An Early Homo Sapiens Left Africa, Mated With Neanderthals and Went Extinct

Discovery of human genes in Neanderthals dating back 100,000 years ago changes the timeline of interspecies human mixing.

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Denisova Cave in Siberia, Russia, where the findings the research relies upon were found.
Denisova Cave in Siberia, Russia, where the findings the research relies upon were found. Credit: Bence Viola

We now know that all non-Africans bear Neanderthal DNA, and some have Denisovan DNA too. We always assumed “they” mixed with “us.” Now a new genomic analysis of a Neanderthal finger-bone found in Siberia indicates that modern man shouldn’t throw stones at glass caves. That Neanderthal had human genes, but not ours – they were genes from a human dating back 100,000 years.

So, early men predating the great exit from Africa mated with early Neanderthals – “we” mixed with “them” too. Hybrids that had been half-human and half-Neanderthal had to have existed, says Dr. Ilan Gronau of the Interdisciplinary Center, Herzliya, expert on computational genetics.

Evidently, the timeline of modern man’s migrations needs rewriting again. All of today’s non-African humans are believed to have originated with a group of Homo sapiens that left Africa some 65,000 years ago. The new discovery suggests that a group of Homo sapiens split off, left Africa earlier, mated with Neanderthals at least 100,000 years ago and then went extinct.

The Neanderthal finger-bone that led to these startling conclusions was found in the Denisovan cave in Siberia, where remains of the hominin species called “Denisovans” was first discovered in 1997. The finds are described in “Genomics: Close encounters of the first kind” on the website. (The Denisovans did leave genetic marks on modern humans, but had no modern human genes – they mixed with us, not we with them; they also had traces of Neanderthal DNA. )

Love in the Levant

Homo neanderthalensis were generally bigger and brawnier than Homo sapiens, and had bigger brains per poundage, though they weren’t thought to be “smarter,” but to have bigger brain areas devoted to vision and body control. Neanderthal and man are believed to have diverged from a common ancestor, maybe Homo heidelbergensis, between 350,000 and 400,000 years ago.

The humans and Neanderthals are thought to have had their interspecies tryst in the Levant tens of thousands of years before our modern ancestors left Africa for Europe and Asia.

The Levant region, and Israel in particular, are rich in signs of prehistoric hominins and human-Neanderthal coexistence. They shared cave space. But genetics aside, finding smoking guns attesting to actual interspecies sex is harder, though humans and Neanderthals coexisted until the latter’s final extinction some 30,000 years ago. (The Levant is evidently as far south as the cold-adapted Neanderthals went – they are not believed to have reached Africa.)

One of very few hybrid remains to have been identified was a jawbone found in March 2013 in northern Italy from 30,000-40,000 years ago. That individual had Neanderthal mitochondria (which come from the mother alone) but human attributes, leading the scientists to conclude that its mother was a Neanderthal who paired with a male Homo sapiens. The discovery a couple of years later, of a human cranium dating to about 55,000 years ago in Manot Cave in Israel, was hailed as “the earliest evidence of anatomically modern humans outside Africa.” That discovery lends credence to the theory that the species of men met and mated here.

Multiple gene flows

Reconstruction of Neanderthals at the Neanderthal Museum in Mettmann, Germany.Credit: Wikimedia Commons

The Neanderthal genome was first partially sequenced in 2010. Four years later, in 2014, a Neanderthal woman from the Altai Mountains was sequenced, leading to the unhappy discovery that her parents had evidently been half-siblings, and that her clan had been prone to incest (“mating among close relatives”), which spurred a host of new theories about Neanderthal extinction.

Muddying the picture a little more, based on archaic and present-day genomes, the researchers concluded that multiple gene flow events occurred among Neanderthals, Denisovans and early modern humans (even possibly including gene flow into Denisovans from an unknown archaic group of hominins). “Thus, interbreeding, albeit of low magnitude, occurred among many hominin groups in the Late Pleistocene,” they conclude.

And so we wound up with Neanderthal DNA – and they wound up with ours, it has now been shown.

What that Neanderthal DNA did to us is still being elucidated. Different modern humans, it turns out, have different Neanderthal genes – we don’t all have the same set. Recent studies have linked our Neanderthal heritage to various maladaptations, including depression and even obesity and heart disease.

Studying the effects of Neanderthal genes on our state of being began with identifying that non-African humans have about 135,000 Neanderthal genetic variations. Then the scientists analyzed the genetic data and health records of more than 28,000 adults of European ancestry – to find correlations between possessing Neanderthal genes and illness.

Such correlations, dear reader, were found, including to urinary tract problems, heart disease, our mental state and even arthritis. Did the Neanderthal genes do us no good? Probably, back when, maybe, especially when life spans were short. Take genes that expedite blood clotting: That’s great if you’re a young Neanderthal chasing gazelles and fighting off Syrian brown bears, but it’s less useful if you’re an aging Westerner with a bad temper and propensity to stroke.