DNA study finds less than 2 percent of the human genome is “human”

For all the progress Homo sapiens has made as a species over the hundreds of thousands of years of our existence, our genome tells a different story.

In this biological version of the story, humans have not come as far as we think from our more archaic ancestors — at least on the molecular level. In a new landmark paper published Friday in the journal Science Advances, researchers detail a telling discovery about our genes — finding that far less of our genome is actually wholly ours.

The discovery — In the new study, the researchers construct an evolutionary family tree for Homo sapiens, based on the sequenced genomes of modern humans, Neanderthals, and Denisovans. They make two discoveries from their close analysis of these data:

First, as little as 1.5 percent and as much as 7 percent of the modern human genome is unique to our species. In other words, at least 93 percent of the modern human genome is shared between our species and the two other ancient hominins.

Fernando Villanea, a population geneticist at the University of Colorado, Boulder, who was not involved in the study, tells Inverse that the findings are impressive in what they tell us about how the three species may have mixed.

“Their results support the most exciting new views on the interactions between humans, Neanderthals, and Denisovans,” Villanea says.

Second, in the last 600,000 years, our genetic adaptations largely were to do with brain development and function only — perhaps when we think of human uniqueness, this is what we should consider as primal, Nathan Schaefer, a bioinformatician at the University of California, San Francisco, and the paper’s lead author, tells Inverse.

“Maybe we’ve gotten a first glimpse at what to look at next for what might make humans special,” Schaefer says.

How they did it — Schaefer and his team used a genetic analysis technique called an ancestral recombination graph to make their discovery. Using publicly available data of modern human, Neanderthal, and Denisovan genomes, they then sequenced these genomes themselves and then used the ancestral recombination graph tool to sketch out a genetic tree encompassing the three species.

“If you sequence a bunch of people, you could make a tree that would show how everyone's related, on average, across the whole genome,” Schaefer explains.

Applied to the three species, it works in a similar way — mapping how they are related across the genome, finding shared regions and distinct ones.

“They can look at all human populations at once under the same scope,” Villanea says.

“We are very similar to Neanderthals.”

Why it matters — By recreating these evolutionary trees, researchers today can pinpoint critical moments when H. sapiens adapted and diverged from our ancestors and other hominin lineages.

But to understand how we relate to Neanderthals and Denisovans, it is important to look not only at genes — but also at what happens when those genes are translated into proteins.

“When you ask that question, we are very similar to Neanderthals,” Schaefer says.

“We have, you know, around 20,000 genes, and somewhere around 40 of them have these actual coding differences that all humans have one version, and the Neanderthals have the other version,” he says.

“That’s already like, ‘Wow, we’re really, really close to them.’”

As for the subsequent finding about cognitive adaptations, Schaefer says the genomes hint at the true difference between humans and other ancient peoples has to do with our brain development. The pressures that gave rise to these differences are likely incredibly ancient themselves.

“These adaptation events which define our species possibly happened around [600,000] and [200,000] years ago in Africa,” Villanea says.

What’s next — This tree offers a peek at the “adaptation events” in the last 600,000 that hold the key to our cognitive development — and more metaphysically perhaps, human uniqueness. The tree hints that what could make us genetically unique from Neanderthals and Denisovans could be all in our heads — that is to say, our brains.

“What I’m interested in doing now is trying to learn more about how genes work and what these genes do,” Schaefer says. For example, which mutations in the human genome are even functional, in that they have a measurable effect on our behavior.

The study offers a little more light too on Denisovans as a species. As the study details, much more information is known about how modern human DNA reflects our species’ past interactions with Neanderthals purely because more Neanderthal remains have been discovered and more of their genomes are available to science.

Currently, our knowledge of the Denisovan genome comes from a single pinkie bone found in a cave in Siberia, and Villanea says much of the work ahead will need to focus on understanding this elusive population of ancient hominin — and if there are more ancient peoples out there still to discover.

“Who knows,” he says. Only more time — and data — can tell.

Abstract: Many humans carry genes from Neanderthals, a legacy of past admixture. Existing methods detect this archaic hominin ancestry within human genomes using patterns of linkage disequilibrium or direct comparison to Neanderthal genomes. Each of these methods is limited in sensitivity and scalability. We describe a new ancestral recombination graph inference algorithm that scales to large genome-wide datasets and demonstrate its accuracy on real and simulated data. We then generate a genome-wide ancestral recombination graph including human and archaic hominin genomes. From this, we generate a map within human genomes of archaic ancestry and of genomic regions not shared with archaic hominins either by admixture or incomplete lineage sorting. We find that only 1.5 to 7% of the modern human genome is uniquely human. We also find evidence of multiple bursts of adaptive changes specific to modern humans within the past 600,000 years involving genes related to brain development and function.