Sizeable Neanderthal Genome Still Exists in Modern Humans

A substantial fraction of the Neanderthal genome has been found to persist in modern human populations. A new strategy for analyzing whole-genome sequencing data from 665 people from Europe and East Asia revealed that more than 20% of the Neanderthal genome survives in the DNA of this contemporary group.

The genetic data gathered are part of the 1000 Genomes Project (Bethesda, MD, USA). Significant amounts of population-level DNA sequences might be obtained from extinct groups even in the absence of fossilized remains, because these archaic sequences might have been inherited by other individuals from whom scientists can collect genomic data.

Earlier research suggests that someone of non-African descent may have inherited about 1%–3% of his/her genome from Neanderthal ancestors. These archaic DNA sequences can vary from one person to another and they were aggregated in the present study to determine the degree of the Neanderthal genome remaining in the study group as a whole. The findings are a beginning to identifying the location of specific pieces of Neanderthal DNA in modern humans and a beginning to creating a collection of Neanderthal lineages surviving in present-day human populations.

Scientists Drs. Benjamin Bernot and Joshua M. Akey, both population geneticists from the department of genome sciences, University of Washington (Seattle, USA), reported their findings January 29, 2014, in the journal Science Express. Dr. Vernot is a graduate student and Dr. Akey is an associate professor.

To verify the accuracy of their strategy, Dr. Vernot ran their analysis before comparing the suspected Neanderthal sequences they found in modern humans to the recently mapped Neanderthal genome obtained from DNA taken from bone. This genome came from the paleogenetics laboratory of Dr. Svante Paabo of the Max Planck Institute for Evolutionary Anthropology (Leipzig, Germany).

“We wanted to know how well our predictions matched the Neanderthal reference genome,” Dr. Akey said. “The analysis showed that, after more refinement of these methods, scientists might not need a reference genome from an archaic species to do this type of study.”

The new findings suggest that substantial amounts of population-level DNA sequences might be obtained from extinct groups even in the absence of fossilized remains, because these ancient sequences might have been inherited by other individuals from whom scientists can gather genomic data, according to Dr. Akey. Here, lies the potential to find and characterize earlier unknown archaic humans that bred with early humans.

“In the future, I think scientists will be able to identify DNA from other extinct hominin, just by analyzing modern human genomes,” Dr. Vernot stated. “From our end, this was an entirely computational project. I think it’s really interesting how careful application of the correct statistical and computational tools can uncover important aspects of health, biology, and human history. Of course, you need good data, too.”

Neanderthals became extinct about 30,000 years ago. The time they lived on Earth, and some of their geographic range, overlapped with humans who were anatomically similar. The two closely related groups mated and generating some fertile offspring, such that parts of Neanderthal DNA were passed along to the next generations. In a proposed model, this combination of DNA could have occurred both before and after the evolutionary divergence of non-African modern humans from a common ancestral population.

It did not necessarily take a lot of individual hybrid offspring to introduce Neanderthal genes into early human populations. Nevertheless, Dr. Akey noted that it is not known how many Neanderthal ancestors modern-day humans have had. However, past interactions between the groups, Dr. Akey noted, is possibly more complicated than earlier believed. “In addition, the analysis of surviving archaic lineages points to the possibility that there were fitness costs to the hybridization of Neanderthal and humans,” Dr. Akey said.

Dr. Vernot noted, “I think what was most surprising to me, is that we found evidence of selection. In 2013, I would have bet that a Neanderthal/human hybrid would have been as fit as a fully modern human. This was mostly because we haven't been separated from them that long, on an evolutionary scale.”

Nevertheless, the Neanderthals were also a probable source for at least a few genetic variations that were adaptive for their human descendants. Neanderthal DNA sequences were discovered in regions of the genome that have been associated with skin pigmentation regulation. The procurement of these variants by breeding with the Neanderthals may have been a fast way for humans to adapt to local conditions. “We found evidence that Neanderthal skin genes made Europeans and East Asians more evolutionarily fit,” Dr. Vernot said, “and that other Neanderthal genes were apparently incompatible with the rest of the modern human genome, and thus did not survive to present day human populations.”

The researchers discerned that specific chromosomes arms in humans are revealingly lacking in Neanderthal DNA sequences, perhaps due to disparities between the two species along specific portions of their genetic materials. They noticed, for instance, a strong depletion of Neanderthal DNA in a region of human genomes that contains a gene for a factor thought to play an important role in human speech and language.

According to the scientists, the “fossil-free” application of sequencing archaic genomes not only has potential in revealing aspects of the evolution of now-extinct ancient humans and their characteristic population genetics, it also might provide insights into how interbreeding influenced current patterns of human diversity. Moreover, these studies might also help researchers target in on genetic alterations not found in any other species, and determine if these changes helped bestow early people with uniquely human characteristics.

The goal of the 1000 Genomes Project is to find most genetic variants that have frequencies of at least 1% in the populations studied.

1000 Genomes Project
University of Washington
Max Planck Institute for Evolutionary Anthropology

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