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sábado, 9 de septiembre de 2017
NEW SCIENTIFIC ISSUES FROM QUANTA MAGAZINE
lunes, 28 de agosto de 2017
How Neanderthals Gave Us Secret Power
Interbreeding with our fellow hominins appears to
have helped humans survive harsh climates.
· MAY 31, 2016
Native Tibetans make use of
a gene derived from Denisovans to stay healthy at high altitudes.
·
By EMILY SINGER
TEXT SIZE
Early human history was a promiscuous affair.
As modern humans began to spread out
of Africa roughly 50,000 years ago, they encountered other species that looked
remarkably like them—the 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.
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 population—one variant, for example, is present
in 70 percent of Europeans—suggesting 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.”
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. “It’s not just noise, it’s a very
important substantial part of who we are.
* * *
The Tibetan plateau is a vast stretch of
high-altitude real estate isolated by massive mountain ranges. The scant oxygen
at 14,000 feet—roughly 40 percent lower than the concentrations at sea
level—makes 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 don’t make as many red blood
cells 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 it’s 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. “That’s 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 challenges—different 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 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 years—enough 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.
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
DNA—those that don’t help the carrier—are 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
Akey’s 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 it’s not
clear exactly how. Skin can have 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 this—we don’t 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 smallest—novel
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 DNA—143,000 DNA base-pairs long—that
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 humans—two from Neanderthals and one from Denisovans.
To figure
out what those variants do, Kelso’s 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 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 don’t 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. “It’s 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 Kelso’s 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 didn’t focus on
adaptive DNA, so it’s 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 problems—most of these databases were
designed to find genes 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 see—some process is purging the archaic material from these regions,”
Sankararaman said. “Perhaps they are functionally important
for modern humans.”
SOURCE: https://www.quantamagazine.org/how-neanderthal-dna-helps-humanity-20160526/?utm_source=Quanta+Magazine&utm_campaign=510f4dd932-EMAIL_CAMPAIGN_2017_08_24&utm_medium=email&utm_term=0_f0cb61321c-510f4dd932-389390733
sábado, 19 de agosto de 2017
SCIENTIFIC AMERICAN REVIEW STATES.......
White Nationalists Are Flocking to Genetic Ancestry Tests--with Surprising Results
Sometimes they find they are not as “white” as they’d hoped
It was a strange moment of triumph against racism: The gun-slinging white supremacist Craig Cobb, dressed up for daytime TV in a dark suit and red tie, hearing that his DNA testing revealed his ancestry to be only “86 percent European, and … 14 percent Sub-Saharan African.” The studio audience whooped and laughed and cheered. And Cobb—who was, in 2013, charged with terrorizing people while trying to create an all-white enclave in North Dakota—reacted like a sore loser in the schoolyard.
“Wait a minute, wait a minute, hold on, just wait a minute,” he said, trying to put on an all-knowing smile. “This is called statistical noise.”
Then, according to the Southern Poverty Law Center, he took to the white nationalist website Stormfront to dispute those results. That’s not uncommon: With the rise of spit-in-a-cup genetic testing, there’s a trend of white nationalists using these services to prove their racial identity, and then using online forums to discuss the results.
But like Cobb, many are disappointed to find out that their ancestry is not as “white” as they’d hoped. In a new study, sociologists Aaron Panofsky and Joan Donovan examined years’ worth of posts on Stormfront to see how members dealt with the news.
It’s striking, they say, that white nationalists would post these results online at all. After all, as Panofsky put it, “they will basically say if you want to be a member of Stormfront you have to be 100 percent white European, not Jewish.”
But instead of rejecting members who get contrary results, Donovan said, the conversations are “overwhelmingly” focused on helping the person to rethink the validity of the genetic test. And some of those critiques—while emerging from deep-seated racism—are close to scientists’ own qualms about commercial genetic ancestry testing.
Panofsky and Donovan presented their findings at a sociology conference in Montreal on Monday. The timing of the talk—some 48 hours after the violent white nationalist rally in Charlottesville, Va.—was coincidental. But the analysis provides a useful, if frightening, window into how these extremist groups think about their genes.
RECKONING WITH RESULTS
Stormfront was launched in the mid-1990s by Don Black, a former grand wizard of the Ku Klux Klan. His skills in computer programming were directly related to his criminal activities: He learned them while in prison for trying to invade the Caribbean island nation of Dominica in 1981, and then worked as a web developer after he got out. That means this website dates back to the early years of the internet, forming a kind of deep archive of online hate.
