The other man: Neanderthal findings test our power of imagination
Counting down 2024’s three biggest ancient DNA findings: number 2
The ancient-DNA era for the human species is not yet 15 years old. It kicked off with the 2010 paper Paleo-Eskimo genome (followed by blockbusters on Neanderthals and Denisovans). Today, remains from tens of thousands of ancient humans offer us decipherable DNA information, each contributing to fill in gaps in our understanding of prehistory.
No matter the brilliance and insight of its practitioners and theorists, human prehistory’s age of genetic inference, when we were limited to examining modern genomes to learn about ancient peoples, was like trying to comprehend the world’s oceans solely from the activity observable in its brightly lit uppermost layers, the photic zone that reaches down at most about 200 meters. Though some key insights date to the before times, the paleogenomic era since 2010 has been absolutely revolutionary and transformative. Name a superlative, and it probably isn’t strong enough.
This year, year 14 of our ancient-DNA golden age if you’re keeping count, was no exception to the relentless pace of revolution and transformative progress in the field. And yet, from my vantage, three topics charted particularly spectacular gains this year. As 2024 gives way to 2025, I have three short pieces for you sharing my picks for this year’s most exciting leaps forward in ancient DNA.
In third place, my pick was a September 2024 preprint I’m confident will prove a landmark in the field. The culmination of years of work, it takes ancient DNA far beyond phylogeny, throwing open the gates to vast new landscapes of evolutionary dynamics. Humans are an expansive species that has spread across the planet, adapting to every locale, and this paper now turns our long history into one of evolution’s premier laboratories.
Today, in second place, a blockbuster paper published in Cell’s September 2024 issue, sheds important new light on our Neanderthal cousins: they were diverse, just like us. For hundreds of thousands of years, Neanderthals occupied both all of Europe and parts east, so it stands to reason that they would be at least as diverse as our species. But this new ancient DNA finding demonstrates that in some ways Neanderthal social behavior also looks startlingly foreign to our sociable clan; the remains found demonstrate that they maintained genetic and cultural separation for tens of thousands of years from even their nearest Neanderthal neighbors.
The Other Man: Neanderthal findings test our power of imagination
When I was growing up, the figure of the hulking Neanderthal was a major fixture within paleoanthropology and popular culture. William Golding’s 1955 novel The Inheritors featured them, Jean Auel’s 1980’s Clan of the Cave Bear books were bestsellers and became a movie starring Darryl Hannah, and Neanderthal-like humans again starred in 1981’s Quest for Fire. We flung around the term “Neanderthal” to paint someone as uncouth, primitive, maybe even bestial. They may not have been apes, but the Neanderthals of our imagining were most certainly not Homo sapiens. They were a failed experiment, long since consigned to the dustbins of prehistory (albeit creatively revived in the 2007 TV show Cavemen, spinoff from a hit GEICO insurance commercial).
When in 2010, a first Neanderthal genome was decoded, overnight, we had to scoot over a little to let them into the human family portrait. The first whole genome of a Neanderthal, analyzed by Svante Paabo’s team in 2010, made clear that modern human and Neanderthal lineages had mixed. The team found that all contemporary humans outside of Africa harbored easily detectable Neanderthal ancestry (1.5-2.25%), while today we know that all Africans save for a few isolated tribes also carry some Neanderthal ancestry contributed by forebears who later back-migrated into the continent from Eurasia. In light of our species’ ubiquitous Neanderthal heritage, our cousins were hurriedly humanized in popular conception. Artistic renderings were spruced up, our burly relatives given red hair (a characteristic supported by some early genetic analysis) and reimagined with an upgraded dash of sensitivity.
