Arthritic and inbred (Image: John Reader/Science Photo Library)

TALK about an inauspicious beginning. For thousands of years our ancestors lived in small, isolated populations, leaving them severely inbred, according to a new genetic analysis. The inbreeding may have caused a host of health problems, and it is likely that small populations were a barrier to the development of complex technologies.

In recent years, geneticists have read the genomes of long-dead humans and extinct relatives like Neanderthals. David Reich of Harvard Medical School in Boston has now sequenced the Neanderthal genome and that of another extinct human, the Denisovan, to an unprecedented degree of accuracy. He presented his findings at a Royal Society meeting on ancient DNA in London on 18 November.

Describing the genomes as “nearly error-free”, Reich says both species were severely inbred due to small populations. “Archaic populations had low genetic diversity, really extraordinarily low,” he said. “It’s among the lowest diversity of any organism in the animal kingdom.”


One Neanderthal, whose DNA Reich obtained from a toe bone, had almost no diversity in about one-eighth of the genome: both copies of each gene were identical. That suggests the individual’s parents were half-siblings.

That’s in line with previous evidence of small populations, says Chris Stringer of the Natural History Museum in London. “In the distant past, human populations were probably only in the thousands or at best tens of thousands, and lived locally, exchanging mates only with their nearest neighbours.”

Our genomes still carry traces of these small populations. A 2010 study concluded that our ancestors 1.2 million years ago had a population of just 18,500 individuals, spread over a vast area (PNAS, doi.org/dv75x8).

Fossils suggest the inbreeding took its toll, says Erik Trinkaus of Washington University in St Louis, Missouri. Those he has studied have a range of deformities, many of which are rare in modern humans. He thinks such deformities were once much more common (PLoS ONE, doi.org/p6r).

Despite the impact on health, it is unclear whether inbreeding could have killed off the Neanderthals and Denisovans. More likely is the effect of small populations on culture and technology, says Mark Thomas of University College London. Larger populations retain more knowledge and find ways to improve technologies. This “cumulative culture” is unique to humans, but it could only emerge in reasonably large populations. In small populations, knowledge is easily lost, which explains why skills like bone-working show up and then vanish, says Trinkaus.

Tiny populations may have prevented Neanderthals and Denisovans from developing cumulative culture. “It would place some limits on their cultural complexity,” says Thomas. The same thing held our species back, until the population reached a critical density, unleashing the power of culture – at which point there was no stopping us.

“Tiny populations may have prevented Neanderthals from developing more advanced technologies”

The genomes also show that early human species interbred with other hominins (see “We’re all Homo, aren’t we?“). Many of us carry genes from Neanderthals, or from the mysterious Denisovans, who are known only from a single cave in Siberia.

We’re all Homo, aren’t we? Early hominins weren’t picky about their sexual partners. We already knew that our species, Homo sapiens, interbred with two other hominin species, the Neanderthals and Denisovans. Now it looks like the Denisovans did some interbreeding of their own. Some stretches of the Denisovan genome look much older than the rest, says David Reich of Harvard Medical School. The most likely explanation, he says, is that the Denisovans interbred with an unidentified species and picked up some of their DNA. The question is, who? It could be evidence of a new species of hominin, as yet unknown to science. Alternatively, it could be the first genetic record of one of the many known species. Johannes Krause of the University of Tübingen in Germany suspects it was the latter, since many hominin species identified from their fossils have never been genetically analysed. The most likely candidate is Homo heidelbergensis, says Chris Stringer of London’s Natural History Museum. This species lived between 600,000 and 250,000 years ago, and spread from Africa into Europe and western Asia. That means Denisovans, whose ancestors followed a similar path, could well have met them.

This article appeared in print under the headline “Inbreeding shaped human evolution”