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How Neanderthals Gave Us Secret Powers

Interbreeding with our fellow hominins appears to have helped humans
survive harsh climates.

Native Tibetans make use of a gene derived from Denisovans to stay healthy at high altitudes.
Nicols Marino / Quanta
EMILY SINGER TEXT SIZE
MAY 31, 2016 | SCIENCE

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Early human history was a promiscuous affair. As modern humans began

to spread out of Africa roughly 50,000 years ago, they encountered other

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species that looked remarkably like themthe Neanderthals and

Denisovans, two groups of archaic humans that shared an ancestor with us
roughly 600,000 years earlier. This motley mix of humans coexisted in
Europe for at least 2,500 years, and we now know that they interbred,
leaving a lasting legacy in our DNA. The DNA of non-Africans is made up
of roughly 1 to 2 percent Neanderthal DNA, and some Asian and Oceanic
island populations have as much as 6 percent Denisovan DNA.

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Over the last few years, scientists have dug deeper into the Neanderthal
and Denisovan sections of our genomes and come to a surprising
conclusion. Certain Neanderthal and Denisovan genes seem to have
swept through the modern human populationone variant, for example,
is present in 70 percent of Europeanssuggesting that these genes
brought great advantage to their bearers and spread rapidly.

In some spots of our genome, we are more Neanderthal than human,

said Joshua Akey, a geneticist at the University of Washington. It seems
pretty clear that at least some of the sequences we inherited from archaic
hominins were adaptive, that they helped us survive and reproduce.

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But what, exactly, do these fragments of Neanderthal and Denisovan

DNA do? What survival advantage did they confer on our ancestors?
Scientists are starting to pick up hints. Some of these genes are tied to our
immune system, to our skin and hair, and perhaps to our metabolism and
tolerance for cold weather, all of which might have helped emigrating
humans survive in new lands.

What allowed us to survive came from other species, said Rasmus

Nielsen, an evolutionary biologist at the University of California,
Berkeley. Its not just noise, its a very important substantial part of who
we are.

Illustration by Lucy Reading-Ikkanda for Quanta Magazine, based on a map by Sriram Sankararaman.

***

The Tibetan plateau is a vast stretch of high-altitude real estate isolated by

massive mountain ranges. The scant oxygen at 14,000 feetroughly 40
percent lower than the concentrations at sea levelmakes it a harsh
environment. People who move there suffer higher rates of miscarriage,
blood clots, and stroke on account of the extra red blood cells their bodies
produce to feed oxygen-starved tissue. Native Tibetans, however, manage
just fine. Despite the meager air, they dont make as many red blood cells

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as the rest of us would at those altitudes, which helps to protect their

health.

In 2010, scientists discovered that Tibetans owe their tolerance of low

oxygen levels in part to an unusual variant in a gene known as EPAS1.
About 90 percent of the Tibetan population and a smattering of Han
Chinese (who share a recent ancestor with Tibetans) carry the high-
altitude variant. But its completely absent from a database of 1,000
human genomes from other populations.

The unique gene then flourished in those who lived

at high altitudes and faded away in descendants
who colonized less harsh environments.

In 2014, Nielsen and colleagues found that Tibetans or their ancestors

likely acquired the unusual DNA sequence from Denisovans, a group of
early humans first described in 2010 that are more closely related to
Neanderthals than to us. The unique gene then flourished in those who
lived at high altitudes and faded away in descendants who colonized less
harsh environments. Thats one of the most clear-cut examples of how
[interbreeding] can lead to adaptation, said Sriram Sankararaman, a
geneticist and computer scientist at the University of California, Los
Angeles.

The idea that closely related species can benefit from interbreeding,
known in evolutionary terms as adaptive introgression, is not a new one.
As a species expands into a new territory, it grapples with a whole new set
of challengesdifferent climate, food, predators, and pathogens. Species
can adapt through traditional natural selection, in which spontaneous
mutations that happen to be helpful gradually spread through the

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population. But such mutations strike rarely, making it a very slow

process. A more expedient option is to mate with species that have already
adapted to the region and co-opt some of their helpful DNA. (Species are
traditionally defined by their inability to mate with one another, but
closely related species often interbreed.)

This phenomenon has been well documented in a number of species,

including mice that adopted other species tolerance to pesticides and
butterflies that appropriated other species wing patterning. But it was
difficult to study adaptive introgression in humans until the first
Neanderthal genome was sequenced in 2010, providing scientists with
hominin DNA to compare to our own.

Neanderthals and Denisovans would have been a good source of helpful

DNA for our ancestors. They had lived in Europe and Asia for hundreds of
thousands of yearsenough time to adjust to the cold climate, weak sun
and local microbes. What better way to quickly adapt than to pick up a
gene variant from a population that had probably already been there for
300,000 years? Akey said. Indeed, the Neanderthal and Denisovan
genes with the greatest signs of selection in the modern human genome
largely have to do with how humans interact with the environment, he
said.

