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Natural Selection Removed Many Neanderthal Genes from Human Genome, Scientists Say

According to a team of researchers at the University of California, Davis, only a very small percentage of Neanderthal DNA is present in the genomes of modern humans because, after interbreeding, natural selection removed large numbers of ‘bad’ Neanderthal gene variants.

Reconstruction of a Neanderthal. Image credit: Neanderthal Museum.

Reconstruction of a Neanderthal. Image credit: Neanderthal Museum.

Neanderthals split from our African ancestors over 500,000 years ago, and lived in Europe and Central Asia until a few tens of thousands of years ago.

When anatomically modern Homo sapiens left Africa about 50,000 to 80,000 years ago and spread through Europe and Asia, they interbred with Neanderthals.

The first hybrid offspring would have been, on average, a 50/50 mix of modern human and Neanderthal genes, and could then have themselves bred with modern humans, Neanderthals or other hybrids.

Thanks to DNA samples retrieved from a number of fossils, we have enough data on the Neanderthal genome to identify their genes among ours.

Today, Neanderthal genes are only 1-4% of the genome of people of European ancestry, a little more common in people of East Asian descent, and almost absent in people of African ancestry.

“For a while now we have known that humans and Neanderthals hybridized. Many Europeans and Asians — along with other non-African populations — are the descendants of those hybrids,” said Dr. Ivan Juric, a researcher in the Department of Evolution and Ecology and the Center for Population Biology at the University of California, Davis, and lead author on the current study.

To understand how modern humans lost their Neanderthal genetic material and how humans and Neanderthals remained distinct, Dr. Juric and co-authors developed a novel method for estimating the average strength of natural selection against Neanderthal genetic material.

They found that natural selection removed many Neanderthal alleles from the genome that might have had mildly negative effects.

“Previous work has shown that, following hybridization, many Neanderthal gene variants were lost from the modern human population due to selection. We wanted to better understand the causes of this loss,” Dr. Juric said.

The team estimates that these gene variations were able to persist in Neanderthals because they 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.

“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 hybridization. Once in the larger human population, those deleterious variants were slowly purged by natural selection,” Dr. Juric said.

The work also confirms previous reports that East Asian people had somewhat higher initial levels of Neanderthal ancestry than Europeans.

“The key finding of our study 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,” Dr. Juric explained.

“The human population size has historically been much larger, and this is important since selection is more efficient at removing deleterious variants in large populations. Therefore, weakly deleterious variants that could persist in Neanderthals could not persist in humans.”

“We think that this simple explanation can account for the pattern of Neanderthal ancestry that we see today along the genome of modern humans.”

The findings were published online Nov. 8, 2016 in the journal PLoS Genetics.

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I. Juric et al. 2016. The Strength of Selection against Neanderthal Introgression. PLoS Genet 12 (11): e1006340; doi: 10.1371/journal.pgen.1006340

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