Our explosive past: on cataclysms and demographics
The continuing quest to pinpoint what propelled modern humans to every corner of the earth
74,000 years ago, a volcano erupted at western Indonesia’s Lake Toba, leaving half a foot of ashfall as far west as India. The most powerful explosion of the last 2.5 million years, the Toba eruption triggered a decade-long cold snap that wrought havoc even amid the last Ice Age’s already inclement conditions. When the cataclysm hit, Neanderthals had reigned supreme from the Atlantic to the Siberian Altai for hundreds of thousands of years, while their Denisovan cousins dominated East Asia. To the south, diminutive small-brained human populations occupied Indonesia’s Flores islands and Luzon in the Philippines, coexisting with both modern humans and Denisovans. But thirty thousand years after Toba, a blink of the eye in geological time, the landscape of human geography was abruptly transformed. Neanderthals, Denisovans and Southeast Asia’s enigmatic hominins were extinct or under extreme, terminal pressure from African newcomers. Neanderthals, by then resident in Europe for over 500,000 years, disappeared 5,000 years after that mass arrival of African humans to northwest Eurasia. Denisovans, by then as far into their East Asian sojourn as Neanderthals their western one, disappeared soon after their cousins. Finally, the small human populations of Flores and the Philippines also died out 50,000 years ago, after modern humans’ final expansion. This radical homogenization of Eurasian humanity is associated with the expansion of the Initial Upper Paleolithic (IUP) archaeological culture, which radiated out of the Middle East 50,000 years ago, washing over the whole of Asia, Europe and Australia by 45,000 years ago.
In 2004, when Stanford paleoanthropologist Richard Klein wrote The Dawn of Human Culture, the IUP conquest of the world was considered conterminous with the rise of humans qua humans. Today we know this is wrong. Modern humans, from the ancestors of southern Africa’s San Bushmen to those of the indigenous Aboriginal people of Australia, began to diversify into distinct lineages more than 100,000 years ago, when Neanderthals and Denisovans were flourishing across Eurasia's whole breadth. Additionally, the bearers of the IUP toolkit were not even the first modern African-derived humans in Eurasia; archaeological finds in Laos place modern populations with our delicately built, gracile stature in Southeast Asia 85,000 years ago, 10,000 years before Toba. But ancient and modern genomic data exclude the possibility that today’s Southeast Asians descend from these African-related Asians that flourished before Toba. Instead, all modern Europeans, Asians, Australians and New World peoples, indeed 85% of humans alive today, descend from the tribes that diversified 40-45,000 years ago, correlating precisely with the spread of the IUP, and its immediate successor culture in western Eurasia, the Aurignacians. Additional genetic data now indicate that these IUP populations did not exit Africa 50,000 years ago in a single sweep, setting right to worldwide conquest. Instead, the ancestors of all non-Africans existed as a coherent and isolated breeding group for tens of thousands of years before their clear demographic explosion, one enduring legacy of which is the striking biological homogeneity unmistakable in the genes of all non-Africans.
Today the synthesis of archaeology, genomics and ancient DNA converges upon the outlines of a complex narrative much more nuanced and intricate than the clear, stark story of world conquest Klein’s book outlined. Yes, all non-Africans descend from a people that embarked upon settling the world outside the mother continent 50,000 years ago. Still, it is also clear that within Africa, more than 100,000 years ago, our species had already begun to diversify into the branches recognizable today. The out-of-Africa event was more capstone than prologue to the human story. Earlier waves of modern-looking African humans had even expanded out of the continent long before the IUP expansion. They left their tools and remains across Eurasia more than 100,000 years ago, as well as their genes in prehistoric Siberian Neanderthals. Finally, even the expansion of IUP-equipped humans out of Africa was not a singular event marking a transition out of the ancestral continent in a single step; even the modern human explosion of 50,000 years ago was a series of expansions. The out-of-Africa event was the culminating ignition of a long evolutionary fuse. It began with a single tribe whose origins go back tens of thousands of years earlier, to the time of the Toba event, when the ancestors of modern non-Africans were a small, isolated population on the ancestral continent’s edge.