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Illustration by Lucy Reading-Ikkanda for Quanta Magazine, based on a map by Sriram Sankararaman.

To find these adaptive segments, scientists search the genomes of

contemporary humans for regions of archaic DNA that are either more
common or longer than expected. Over time, useless pieces of
Neanderthal DNAthose that dont help the carrierare likely to be lost.
And long sections of archaic DNA are likely to be split into smaller
segments unless there is selective pressure to keep them intact.

In 2014, two groups, one led by Akey and the other by David Reich, a
geneticist at Harvard Medical School, independently published genetic
maps that charted where in our genomes Neanderthal DNA is most likely
to be found. To Akeys surprise, both maps found that the most common
adaptive Neanderthal-derived genes are those linked to skin and hair
growth. One of the most striking examples is a gene called BNC2, which is
linked to skin pigmentation and freckling in Europeans. Nearly 70 percent
of Europeans carry the Neanderthal version.

Scientists surmise that BNC2 and other skin genes helped modern humans
adapt to northern climates, but its not clear exactly how. Skin can have

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many functions, any one of which might have been helpful. Maybe skin
pigmentation, or wound healing, or pathogen defense, or how much water
loss you have in an environment, making you more or less susceptible to
dehydration, Akey said. So many potential things could be driving
thiswe dont know what differences were most important.

***

One of the deadliest foes that modern humans had to fight as they
ventured into new territories was also the smallestnovel infectious
diseases for which they had no immunity. Pathogens are one of the
strongest selective forces out there, said Janet Kelso, a bioinformatician
at the Max Planck Institute for Evolutionary Anthropology in Leipzig,
Germany.

Earlier this year, Kelso and collaborators identified a large stretch of

Neanderthal DNA143,000 DNA base-pairs longthat may have played
a key role in helping modern humans fight off disease. The region spans
three different genes that are part of the innate immune system, a
molecular surveillance system that forms the first line of defense against
pathogens. These genes produce proteins called toll-like receptors, which
help immune cells detect foreign invaders and trigger the immune system
to attack.

Modern humans can have several different versions of this stretch of

DNA. But at least three of the variants appear to have come from archaic
humanstwo from Neanderthals and one from Denisovans. To figure out
what those variants do, Kelsos team scoured public databases housing
reams of genomic and health data. They found that people carrying one of
the Neanderthal variants are less likely to be infected with H. pylori, a

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microbe that causes ulcers, but more likely to suffer from common
allergies such as hay fever.

Kelso speculates that this variant might have boosted early humans
resistance to different kinds of bacteria. That would have helped modern
humans as they colonized new territories. Yet this added resistance came
at a price. The trade-off for that was a more sensitive immune system
that was more sensitive to nonpathogenic allergens, said Kelso. But she
was careful to point out that this is just a theory. At this point, we can
hypothesize a lot, but we dont know exactly how this is working.

Most of the Neanderthal and Denisovan genes found in the modern

genome are more mysterious. Scientists have only a vague idea of what
these genes do, let alone how the Neanderthal or Denisovan version might
have helped our ancestors. Its important to understand the biology of
these genes better, to understand what selective pressures were driving
the changes we see in present-day populations, Akey said.

A number of studies like Kelsos are now under way, trying to link
Neanderthal and Denisovan variants frequently found in contemporary
humans with specific traits, such as body-fat distribution, metabolism or
other factors. One study of roughly 28,000 people of European descent,
published in Science in February, matched archaic gene variants with data
from electronic health records. Overall, Neanderthal variants are linked to
higher risk of neurological and psychiatric disorders and lower risk of
digestive problems. (That study didnt focus on adaptive DNA, so its
unclear how the segments of archaic DNA that show signs of selection
affect us today.)

At present, much of the data available for such studies is weighted toward
medical problemsmost of these databases were designed to find genes

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linked to diseases such as diabetes or schizophrenia. But a few, such as the

U.K. Biobank, are much broader, storing information on participants
vision, cognitive test scores, mental health assessments, lung capacity and
fitness. Direct-to-consumer genetics companies also have large, diverse
data sets. For example, 23andMe analyzes users genetics for clues about
ancestry, health risk and other sometimes bizarre traits, such as whether
they have a sweet tooth or a unibrow.

Of course, not all the DNA we got from Neanderthals and Denisovans was
good. The majority was probably detrimental. Indeed, we tend to have
less Neanderthal DNA near genes, suggesting that it was weeded out by
natural selection over time. Researchers are very interested in these parts
of our genomes where archaic DNA is conspicuously absent. There are
some really big places in the genome with no Neanderthal or Denisovan
ancestry as far as we can seesome process is purging the archaic material
from these regions, Sankararaman said. Perhaps they are functionally
important for modern humans.

This post appears courtesy of Quanta Magazine.

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