To find relevant comments in the 12 million posts written by over 300,000 members, the authors enlisted a team at the University of California, Los Angeles, to search for terms like “DNA test,” “haplotype,” “23andMe,” and “National Geographic.” Then the researchers combed through the posts they found, not to mention many others as background. Donovan, who has moved from UCLA to the Data & Society Research Institute, estimated that she spent some four hours a day reading Stormfront in 2016. The team winnowed their results down to 70 discussion threads in which 153 users posted their genetic ancestry test results, with over 3,000 individual posts.
About a third of the people posting their results were pleased with what they found. “Pretty damn pure blood,” said a user with the username Sloth. But the majority didn’t find themselves in that situation. Instead, the community often helped them reject the test, or argue with its results.
Some rejected the tests entirely, saying that an individual’s knowledge about his or her own genealogy is better than whatever a genetic test can reveal. “They will talk about the mirror test,” said Panofsky, who is a sociologist of science at UCLA’s Institute for Society and Genetics. “They will say things like, ‘If you see a Jew in the mirror looking back at you, that’s a problem; if you don’t, you’re fine.'” Others, he said, responded to unwanted genetic results by saying that those kinds of tests don’t matter if you are truly committed to being a white nationalist. Yet others tried to discredit the genetic tests as a Jewish conspiracy “that is trying to confuse true white Americans about their ancestry,” Panofsky said.
But some took a more scientific angle in their critiques, calling into doubt the method by which these companies determine ancestry—specifically how companies pick those people whose genetic material will be considered the reference for a particular geographical group.
And that criticism, though motivated by very different ideas, is one that some researchers have made as well, even as other scientists have used similar data to better understand how populations move and change.
“There is a mainstream critical literature on genetic ancestry tests—geneticists and anthropologists and sociologists who have said precisely those things: that these tests give an illusion of certainty, but once you know how the sausage is made, you should be much more cautious about these results,” said Panofsky.
A COMMUNITY’S GENETIC RULES
Companies like Ancestry.com and 23andMe are meticulous in how they analyze your genetic material. As points of comparison, they use both preexisting datasets as well as some reference populations that they have recruited themselves. The protocol includes genetic material from thousands of individuals, and looks at thousands of genetic variations.
“When a 23andMe research participant tells us that they have four grandparents all born in the same country—and the country isn’t a colonial nation like the U.S., Canada, or Australia—that person becomes a candidate for inclusion in the reference data,” explained Jhulianna Cintron, a product specialist at 23andMe. Then, she went on, the company excludes close relatives, as that could distort the data, and removes outliers whose genetic data don’t seem to match with what they wrote on their survey.
But specialists both inside and outside these companies recognize that the geopolitical boundaries we use now are pretty new, and so consumers may be using imprecise categories when thinking about their own genetic ancestry within the sweeping history of human migration. And users’ ancestry results can change depending on the dataset to which their genetic material is being compared—a fact which some Stormfront users said they took advantage of, uploading their data to various sites to get a more “white” result.
J. Scott Roberts, an associate professor at the University of Michigan, who has studied consumer use of genetic tests and was not involved with the study, said the companies tend to be reliable at identifying genetic variants. Interpreting them in terms of health risk or ancestry, though, is another story. “The science is often murky in those areas and gives ambiguous information,” he said. “They try to give specific percentages from this region, or x percent disease risk, and my sense is that that is an artificially precise estimate.”
For the study authors, what was most interesting was to watch this online community negotiating its own boundaries, rethinking who counts as “white.” That involved plenty of contradictions. They saw people excluded for their genetic test results, often in very nasty (and unquotable) ways, but that tended to happen for newer members of the anonymous online community, Panofsky said, and not so much for longtime, trusted members. Others were told that they could remain part of white nationalist groups, in spite of the ancestry they revealed, as long as they didn’t “mate,” or only had children with certain ethnic groups. Still others used these test results to put forth a twisted notion of diversity, one “that allows them to say, ‘No, we’re really diverse and we don’t need non-white people to have a diverse society,'” said Panofsky.
That’s a far cry from the message of reconciliation that genetic ancestry testing companies hope to promote.
“Sweetheart, you have a little black in you,” the talk show host Trisha Goddard told Craig Cobb on that day in 2013. But that didn’t stop him from redoing the test with a different company, trying to alter or parse the data until it matched his racist worldview.
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