[Razib Khan] We're not the man we used to be. Over the last twenty years, genomics, ancient DNA and paleoanthropology have joined forces to completely overhaul our understanding of the origin of our species. The true diversity and complexity of human evolution over the last few hundred millennia surpasses even the most unhinged imaginings we might have hazarded just a short generation ago. But greater clarity has left us with a messier and less elegant narrative. Our species’ status, it turns out, is "complicated."In the year 2000, the orthodoxy was that humans spread across the world 60,000 years ago, and were descended exclusively from a small population in Africa. Neanderthals and various other human groups (and yes, we didn’t even deign to give them all names) were evolutionary "dead ends." Of interest mostly to scholars, they were dismissed as failed experiments in a world our ancestors won. Today, this tidy story of us no longer passes a basic fact check.
In 2010, genomes recovered from ancient remains of "archaic hominins" in Eurasia turned out to have genetic matches in many modern humans. It seems they weren’t quite as "archaic" as we thought. In addition, we had to get used to the new reality that a solid 2-3% of the ancestry of all humans outside Africa is Neanderthal. About 5% of the ancestry of Melanesian groups, like the Papuans of New Guinea, actually comes from a previously unimagined new human lineage discovered in Denisova cave, in Siberia of all places.
Since these first major overhauls, the genetic picture has only grown more complex. Trace, but detectable (0.2% or so), levels of "Denisovan" ancestry are found across South, Southeast, and East Asia (as well as among indigenous people of the Americas). Similarly, trace but detectable levels of Neanderthal ancestry actually appear in most African populations. And, though we have no ancient genomes to make the triumphant ID, a great deal of circumstantial DNA evidence indicates that many African groups harbor silent "archaic" lineages equivalent to Neanderthals and Denisovans. We call them "ghost" populations. We know they’re there in the genomes, but we have no fossils to identify them with.
Even the canonical "Out of Africa" migration itself has turned out to be less neat and tidy than we thought. Outside Africa, whether you are an indigenous Australian, Amazonian native or a German burgher, fully 90-99% of your ancestry derives from a single ancestral human population pulse 60,000 years ago. Somehow, an isolated African tribe of 1,000 to 10,000 people, who became genetically homogenous due to their initial small population size, swept across Eurasia. By 50,000 years ago, they reached Australia. They had replaced the last Neanderthals and Denisovans by 40,000 years ago, if not earlier. They even migrated to North and South America 15,000 years ago.
But inside of Africa, the story is much richer and still not fully grasped. Many African populations started separating from each other 200,000 years ago, becoming distinct lineages such as Khoisan and West Africans. The emergence of modern humans within the continent was not an explosion, but a gradual evolution of interacting lineages. A slow burn. The ancestors of modern non-Africans were part of this dance, but were isolated at some point for tens of thousands of years, passing through the "great bottleneck." Where? When? Who knows? We can’t be sure at this point. Best to just come out and admit it: this chapter of the story is still provisional.