Between 400,000 and 45,000 years ago, Neanderthals had most of Eurasia to themselves, hunting large game, harvesting plants, expertly knapping stone tools, and fashioning clothing from animal skins. But their existence was precarious. Two new studies show many Neanderthals lived in small, far-flung groups; likely experienced significant inbreeding; and survived a close brush with extinction about 75,000 years ago.
The findings, based on ancient DNA obtained in some cases from bone fragments no bigger than a french fry, reveal how advances in fossil identification and genomics are helping scientists tell new stories about our ancient cousins. “We’re finding little pieces in lots of places,” says Hélène Rougier, a paleoanthropologist at California State University, Northridge who co-authored one of the new papers, published today in the Proceedings of the National Academy of Sciences. “And with the methods geneticists have now, they can really make them talk.”
One paper details genomic insights from a fragment of Neanderthal bone just 2.5 centimeters in length. It was found in the back of Denisova Cave, a vaulted chamber in the Altai region of southern Siberia, where Neanderthals and another extinct ancient cousin, the Denisovans, found shelter from harsh conditions more than 100,000 years ago.
By comparing the newly sequenced genome with two others from the same region and a more recent specimen from a cave in Croatia, the team found that Neanderthals accumulated lots of genetic differences relatively quickly. The pattern likely reflects inbreeding in small, far-flung populations of just a few dozen individuals, especially in the east where Neanderthal populations were at the far edge of their range, the researchers say. “Neanderthals were more likely to reproduce between close relatives,” says Yale University geneticist Diyendo Massilani, a co-author of the Denisova Cave paper. As a result, the groups rapidly accumulated different sets of mutations, causing them to diverge genetically.
“Evolution happens faster in smaller populations,” says Joshua Akey, a Princeton University geneticist who did not work on either paper. “What they’re observing is that the global population of Neanderthals was small—maybe a couple of thousand breeding individuals—and on top of that, spread out over a large geographic range.”
Harmful mutations can accumulate through inbreeding. Yet somehow Neanderthals managed to survive across most of Eurasia for nearly 400,000 years, longer than modern humans have been on Earth. Perhaps, Massilani speculates, the mutations posed few problems so long as the surrounding environment was stable. “If a population or family are well-adapted to the environment, and the environment stays constant, maybe it’s not necessary for them to change so much to survive,” he says.
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The second study supports that conjecture. Hoping to examine the fate of Europe’s Neanderthal population over the course of the past 130,000 years, researchers linked the distributions of Neanderthals across Europe to genetic information from the mitochondrial DNA—a smaller subset of genetic material passed down from mothers to their offspring—of dozens of individuals.
The team found that Neanderthal sites and skeletal remains were widely distributed across the continent, and their genomes relatively diverse, until about 75,000 years ago. Then, as an ice age gripped the continent between 75,000 and 65,000 years ago, “we see the number of sites decline,” says Rougier, who co-authored the paper. Archaeological data show some Neanderthals found refuge in southwestern Europe, taking shelter inside caves in the valleys of southern France, while abandoning or dying out in the rest of the continent.
When the ice melted, the surviving Neanderthals spread out again, chasing big game from Spain to the mountains of the Caucasus. However, “All the genetic diversity we saw in mitochondrial DNA before 60,000 years ago vanishes, and one single line survives,” explains University of Tübingen paleogeneticist Cosimo Posth, also a study author.
Yet even as they expanded throughout Eurasia once more, genetic data show the number of breeding individuals—what geneticists call “effective population size”—remained small for millennia. “Maybe the resources available aren’t enough to sustain large groups,” Posth speculates.
About 45,000 years ago, sharp swings in climate conditions coincided with the arrival of anatomically modern humans in Europe. Those two events may have been disastrous for these fragile, inbred survivors, says Qiaomei Fu, a geneticist at the Chinese Academy of Sciences’s Institute of Vertebrate Paleontology and Paleoanthropology who was not part of either study. “When the environment changes, it’s not easy for them to adapt.”
Within 3000 years, the genetic data show Neanderthals’ effective population size plummeting again, hitting a low about 42,000 years ago before winking out entirely. “It’s pretty striking to see how fast they go down,” says University of Toronto paleoanthropologist Bence Viola, who was not involved with either paper. “Climate could have weakened them, and then modern humans come in and were so much larger a population that Neanderthals get swallowed up and diluted.”
The story of Neanderthals may shed light on our own, as well. By comparing our close cousins’ fate with that of the modern humans living in the same region, researchers have what amounts to a natural experiment that may point to which factors allowed our species to prevail while our ancient relatives died out. “One criticism of evolutionary theory is that you can’t run the experiment twice,” says Hugo Zeberg, a geneticist at the Max Planck Institute for Evolutionary Anthropology. “But with more information on how Neanderthals and Denisovans expanded into Europe and Asia, it’s almost like we can run the experiment three times and understand why modern humans were so different.”