And yet from a genomic perspective ,so much remained and yet remains unknown. We still have only a handful of Neanderthal whole genomes, with varying levels of data quality (just three so far are “high quality,” the standard we require for our own medical testing purposes). Imagine trying to understand our own lineage’s twists and turns over millennia from just a dozen random humans arbitrarily scattered across a couple continents and a few hundred thousand years of prehistory. For some 500,000 years, Neanderthals and their ancestors occupied Europe, Central Asia, western Siberia and parts of West Asia. By any measure, their tenure was incredibly successful. Robust, with massive craniums, they specialized in harsh northern climes, but they also survived five warmer interglacials. The last, the Eemian from 130,000-115,000 years ago, averaged 2 degrees celsius warmer than the planet as we know it today. Forests reached northern Norway, and elephants, rhinoceros and hippopotamus all flourished in Britain. And yet the cold-specialized Neanderthals came out of it still the dominant human lineage across the Northern Hemisphere. And when a colder climate returned after 115,000 years ago, they even pushed southward into modern Israel. Neanderthal fossils have been found in the Palestinian West Bank dating to as late as 60,000 years ago.
But this was a last hurrah. A switch flipped 50,000 years ago, when modern humans pushed deep into Neanderthal territory. The last Neanderthal sites date to 40,000 years ago, whereupon they suddenly disappear all across their range, replaced by newcomers who were our ancestors. Of course, some Neanderthal populations were absorbed into our forebears’ expanding Upper Paleolithic societies. The genomic imprint of Neanderthal ancestry in modern populations dates to some time between 45,000 and 50,000 years ago, likely in West Asia. Genetically, Neanderthals are still with us. You can reconstruct some 30% of the Neanderthal genome from bits and pieces floating in modern human genomes. But a human population is more than genes, and 500,000 years of unique history, culture and tradition disappeared with Homo sapiens’ rise.
When our understanding rests upon such a paucity of data, any new scrap of information can be transformative. This is why a 2024 paper in Cell, Long genetic and social isolation in Neanderthals before their extinction, marks such a profound contribution. The team, led by Ludovic Slimak, uncovered an extremely well preserved Neanderthal individual (the remains include many miraculously complete entire bones) who died about 50,000 years ago in southeast France’s Grotte Mandrin cave high on a bank above the Rhone river. They nicknamed the individual “Thorin,” after Tolkein’s dwarf king who led his band on a quixotic adventure to reclaim his ancestral mountain home from the dragon Smaug in The Hobbit. The Grotte Mandrin site is already special because before Thorin’s folk occupied it, it seems to have already played home to bands of modern humans between 57,000 and 52,000 years ago. This earlier population would have pre-dated humans’ Initial Upper Paleolithic expansion that began 50,000 years ago, thus representing a wave of human migration heretofore unknown and unexpected.
Slimak and his collaborators obtained whole-genome data from one of Thorin’s molars, and from it could conclude that despite those background details of his apparent residence, he did not have elevated modern human ancestry compared to other contemporary or earlier Neanderthal samples. The last Neanderthals at Grotte Mandrin, (last because Thorin’s people were likely the last of the Neanderthals to occupy the site before their lineage’s extinction), entirely replaced the modern humans who had occupied the site for the five millennia before them. This apparent aversion to social interaction is not shocking in light of what they discovered next: Thorin was an exemplar of a lineage of Neanderthals who had remained genetically entirely distinct from the broader Neanderthal lineage to the north and east for 50,000 years (even though their nearest neighbor population was a week’s walk away).
Humanity’s history truly offers no informative analogy here; it would be like modern Italians not only entirely sidestepping Europe’s millennia of waves of new genetic inputs from Gravettian foragers, Anatolian farmers, Yamnaya pastoralists and more, but also remaining completely hermetically sealed off from their neighbors in France since arriving in Europe more than 40,000 years ago. Thorin’s curious (and frankly inbred: their effective breeding population narrowed to as few as 100 individuals, textbook bottleneck-scale) kind lived out a tenure of isolation on a scale we can barely comprehend. All while Neanderthal neighbors as nearby as today’s Croatia were actually mixing and migrating at distance on the scale of the whole supercontinent; Mongolian and Croatian samples are more closely related (and their sites share material culture signatures)... than the Croatians were to Thorin’s band.
