Research suggests the severe inbreeding may have created many health problems and the small populations were likely a barrier to the development of complex culture and technologies, NewScientist.com reported Thursday.
David Reich of Harvard Medical School in Boston -- who has sequenced the genome of Neanderthals and that of another extinct human, the Denisovans -- said 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."
The DNA of one Neanderthal, 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, Reich said.
That's common in small populations, said 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 neighbors," Stringer said.
A previous study has suggested Earth's total human population 1.2 million years ago was just 18,500, spread over a wide area of the globe.