It is well known that modern humans interbred with Neanderthals, but we have surprisingly little of our predecessors’ DNA.

A new study suggests that once Neanderthal genetic material merged with the DNA of modern humans, natural selective mechanisms acted to weed it out.

Humans and Neanderthals interbred tens of thousands of years ago, but today, Neanderthal DNA makes up only 1 to 4 per cent of the genomes of modern non-African people. 

Using a novel method for estimating the average strength of natural selection against Neanderthal genetic material, researchers from the University of California have found that natural mechanisms removed many Neanderthal alleles from the genome that might have had mildly negative effects. 

The scientists estimate that these gene variations were able to persist in Neanderthals because Neanderthals had a much smaller population size than humans.  

Once transferred into the human genome, however, these alleles became subject to natural selection, which was more effective in the larger human populations and has removed these gene variants over time.

The study is one of the first attempts to quantify the strength of natural selection against Neanderthal genes, and sheds new light on the role of population size on losing or maintaining Neanderthal ancestry in humans.

“For a while now we have known that humans and Neanderthals hybridised,” said researcher Ivan Juric.

“Many Europeans and Asians - along with other non-African populations - are the descendants of those hybrids.

“Previous work has also shown that, following hybridisation, many Neanderthal gene variants were lost from the modern human population due to selection.

“Our results are compatible with a scenario where the Neanderthal genome accumulated many weakly deleterious variants, because selection was not effective in the small Neanderthal populations. Those variants entered the human population after hybridisation. Once in the larger human population, those deleterious variants were slowly purged by natural selection.

“The key finding of our study therefore is that the current levels of Neanderthal ancestry in modern humans are in part due to long-term differences in human and Neanderthal population sizes.

“From our study, we cannot conclude that differences in demography explain everything.

“Still, I find it fascinating to think that if the Neanderthals had reached larger population sizes in Europe, or if modern human populations had grown slower, some of us today would probably carry a lot more Neanderthal ancestry in our genome.”

The full study is accessible here.