Neandersovans and Neanderhumans
A genetic narrative illuminating the recent origin of modern humans outside of Africa begins with an essential piece of cellular machinery, the mitochondrion. This organelle is the workhorse of the cell, generating energy that powers our body’s external mechanics and internal physiology. The average cell is packed with thousands of mitochondria, and every single one has its own DNA, the legacy of a past, hundreds of millions of years ago when they were independent, free-living bacteria. These bacteria were absorbed into larger microorganisms, who eventually became the cellular constituents of eukaryotes. For the purposes of phylogenetics, it is critical to observe that mitochondria in every cell are only inherited from the eggs, rather than the sperm, meaning that every human obtains these cell-scale power plants exclusively from their mother. Because each cell harbors so much mtDNA. it was already easy to extract, amplify and analyze the mitochondrial genetic code with crude 20th-century methods. This resulted in much of our first understanding of human evolutionary phylogenetics being mediated through the direct maternal lineage, an unbroken line from mother to daughter coalescing back to a common ancestress, “mitochondrial Eve.” This project, in the spotlight throughout the 1980’s and 1990’s, established that mtDNA Eve lived 200,000 years ago in Africa. All non-Africans could be nested within the family trees of various African populations, all of whom were much more genetically diverse than non-Africans. Human mtDNA can be sorted into seven major lineages, macro-haplogroups, all of which are labeled with the letter L and a number. Of these, one: L3, has seven descendants, only two of which, haplogroups M and N, are found outside of Africa. So it is M and N alone that define the maternal lineages for the 85% of humans whose heritage derives back to the out-of-Africa event.
When the first Neanderthal mtDNA was analyzed in 1998 it proved very different from all modern lineages. The best estimates of the time of divergence placed the split between Neanderthal mtDNA and that of modern humans 300-400,000 years ago, well before Mitochondrial Eve. And it’s not just the direct maternal lineage. Just as we have mtDNA Eve, a last common mitochondrial ancestor, so we have Y-chromosomal Adam, the last paternal ancestor of all men, whose lineage has been passed uninterrupted from father to son. Y-chromosomal DNA from ancient Neanderthal remains also shows the same pattern as mtDNA, where Neanderthal branches diverged 300-400,000 years ago, 100,000 years before the last common modern human male Y (like mtDNA haplogroups, for the Y chromosome, non-African lineages are all nested within African ones, reflecting the same broad history for men and women). So far so good. These results bolstered the contention at the time of paleoanthropologists like Chis Stringer, drawing on fossil evidence, that Neanderthals were indeed a separate species that did not contribute to the genes of modern populations in Europe,
But the ancient DNA revolution did not end with Neanderthals; in 2010 a new mtDNA lineage was discovered in Siberia that diverged from that of modern humans and Neanderthals almost a million years ago. Initially dubbed “X-woman,” this individual was immediately touted as representative of a newly discovered human lineage. That was correct. She was a member of the population we now call Denisovan. Like the mtDNA, the Denisovan Y chromosome differs from those of modern humans and Neanderthals, having diverged 700,000 years ago. But here fissures in our tidy narrative start emerging. The vast majority of the tracts of DNA sequence within Denisovan and Neanderthal genomes indicate that they were much genetically closer to each other overall than they were to the African ancestors of modern humans. Denisovans and Neanderthals shared a lineage that separated from modern humans more than 600,000 years ago, which then itself bifurcated into their two distinct lineages 500,000 years ago. We now call the ancestral population to these two lineages, before they went their separate ways to western and eastern Eurasia, “Neandersovans.” Putting the genomics and fossil evidence together, we conclude that Neanderthals and Denisovans were the outcome of a separate, extremely ancient and forgotten out-of-Africa migration.
We have a contradiction then according to which method we favor; the implication of the male and female lineages contradicts what looking purely at the genomes in a one-to-one comparison across billions of bases might suggest. A human family tree based on Y chromosomes and mtDNA places Neanderthals and modern humans together on a single branch, whereas one derived from the whole genome places Neanderthals and Denisovans together. The answer to this conundrum is that by chance, ancestral Neanderthal Y and mtDNA lineages specifically were replaced wholesale more than 100,000 years ago by those more closely related to modern humans. Older Neanderthal lineages extracted from ancient DNA are genetically closer to Denisovan Y and mtDNA, reflecting a divergence 600,000 years ago, in line with expectations from the whole genome.
This reinforces the reality that instead of charting separations and isolations that lend themselves to diagrams of sharply branching phylogenetic trees, various human lineages were interacting and interbreeding, long before the explosion of the IUP people 50,000 years ago. Though the admixture of Neanderthals and Denisovans into modern human lineages about 55,000 and 45,000 years ago respectively is well attested, it is also clear that Siberian Neanderthals absorbed ancestry from populations of ancient moderns more than 100,000 years ago. Even more improbably, in Siberia researchers have found the remains of a child dating to 90,000 years ago whose father was Denisovan and whose mother was Neanderthal, an evolutionary “dead-end” that illustrates the human propensity to mate across the genetic and evolutionary chasm.
Our naive late-20th-century idea held that a single modern tribe burst out of East Africa 50,000 years ago, replacing Neanderthals and other human lineages inexorably and in totality. In reality, almost all modern humans have some Neanderthal ancestry, while Denisovans contribute nearly 4% of the genome of Papuans and other Melanesians. But it remains true that the entire world’s genetic legacy outside Africa today does come from a single intrepid tribe, a lone population with a unified early history. But these were not the first Africans to venture out of their ancient homeland; they were the last.