And it’s not as if Neanderthals weren’t human enough to have mixed with our own forebears. Thorin’s lineage and other Neanderthals in Western Europe reflect influence by the cultural traditions the new humans bore into their midst from the east 45,000 years ago. But they were also profoundly different. Neanderthals’ ancestors had gone their own way from African humans’ ancestors more than 500,000 years ago. Though Neanderthals produced viable offspring with African humans expanding into their territories, our existence provides strong genomic evidence that they were different enough that the mixing came with serious costs. Our Neanderthal heritage concentrates tellingly in areas of the genome that are not functional (where selection doesn’t operate). This underscores that Neanderthal and modern human biology had genuinely parted ways, and reuniting the two lines exposed myriad incompatibilities.
Obviously anthropologists cannot go live in a Neanderthal band and observe all their differences from other human cultures, so genes and material remains grant our best window onto their distinctiveness. Like most modern human populations, Neanderthals seem to have been patrilineal; females moved between bands. But the handful of samples we have indicate they were genetically very homogeneous, probably living in smaller bands that did not interact as consistently as our ancestors’ did. Neanderthals had a very wide geographic distribution, from Gibraltar to Israel to Mongolia, but all the genomes found prior to Thorin had suggested very little population structure. Siberian Neanderthal remains sequenced from the Denisovan site in the Altai dating to 120,000 and 55,000 years ago revealed populations with no relationship to each other; the earlier Altai Neanderthals left no descendents. Instead, the Neanderthals in the Altai by the later date closely resembled their contemporary populations far to the west in Eastern Europe. This tells us Neanderthal populations suffered population crashes that drove extinct whole lineages, before a few local survivor groups would expand into those abandoned domains.
Thorin is unique, because his lineage’s genetic distinctness, an isolate lodged within Western Europe’s fertile heartland, the Rhone valley of France, shows that replacement was not necessarily total, and we simply needed more samples. After the expansion of ice sheets 115,000 years ago, Thorin’s ancestors split from the main lineage of Neanderthals that prior data suggests dominated from Europe to Mongolia, and proceeded to seal themselves off genetically and culturally for 50,000 years. This finding genuinely astounds because such behavior in a species remotely resembling our compulsively sociable, gregarious Homo sapiens lineage is basically unthinkable. Neanderthals must have had another way of being human.
Slimak, an archaeologist who has studied Neanderthal material culture for decades, and authored The Naked Neanderthal: A New Understanding of the Human Creature, believes that we’ve taken understanding our cousins in terms of ourselves too far. Neanderthals were profoundly different, Slimak concludes, an assessment he arrives at, from among myriad other lines of inquiry, comparing the cunning originality and uniqueness of their tools versus the more mass-produced character of those our ancestors fashioned. Neanderthals famously had brains on average larger than we do, but if Slimak is right that they surely thought and behaved radically differently from our modern human ancestors, that considerable brainpower was deployed to wholly different ends.
Because DNA degradation is a function of age, we will always obtain less DNA from the time period of Neanderthals, more than 40,000 years ago, than we can hope to from the last 10,000 years. Additionally, our lineage was always much more numerous than Neanderthals, so we can always expect to find many more of our own ancient whole genomes than our cousins’. But at some point soon we can expect to graduate from ~20 whole-genome caliber ancient samples to ~200. At that scale, we can hope to begin grasping Neanderthals not only in their unitary essence, but also in their diversity, because we will obtain enough chronological and geographical variation to actually hypothesize about their demographic history with some real granularity. Thorin’s existence argues for both similarities and differences between sapiens and neanderthalensis; like our own lineage, Neanderthals did exhibit population structure, and it seems likely that the Neanderthal population structure was far greater than can be found across branches of Homo sapiens. We will never know the exact details of how Neanderthals and our ancestors interacted, but we can now see in ever more detail that they were at once both aliens and our own flesh and blood.
Great summation. Thank you
Thank you for this and happy new year