell's mitochondria, which is always inherited from an organism's mother—could be extracted, and not the more comprehensive DNA from cell nuclei that is needed for a full genome.

"The overall low preservation of aDNA did not allow us to extract nuclear aDNA," Barbieri explains. But "that might be possible with future sampling."

He says the fetus was probably buried when its mother died, but that her remains had never been found.

In addition to the ancient genetic analysis, Barbieri and his team also micro CT-scanned and conducted anatomical research on the fossilized fetus, some of which is detailed in a not-yet-peer-reviewed paper uploaded to the preprint server bioRxiv in late February.

For that preprint, Barbieri and his colleagues used their findings from the PNAS study as a baseline for research on new details about Neanderthal development before birth, including prenatal bone development. That, in turn, enabled them to compare the Neanderthal fetus with a modern human fetus, Barbieri says.

Both research efforts present new details of Neanderthals and the extent to which they were similar—and different—to modern humans. Scientists don't yet know all the factors that led to the ultimate demise of Neanderthals about 40,000 years ago, but the latest studies are crucial pieces of the puzzle.